[gmx-users] problem in applying position restrain on protein
Dear all, I am encountering problem in applying position restrain on my protein which is with lipid bilayer . Actually I want to do simulation of system protein-lipid bilayer to pack lipid around the protein for this I want to keep my protein constant and lipid should move around this .I am doing this by applying strong position restrain on protein with force constant 10. But the restrain not working on protein. I have included these lines in my topol_A.itp file and topol_B.itp file- ; Include position restrain file #ifdef POSRES #include "posre_A.itp" #endif I have also included- define = -DPOSRES in em.mdp file. also edited posre.itp file with force constant 10. Even after doing these things the restrain not working on protein thats why my protein structure being disturbed . Can any one help me in solving this problem. Thanks a lot in advance. Nitu sharma ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ffgmx:diffusion of oxygen
Respectable Experts Thank you very much David. Yes the msd curve tries to improve if I run for 100ns. But my system is very small 1oxygen molecule in 255 molecules of water. I want to calculate the self diffusion coefficient of oxygen . What I have found that people do such simulations for mostly not more than 10 ns. I also got to see your paper on dynamic property of water/alcohol mixture where you have used time less than 10 ns. Which msd curve is to take ? Another query : I want to simulate the system in a bit higher temperature 310 K . What are the parameters I should change in the mdp file. I saw the previous mails about it. Eric says that only time step should be small in order to constrain the bonds. Are there any other things? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ffgmx:diffusion of oxygen
Sunil Thapa wrote: Respectable Experts Thank you very much David. Yes the msd curve tries to improve if I run for 100ns. But my system is very small 1oxygen molecule in 255 molecules of water. I want to calculate the self diffusion coefficient of oxygen . What I have found that people do such simulations for mostly not more than 10 ns. I also got to see your paper on *dynamic property of water/alcohol mixture* where you have used time less than 10 ns. Which msd curve is to take ? The problem is that you have only one molecule. If you have a liquid you can average over all the molecules. Another query : I want to simulate the system in a bit higher temperature 310 K . What are the parameters I should change in the mdp file. I saw the previous mails about it. Eric says that only time step should be small in order to constrain the bonds. Are there any other things? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Questions
Hi Lin, I bounce this mail to the gromacs user list as the issues are well off to be archived. > I have two stupid questions here. Well, that's up to us to decide ;) > 1. I want to get the proper structure of lysozyme. > > From your tutorials, 1LW9.pdb file is used. Potassium (K), chloride (CL) and > 2-hydroxethyl disulfide (HED) are removed. > > http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ > > Further, I remove the water, such as HOH, AHOH and BHOH. > > I don't know what is the differece between HOH, AHOH and BHOH. The answer to this question is in the format specification of the PDB file. The A and B are alternative identifiers and indicate that the electron density can be explained by a water molecule that is partially present at two sites. If you look at the occupancy field you'll notice that the corresponding values are less than 1. In fact, if you sum the occupancies for equivalent atoms in for A and B, they will add up to 1. > Then, I add all missing H atoms. => made the new pdb file => it is attached. > > Would you please take a look if the pdb file is corrct? No, I'm not going to do that. Have a look at the structure to see if it is okay and be sure to take into account whether you used a united atom force field or an all atom one. > In your tutorial, why don't you add the missing hydrogen atoms? I do (or rather, I let the students do it ;)). It's one of the things pdb2gmx does. > Is it unnecessary to add the missing H atoms? Each residue/molecule should have atoms (with coordinates) matching with the description in the force field used. So if hydrogen atoms are missing with respect to the force field, then they have to be added. > HETATM 1504 O HOH 445 36.056 19.096 6.798 1.00 34.30 O > HETATM 1535 O AHOH 482 24.352 20.291 2.379 0.50 20.49 O > HETATM 1536 O BHOH 482 24.181 18.429 1.588 0.50 24.50 O > 2. Parallel computing in GROMACS > > What is the maximum number of computers in parallel computers in Gromacs? There are people on the list better equipped to answer this question. But you might be able to find a number of processors that will be optimal for your case by readin the Gromacs 4 paper and doing some tests. > The more computers used in parallel, the less efficiency they have. > For example, I want to see the micelle formation in 2 month and the parallel > computing will be used. > The starting configuration is random-spread of surfactants. > The system is < = 0.25mM => 300 solutes + so many water molecues (TIP3P > water model) > > What is your suggestion of the number of computers used in parallel > computing? I'm sorry, but I can't give an answer to this. If you have constructed your system, you should probably just try different numbers of processors for short (ps) simulations and from that determine what is optimal for your case. Hope it helps :) Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] different result for entropy with normal mode analysis and schlitter-approximation
Dear Gromacs Users,
I'm trying to calculate entropies from a md trajectory using g_anaeig.
There are two ways to go (question at bottom ;-):
1. NMA and quasi-harmonic approximation: Use a bunch of snapshots (maybe
5-20), minimize each of them to very low maximum forces, calculate the
hessian matrix, diagonalize and use g_anaeig to calculate the entropy from
the resulting eigenvector-matrix assuring that there are no negative
eigenvalues in the eigenvectors 7 to N (first six eigenvectors will not be
part of the calculation). - as follows:
# Energy Minimization
grompp_d -f em_nma.mdp -t md.fitted.trr -time $t -c md.gro -p protein.top
-o $t.em.tpr
mdrun_d -v -deffnm $t.em -table table6-12_4r_doublePrecision.xvg -tablep
table6-12_4r_doublePrecision.xvg
# Hessian Matrix
grompp_d -f nma.mdp -t $t.em.trr -c md.gro -p protein.top -o $t.hessian.tpr
mdrun_d -v -deffnm $t.hessian -table table6-12_4r_doublePrecision.xvg
-tablep table6-12_4r_doublePrecision.xvg
# Diagonalization of the Hessian
g_nmeig_d -f $t.hessian.mtx -s $t.hessian.tpr -first 1 -last 1 -v
$t.eigenvec.trr
# Entropy calculation - vibrational (without first 6 modes)
g_anaeig_d -v $t.eigenvec.trr -f $t.em.trr -s $t.hessian.tpr -temp 298.15
-nevskip 6 -entropy 2>&1 | tee out.anaeig.Svib.$t
grep 'The Entropy due to the Quasi Harmonic approximation is'
out.anaeig.Svib.$t | awk '{print $10}' >> result/Svib.nma
I use distance-dependent dielectric e=4r, but that doesn't make much
difference.
2. Schlitter approximation based on covariance: Use all snapshots of the
md trajectory, calculate the covariance matrix (g_covar), - diagonalized
matrix will be returned -, and subsequently calculate the entropy with
g_anaeig. - as follows:
# covariance matrix as time average over configurations
g_covar_d -f md$i.trr -s md.gro -v md$i.eigenvec.trr -mwa -av
average.$i.pdb -ascii covar.$i -xpm covar.$i -xpma covara.$i -l covar.$i
-o md$i.eigenval.xvg <<- EOF
0
0
EOF
# Analysis of the principal components (and entropy calculation)
g_anaeig -v md$i.eigenvec.trr -f md$i.trr -s md.gro -first 1 -last -1
-entropy > out.anaeig.schlitter.$i
grep 'The Entropy due to the Schlitter formula is' out.anaeig.schlitter.$i
| awk '{print $9}' >> result/Svib.schlitter
Somebody before mentioned, he would like to have the undiagonalized
covariance matrix as input for the entropy calculation, I think, that
doesn't make a difference, am I right?
So, practically, I tried to reproduce entropy from Schlitter 1993. A
simulation of a deca-alanine-helix in vacuo in the old gmx force-field
with vdw-cut-off etc. and I could reproduce the value of ca. 700
kJoule/mol K with the Schlitter approximation.
And now the question, why don't I get the same range of values when doing
normal-mode analysis (as described above)?
values of the Schlitter-approximation (for different simulation lengths):
667.365
685.594
681.259
680.269
values given by the quasi-harmonic approximation when calculating from
covariance:
582.731
596.97
590.71
589.07
values from NMA and quasi-harmonic approximation (for 3 snapshots):
21662.9
21674.9
21662.9
So, there is a factor of round 30 between hessian- and covariance-based
entropy!?
I'm totally stuck with this.
If anybody has experience with this phenomenon, any help is appreciated.
Thanx in advance
Oliver Kuhn
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Re: [gmx-users] problem in applying position restrain on protein
nitu sharma wrote: Dear all, I am encountering problem in applying position restrain on my protein which is with lipid bilayer . Actually I want to do simulation of system protein-lipid bilayer to pack lipid around the protein for this I want to keep my protein constant and lipid should move around this .I am doing this by applying strong position restrain on protein with force constant 10. But the restrain not working on protein. Probably due to the excessively large force that you posted as your result of energy minimization. Position restraints don't guarantee that everything stays exactly where it is, they just provide an energy penalty for moving those atoms. Have you done what has been asked of you and inspected the location of the large force? You have to demonstrate that you're using initiative to solve your own problem. I know I've seen at least one post, if not two, that have told you to look at your structure file and deduce the location of the large force. That is usually the information necessary to solve this problem. -Justin I have included these lines in my topol_A.itp file and topol_B.itp file- ; Include position restrain file #ifdef POSRES #include "posre_A.itp" #endif I have also included- define = -DPOSRES in em.mdp file. also edited posre.itp file with force constant 10. Even after doing these things the restrain not working on protein thats why my protein structure being disturbed . Can any one help me in solving this problem. Thanks a lot in advance. Nitu sharma ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] different result for entropy with normal mode analysis and schlitter-approximation
Hi Oliver,
I think the eigenvalues in NMA are not the same (there used to be a
factor of 2PI and the mass weighting). Maybe you can try my script from
the user contributions and see if you get something more reasonable (use
to flag -n to indicate that your eigenvalues are from NMA).
Ran.
oliver.k...@uni-duisburg-essen.de wrote:
> Dear Gromacs Users,
> I'm trying to calculate entropies from a md trajectory using g_anaeig.
> There are two ways to go (question at bottom ;-):
>
> 1. NMA and quasi-harmonic approximation: Use a bunch of snapshots (maybe
> 5-20), minimize each of them to very low maximum forces, calculate the
> hessian matrix, diagonalize and use g_anaeig to calculate the entropy from
> the resulting eigenvector-matrix assuring that there are no negative
> eigenvalues in the eigenvectors 7 to N (first six eigenvectors will not be
> part of the calculation). - as follows:
>
> # Energy Minimization
> grompp_d -f em_nma.mdp -t md.fitted.trr -time $t -c md.gro -p protein.top
> -o $t.em.tpr
> mdrun_d -v -deffnm $t.em -table table6-12_4r_doublePrecision.xvg -tablep
> table6-12_4r_doublePrecision.xvg
>
> # Hessian Matrix
> grompp_d -f nma.mdp -t $t.em.trr -c md.gro -p protein.top -o $t.hessian.tpr
> mdrun_d -v -deffnm $t.hessian -table table6-12_4r_doublePrecision.xvg
> -tablep table6-12_4r_doublePrecision.xvg
>
> # Diagonalization of the Hessian
> g_nmeig_d -f $t.hessian.mtx -s $t.hessian.tpr -first 1 -last 1 -v
> $t.eigenvec.trr
>
> # Entropy calculation - vibrational (without first 6 modes)
> g_anaeig_d -v $t.eigenvec.trr -f $t.em.trr -s $t.hessian.tpr -temp 298.15
> -nevskip 6 -entropy 2>&1 | tee out.anaeig.Svib.$t
>
> grep 'The Entropy due to the Quasi Harmonic approximation is'
> out.anaeig.Svib.$t | awk '{print $10}' >> result/Svib.nma
>
> I use distance-dependent dielectric e=4r, but that doesn't make much
> difference.
>
> 2. Schlitter approximation based on covariance: Use all snapshots of the
> md trajectory, calculate the covariance matrix (g_covar), - diagonalized
> matrix will be returned -, and subsequently calculate the entropy with
> g_anaeig. - as follows:
>
> # covariance matrix as time average over configurations
> g_covar_d -f md$i.trr -s md.gro -v md$i.eigenvec.trr -mwa -av
> average.$i.pdb -ascii covar.$i -xpm covar.$i -xpma covara.$i -l covar.$i
> -o md$i.eigenval.xvg <<- EOF
> 0
> 0
> EOF
>
> # Analysis of the principal components (and entropy calculation)
> g_anaeig -v md$i.eigenvec.trr -f md$i.trr -s md.gro -first 1 -last -1
> -entropy > out.anaeig.schlitter.$i
>
> grep 'The Entropy due to the Schlitter formula is' out.anaeig.schlitter.$i
> | awk '{print $9}' >> result/Svib.schlitter
>
> Somebody before mentioned, he would like to have the undiagonalized
> covariance matrix as input for the entropy calculation, I think, that
> doesn't make a difference, am I right?
>
> So, practically, I tried to reproduce entropy from Schlitter 1993. A
> simulation of a deca-alanine-helix in vacuo in the old gmx force-field
> with vdw-cut-off etc. and I could reproduce the value of ca. 700
> kJoule/mol K with the Schlitter approximation.
> And now the question, why don't I get the same range of values when doing
> normal-mode analysis (as described above)?
>
> values of the Schlitter-approximation (for different simulation lengths):
> 667.365
> 685.594
> 681.259
> 680.269
> values given by the quasi-harmonic approximation when calculating from
> covariance:
> 582.731
> 596.97
> 590.71
> 589.07
>
> values from NMA and quasi-harmonic approximation (for 3 snapshots):
> 21662.9
> 21674.9
> 21662.9
>
> So, there is a factor of round 30 between hessian- and covariance-based
> entropy!?
>
> I'm totally stuck with this.
> If anybody has experience with this phenomenon, any help is appreciated.
> Thanx in advance
>
> Oliver Kuhn
>
>
>
>
>
>
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
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>
>
--
--
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.fried...@bioc.unizh.ch
Skype: ran.friedman
--
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RE: [gmx-users] transport properties
Once you have correlation results then xmgrace software can do the integration. Regards From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of oguz gurbulak Sent: Tuesday, April 28, 2009 10:25 AM To: gmx-users@gromacs.org Subject: [gmx-users] transport properties Dear All, I'm trying to calculate self diffusion coefficient from velocity auto-correlation (VAC) functions using Green-Kubo relation in figure I attached to the mail. I couldn’t solve how to integrate the velocity auto-correlation (VAC) functions to get Diffusion coefficient. Could you please give me some information about this issue ? Could you suggest some software to integrate the VAC function ? Thanks in advance for your helps. Best regards, ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] transport properties
Dear K. Chae, Thank you very much for your answer. I computed velocity auto-correlation (VAC) functions , but how can I integrate velocity auto-correlation (VAC) functions to get Diffusion coefficient using xmgrace software ? I have just used xmgrace to plot md result for analysis. And I have a limited information using xmgrace. Could you please explain the integration procedure in xmgrace ? I will be very grateful if you can help me to learn how to calculate Diffusion coefficient . Thanks in advance for your helps. Best regards, --- On Tue, 4/28/09, kyungchan chae wrote: From: kyungchan chae Subject: RE: [gmx-users] transport properties To: "'Discussion list for GROMACS users'" Date: Tuesday, April 28, 2009, 9:52 AM Once you have correlation results then xmgrace software can do the integration. Regards From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of oguz gurbulak Sent: Tuesday, April 28, 2009 10:25 AM To: gmx-users@gromacs.org Subject: [gmx-users] transport properties Dear All, I'm trying to calculate self diffusion coefficient from velocity auto-correlation (VAC) functions using Green-Kubo relation in figure I attached to the mail. I couldn’t solve how to integrate the velocity auto-correlation (VAC) functions to get Diffusion coefficient. Could you please give me some information about this issue ? Could you suggest some software to integrate the VAC function ? Thanks in advance for your helps. Best regards, -Inline Attachment Follows- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Thermodynamic integration with Martini force field
Dear Martini and GROMACS users, I am trying to perform thermodynamic integration on cg simulations using the Martini FF and GROMACS version 3.3.1 with double precision on a system containing a protein, lipids, water and Cl- ions. In the first test runs I tried to change the Martini atom type Qd to Q0, with a lambda of 0.5 and 0.25. The test simulations (2ns) are running, but the dgdl.xvg file writes out zeros. Also the mdrun option -sepdvdl shows that the energies are zero. I am using the mdp file from the Martini homepage and added the parameters for TI at the very end. I did not change any other parameter in the mdp file. I am right now out of ideas, how to solve this problem. Has anyone experienced this problem before? Caro ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] forcefield for free (neutral) amino acids
Dear chun feng, I am not a user of GROMACS, but I hope someone who's working on protein dynamics can do me a favor here. I am desperately searching for a forcefield for free and neutral amino acids. But it seems that the forcefields such as amber and opls only parametrizes amino acids in peptides (without OH and H) and terminal amino acids on peptides. Yes I know there has to be some forcefield already developed for popular molecules like amino acids, anyone please point me the way! Thanks a million! You could derive your own force field for such amino-acids. You can derive RESP and ESP charges for any molecule or molecular fragment containing chemical elements up to Bromine using the R.E.D. tools. See http://q4md-forcefieldtools.org/ regards, Francois ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Full implementation of CHARMM and AMBER in GROMACS?
Hello, I was jut curious, are there any plans to fully implement any other FF in gromacs. Particulary Im interested in CHARMM and AMBER. By full implementation of CHARMM I mean not simply taking the numbers from the CHARMM text file but calculating CHARMM-specific issues, like Urey-Bradley interactions, 1-4 LJ etc. And what is your opinion about CHARMM - is it any good vs OPLS (considering proteins)? Thanks a lot. SDA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error by pdb2gmx
Dear All users: I was trying to set up a long chain polymer system. I got the following PDB file from WebLab. How can I make changes to the file in order to make it as a GROMACS input pdb file. Then I can use pdb2gmx to get the gro, itp and top file. When I perform the pdb2gmx command, I got the error message: Residue 'MOL' not found in residue topology database Thank you in advance! REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009 ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00 ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00 ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00 ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00 ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00 ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00 ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00 ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00 ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00 ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00 ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00 ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00 ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00 ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 1.00 0.00 ATOM 38 C74 MOL A 1 2.469 1.818 -1.953 1.00 0.00 ATOM 39 C76 MOL A 1 0.160 3.770 0.914 1.00 0.00 ATOM 40 C78 MOL A 1 2.129 2.878 3.056 1.00 0.00 ATOM 41 C80 MOL A 1 2.186 8.538 2.814 1.00 0.00 ATOM 42 Si84 MOL A 1 4.912 7.172 1.476 1.00 0.00 ATOM 43 C84 MOL A 1 8.985 1.172 -7.484 1.00 0.00 ATOM 44 C86 MOL A 1 10.388 2.767 -5.292 1.00 0.00 ATOM 45 C88 MOL A 1 11.402 -0.013 -6.044 1.00 0.00 TER -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error by pdb2gmx
Yanmei Song wrote: Dear All users: I was trying to set up a long chain polymer system. I got the following PDB file from WebLab. How can I make changes to the file in order to make it as a GROMACS input pdb file. Then I can use pdb2gmx to get the gro, itp and top file. When I perform the pdb2gmx command, I got the error message: Residue 'MOL' not found in residue topology database You can't expect pdb2gmx to be magic. A simple search of the list archives and wiki will turn up the following: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database -Justin Thank you in advance! REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009 ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00 ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00 ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00 ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00 ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00 ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00 ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00 ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00 ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00 ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00 ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00 ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00 ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00 ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 1.00 0.00 ATOM 38 C74 MOL A 1 2.469 1.818 -1.953 1.00 0.00 ATOM 39 C76 MOL A 1 0.160 3.770 0.914 1.00 0.00 ATOM 40 C78 MOL A 1 2.129 2.878 3.056 1.00 0.00 ATOM 41 C80 MOL A 1 2.186 8.538 2.814 1.00 0.00 ATOM 42 Si84 MOL A 1 4.912 7.172 1.476 1.00 0.00 ATOM 43 C84 MOL A 1 8.985 1.172 -7.484 1.00 0.00 ATOM 44 C86 MOL A 1 10.388 2.767 -5.292 1.00 0.00 ATOM 45 C88 MOL A 1 11.402 -0.013 -6.044 1.00 0.00 TER -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] ffgmx:diffusion of oxygen
The issue is you don't have enough statistics to get a meaningful result. Three ways you can get more, more particles, more time, or multiply runs. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Sunil Thapa Sent: Tuesday, 28 April 2009 5:40 PM To: gmx-users@gromacs.org Subject: [gmx-users] ffgmx:diffusion of oxygen Respectable Experts Thank you very much David. Yes the msd curve tries to improve if I run for 100ns. But my system is very small 1oxygen molecule in 255 molecules of water. I want to calculate the self diffusion coefficient of oxygen . What I have found that people do such simulations for mostly not more than 10 ns. I also got to see your paper on dynamic property of water/alcohol mixture where you have used time less than 10 ns. Which msd curve is to take ? Another query : I want to simulate the system in a bit higher temperature 310 K . What are the parameters I should change in the mdp file. I saw the previous mails about it. Eric says that only time step should be small in order to constrain the bonds. Are there any other things? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error by pdb2gmx
Dear Justin: Do you have any suggestions on how I can get the itp and gro file for a very long polymer molecules (for example 500 united-atoms), which only consists of Si, O and C atom. I can use PRODRG to generate a short chain. But PRODRG has limitation of atom numbers in a molecule, probably less than 300. So any ideas for building up a long chain based on the short chain? By the way, I already have the force field parameters. Thanks a lot! On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: >> >> Dear All users: >> >> I was trying to set up a long chain polymer system. I got the >> following PDB file from WebLab. How can I make changes to the file in >> order to make it as a GROMACS input pdb file. Then I can use pdb2gmx >> to get the gro, itp and top file. >> >> When I perform the pdb2gmx command, I got the error message: >> >> Residue 'MOL' not found in residue topology database >> > > You can't expect pdb2gmx to be magic. A simple search of the list archives > and wiki will turn up the following: > > http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database > > -Justin > >> Thank you in advance! >> >> REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009 >> ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 >> ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 >> ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 >> ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 >> ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 >> ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 >> ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 >> ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 >> ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 >> ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 >> ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 >> ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 >> ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 >> ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 >> ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 >> ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 >> ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 >> ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 >> ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 >> ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 >> ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 >> ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 >> ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 >> ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00 >> ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00 >> ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00 >> ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00 >> ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00 >> ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00 >> ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00 >> ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00 >> ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00 >> ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00 >> ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00 >> ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00 >> ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00 >> ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 1.00 0.00 >> ATOM 38 C74 MOL A 1 2.469 1.818 -1.953 1.00 0.00 >> ATOM 39 C76 MOL A 1 0.160 3.770 0.914 1.00 0.00 >> ATOM 40 C78 MOL A 1 2.129 2.878 3.056 1.00 0.00 >> ATOM 41 C80 MOL A 1 2.186 8.538 2.814 1.00 0.00 >> ATOM 42 Si84 MOL A 1 4.912 7.172 1.476 1.00 0.00 >> ATOM 43 C84 MOL A 1 8.985 1.172 -7.484 1.00 0.00 >> ATOM 44 C86 MOL A 1 10.388 2.767 -5.292 1.00 0.00 >> ATOM 45 C88 MOL A 1 11.402 -0.013 -6.044 1.00 0.00 >> TER >> >> > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > ___ > gmx-users mailing list gmx-us...@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't pos
RE: [gmx-users] Error by pdb2gmx
If it is a repeating unit, then you can build a .rtp entry then use it as you would for a protein. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. > -Original Message- > From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song > Sent: Wednesday, 29 April 2009 8:59 AM > To: jalem...@vt.edu; Discussion list for GROMACS users > Subject: Re: [gmx-users] Error by pdb2gmx > > Dear Justin: > > Do you have any suggestions on how I can get the itp and gro file for > a very long polymer molecules (for example 500 united-atoms), which > only consists of Si, O and C atom. I can use PRODRG to generate a > short chain. But PRODRG has limitation of atom numbers in a molecule, > probably less than 300. So any ideas for building up a long chain > based on the short chain? By the way, I already have the force field > parameters. > > Thanks a lot! > > On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul > wrote: > > > > > > Yanmei Song wrote: > >> > >> Dear All users: > >> > >> I was trying to set up a long chain polymer system. I got the > >> following PDB file from WebLab. How can I make changes to > the file in > >> order to make it as a GROMACS input pdb file. Then I can > use pdb2gmx > >> to get the gro, itp and top file. > >> > >> When I perform the pdb2gmx command, I got the error message: > >> > >> Residue 'MOL' not found in residue topology database > >> > > > > You can't expect pdb2gmx to be magic. A simple search of > the list archives > > and wiki will turn up the following: > > > > > http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not _found_in_residue_topology_database > > > > -Justin > > > >> Thank you in advance! > >> > >> REMARK Created: Tue Apr 28 15:02:20 US Mountain > Standard Time 2009 > >> ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 > >> ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 > >> ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 > >> ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 > >> ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 > >> ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 > >> ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 > >> ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 > >> ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 > >> ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 > >> ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 > >> ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 > >> ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 > >> ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 > >> ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 > >> ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 > >> ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 > >> ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 > >> ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 > >> ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 > >> ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 > >> ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 > >> ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 > >> ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00 > >> ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00 > >> ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00 > >> ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00 > >> ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00 > >> ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00 > >> ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00 > >> ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00 > >> ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00 > >> ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00 > >> ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00 > >> ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00 > >> ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00 > >> ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 1.00 0.00 > >> ATOM 38 C74 MOL A 1 2.469 1.818 -1.953 1.00 0.00 > >> ATOM 39 C76 MOL A 1 0.160 3.770 0.914 1.00 0.00 > >> ATOM 40 C78 MOL A 1 2.129 2.878 3.056 1.00 0.00 > >> ATOM 41 C80 MOL A
Re: [gmx-users] Error by pdb2gmx
Dear Dallas: Thanks for your response. It consists of many repeating units. Do you mean I can write the rtp entry for one repeating unit and give it a residue name. After that I need to insert this into the force field rtp file, right? How can I do that? It seems I can not change the rtp file. Thanks. On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren wrote: > If it is a repeating unit, then you can build a .rtp entry then use it as you > would for a protein. > > Catch ya, > > Dr. Dallas Warren > Department of Pharmaceutical Biology and Pharmacology > Pharmacy and Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@pharm.monash.edu.au > +61 3 9903 9167 > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > >> -Original Message- >> From: gmx-users-boun...@gromacs.org >> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song >> Sent: Wednesday, 29 April 2009 8:59 AM >> To: jalem...@vt.edu; Discussion list for GROMACS users >> Subject: Re: [gmx-users] Error by pdb2gmx >> >> Dear Justin: >> >> Do you have any suggestions on how I can get the itp and gro file for >> a very long polymer molecules (for example 500 united-atoms), which >> only consists of Si, O and C atom. I can use PRODRG to generate a >> short chain. But PRODRG has limitation of atom numbers in a molecule, >> probably less than 300. So any ideas for building up a long chain >> based on the short chain? By the way, I already have the force field >> parameters. >> >> Thanks a lot! >> >> On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul >> wrote: >> > >> > >> > Yanmei Song wrote: >> >> >> >> Dear All users: >> >> >> >> I was trying to set up a long chain polymer system. I got the >> >> following PDB file from WebLab. How can I make changes to >> the file in >> >> order to make it as a GROMACS input pdb file. Then I can >> use pdb2gmx >> >> to get the gro, itp and top file. >> >> >> >> When I perform the pdb2gmx command, I got the error message: >> >> >> >> Residue 'MOL' not found in residue topology database >> >> >> > >> > You can't expect pdb2gmx to be magic. A simple search of >> the list archives >> > and wiki will turn up the following: >> > >> > >> http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not > _found_in_residue_topology_database >> > >> > -Justin >> > >> >> Thank you in advance! >> >> >> >> REMARK Created: Tue Apr 28 15:02:20 US Mountain >> Standard Time 2009 >> >> ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 >> >> ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 >> >> ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 >> >> ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 >> >> ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 >> >> ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 >> >> ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 >> >> ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 >> >> ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 >> >> ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 >> >> ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 >> >> ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 >> >> ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 >> >> ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 >> >> ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 >> >> ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 >> >> ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 >> >> ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 >> >> ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 >> >> ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 >> >> ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 >> >> ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 >> >> ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 >> >> ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00 >> >> ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00 >> >> ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00 >> >> ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00 >> >> ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00 >> >> ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00 >> >> ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00 >> >> ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00 >> >> ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00 >> >> ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00 >> >> ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.0
Re: [gmx-users] Error by pdb2gmx
Yanmei Song wrote: Dear Dallas: Thanks for your response. It consists of many repeating units. Do you mean I can write the rtp entry for one repeating unit and give it a residue name. After that I need to insert this into the force field rtp file, right? How can I do that? It seems I can not change the rtp file. Thanks. You will need an entry for the repeat units and the terminal/capping groups. You can make a local copy of the .rtp file and edit it in your working directory; pdb2gmx will then read this copy when processing your structure. -Justin On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren wrote: If it is a repeating unit, then you can build a .rtp entry then use it as you would for a protein. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Wednesday, 29 April 2009 8:59 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx Dear Justin: Do you have any suggestions on how I can get the itp and gro file for a very long polymer molecules (for example 500 united-atoms), which only consists of Si, O and C atom. I can use PRODRG to generate a short chain. But PRODRG has limitation of atom numbers in a molecule, probably less than 300. So any ideas for building up a long chain based on the short chain? By the way, I already have the force field parameters. Thanks a lot! On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul wrote: Yanmei Song wrote: Dear All users: I was trying to set up a long chain polymer system. I got the following PDB file from WebLab. How can I make changes to the file in order to make it as a GROMACS input pdb file. Then I can use pdb2gmx to get the gro, itp and top file. When I perform the pdb2gmx command, I got the error message: Residue 'MOL' not found in residue topology database You can't expect pdb2gmx to be magic. A simple search of the list archives and wiki will turn up the following: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not _found_in_residue_topology_database -Justin Thank you in advance! REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009 ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00 ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00 ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00 ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00 ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00 ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00 ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00 ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00 ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00 ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00 ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00 ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00 ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00 ATOM 37 C72 MOL A
RE: [gmx-users] Error by pdb2gmx
That is correct. Fact you can't edit the .rtp file is based on your local computer system permissions. Normally, best idea is to make your own changes to a local copy, and use that. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. > -Original Message- > From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song > Sent: Wednesday, 29 April 2009 9:24 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Error by pdb2gmx > > Dear Dallas: > > Thanks for your response. It consists of many repeating units. Do you > mean I can write the rtp entry for one repeating unit and give it a > residue name. After that I need to insert this into the force field > rtp file, right? How can I do that? It seems I can not change the rtp > file. Thanks. > > On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren > wrote: > > If it is a repeating unit, then you can build a .rtp entry > then use it as you would for a protein. > > > > Catch ya, > > > > Dr. Dallas Warren > > Department of Pharmaceutical Biology and Pharmacology > > Pharmacy and Pharmaceutical Sciences, Monash University > > 381 Royal Parade, Parkville VIC 3010 > > dallas.war...@pharm.monash.edu.au > > +61 3 9903 9167 > > - > > When the only tool you own is a hammer, every problem > begins to resemble a nail. > > > >> -Original Message- > >> From: gmx-users-boun...@gromacs.org > >> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song > >> Sent: Wednesday, 29 April 2009 8:59 AM > >> To: jalem...@vt.edu; Discussion list for GROMACS users > >> Subject: Re: [gmx-users] Error by pdb2gmx > >> > >> Dear Justin: > >> > >> Do you have any suggestions on how I can get the itp and > gro file for > >> a very long polymer molecules (for example 500 united-atoms), which > >> only consists of Si, O and C atom. I can use PRODRG to generate a > >> short chain. But PRODRG has limitation of atom numbers in > a molecule, > >> probably less than 300. So any ideas for building up a long chain > >> based on the short chain? By the way, I already have the > force field > >> parameters. > >> > >> Thanks a lot! > >> > >> On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul > >> wrote: > >> > > >> > > >> > Yanmei Song wrote: > >> >> > >> >> Dear All users: > >> >> > >> >> I was trying to set up a long chain polymer system. I got the > >> >> following PDB file from WebLab. How can I make changes to > >> the file in > >> >> order to make it as a GROMACS input pdb file. Then I can > >> use pdb2gmx > >> >> to get the gro, itp and top file. > >> >> > >> >> When I perform the pdb2gmx command, I got the error message: > >> >> > >> >> Residue 'MOL' not found in residue topology database > >> >> > >> > > >> > You can't expect pdb2gmx to be magic. A simple search of > >> the list archives > >> > and wiki will turn up the following: > >> > > >> > > >> http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not > > _found_in_residue_topology_database > >> > > >> > -Justin > >> > > >> >> Thank you in advance! > >> >> > >> >> REMARK Created: Tue Apr 28 15:02:20 US Mountain > >> Standard Time 2009 > >> >> ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 > 1.00 0.00 > >> >> ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 > 1.00 0.00 > >> >> ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 > 1.00 0.00 > >> >> ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 > 1.00 0.00 > >> >> ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 > 1.00 0.00 > >> >> ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 > 1.00 0.00 > >> >> ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 > 1.00 0.00 > >> >> ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 > 1.00 0.00 > >> >> ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 > 1.00 0.00 > >> >> ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 > 1.00 0.00 > >> >> ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 > 1.00 0.00 > >> >> ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 > 1.00 0.00 > >> >> ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 > 1.00 0.00 > >> >> ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 > 1.00 0.00 > >> >> ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 > 1.00 0.00 > >> >> ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 > 1.00 0.00 > >> >> ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 > 1.00 0.00 > >> >> ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 > 1.00 0.00 > >> >> ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 > 1.00 0.00 > >> >> ATOM 20 C38 MOL A 1
Re: [gmx-users] Full implementation of CHARMM and AMBER in GROMACS?
Hi, in the 4.0.4 version CHARMM is supported with most CHARMM specific energy terms (U-B, dihedrals,...). You can find more about it at http://www.dbb.su.se/User:Bjelkmar/Ffcharmm. The only missing thing in 4.0.4 is CMAP which is added to the latest development/CVS version. As far as I know Amber is also fully supported. But I have never used it. Roland On Tue, Apr 28, 2009 at 3:38 PM, DimitryASuplatov wrote: > Hello, > > I was jut curious, > are there any plans to fully implement any other FF in gromacs. > Particulary Im interested in CHARMM and AMBER. By full implementation > of CHARMM I mean not simply taking the numbers from the CHARMM text > file but calculating CHARMM-specific issues, like Urey-Bradley > interactions, 1-4 LJ etc. And what is your opinion about CHARMM - is > it any good vs OPLS (considering proteins)? > > Thanks a lot. > SDA > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] 10-4 Wall Potential.
Just wanting to confirm: The potential function for the 10-4 wall in GROMACS is of the form: VLJ = c12*density*pi/(5*r^10) - c6*density*pi/(2*r^4) It is NOT the same as the 10-4-3 function which is also sometimes used to model surface-fluid interactions? Thanks, Travis T. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] forcefield for free (neutral) amino acids
FyD wrote: Dear chun feng, I am not a user of GROMACS, but I hope someone who's working on protein dynamics can do me a favor here. I am desperately searching for a forcefield for free and neutral amino acids. But it seems that the forcefields such as amber and opls only parametrizes amino acids in peptides (without OH and H) and terminal amino acids on peptides. Yes I know there has to be some forcefield already developed for popular molecules like amino acids, anyone please point me the way! Thanks a million! You could derive your own force field for such amino-acids. You can derive RESP and ESP charges for any molecule or molecular fragment containing chemical elements up to Bromine using the R.E.D. tools. See http://q4md-forcefieldtools.org/ The "Generalized AMBER Force Field" and the AMBER utility program antechamber is probably also suited to the task. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: transport properties
Please read about obtaining diffusion constant from VAC in the gromacs wiki. I wrote an individual article on that topic. Best, Vitaly Subject: RE: [gmx-users] transport properties > To: Discussion list for GROMACS users > Message-ID: <569363.99887...@web36304.mail.mud.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > Dear K. Chae, > > Thank you very much for your answer. I computed velocity auto-correlation > (VAC) functions , but how can I integrate velocity auto-correlation (VAC) > functions to get Diffusion coefficient using xmgrace software ? I have just > used xmgrace to plot md result for analysis. And I have a limited > information using xmgrace. Could you please explain the integration > procedure in xmgrace ? I will be very grateful if you can help me to learn > how to calculate Diffusion coefficient . > > Thanks in advance for your helps. > > Best regards, > > --- On Tue, 4/28/09, kyungchan chae wrote: > > > From: kyungchan chae > Subject: RE: [gmx-users] transport properties > To: "'Discussion list for GROMACS users'" > Date: Tuesday, April 28, 2009, 9:52 AM > > > Once you have correlation results then xmgrace software can do the > integration. > > Regards > > > > Dear All, > I'm trying to calculate self diffusion coefficient from velocity > auto-correlation (VAC) functions using Green-Kubo relation in figure I > attached to the mail. I couldn’t solve how to integrate the velocity > auto-correlation (VAC) functions to get Diffusion coefficient. Could you > please give me some information about this issue ? Could you suggest some > software to integrate the VAC function ? > Thanks in advance for your helps. > Best regards, > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
