[gmx-users] merge ligand and protein
Dear All I tried to merge the ligand togethere with the protein by using pdb2gmx. However, it doesn't work. Is there another way to merge ligand and protein together. Thank you so much for all of the answers Best RegardKanin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] merge ligand and protein
On Tuesday 12 September 2006 10:00, kanin wichapong wrote: > Dear All >I tried to merge the ligand togethere with the protein by using > pdb2gmx. However, it doesn't work. Is there another way to merge ligand and > protein together. >Thank you so much for all of the answers take a look at http://www.gromacs.org/gromacs/documentation/tutorial.html John Kerrigans drug/enzyme tutorial and another GROMACS intro > > Best Regard > Kanin -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: genion causing atom to be in multiple T-Coupling groups
Una, In your case you can also try the T-coupling groups Protein and Non-Protein, without providing a .ndx file. However, in general give some thoughts to temperature coupling (groups) when setting up your system and try to grasp how groups are treated in gromacs. Hope it helps, Tsjerk On 9/11/06, David van der Spoel <[EMAIL PROTECTED]> wrote: Una Bjarnadottir wrote: > Una Bjarnadottir wrote: > >>> Dear Users, >>> >>> I'm hoping for an answear on my problem with neutralizing my system >>> adding 3 Cl ions with genion. When running grompp after genion with >>> the new generated .gro file I get this error: >>> >>> Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1) >>> >>> which is the last water atom (total in system 33003) and groups 15 >>> and 1 are Cl and protein groups if I on the other hand do not >>> neutralize the system the run goes fine! When looking into the .ndx >>> file atom 33000 is in 4 groups; 0 (system), 11 (non-protein), 14 >>> (SOL) and 16 (other). How can I change the group definitions and >>> make sure the groups do not overlap and to be unique? >>> It seems to be something wrong with how the genion works for me. I >>> followed the tutorial and chose the SOL group and water molecules >>> were replaced by the Cl ions. Than I modifyed the .top file and took >>> 3 sol molecules and added the 3 ions. >>> >>> Please help because have not been able to fix the problem with >>> related letters on the subject on the list. >>> >>> Best regards, Una Bjarnadottir >>> >> >> >>> What do your tcoupl groups look like? > > tc-grps':'Protein OTHER CL- ###where I have to call SOL: OTHER > otherwise error > >>> Could it be System SOL? > >>> The number may be confusing, you should subtract one from them when >>> compared to the output from gmxcheck -n index.ndx >>> So it seems that atom 33000 (numbering in the coordinate file) is in >>> groups 14 and 0. Maybe you should make a new index file after genion. >>> Note that it is good practice to make the ions part of the solvent T >>> coupling group. > > I made the indes file after running genion using the .gro output file > from genion generating it. Also I thought you would have to subtract > one and it was groups 14 and 0 instead of 15 and 1. How would I have > the ions part of the solvent T coupling group? By modifying the .top > file to [ molecules ] > ; Compound#mols > Protein_E 1 > Protein_I 1 > Protein_A 1 > SOL+CL- 9719 > > and than the tc-grps in the .mdp file accordingly to that. How will I > define SOL and CL- together, I tryed SOL+CL- and SOL-CL- but Fatal > error: No such moleculetype SOL+CL- came for both. > Best regards David for your reply, Una David. in make_ndx you type 14 | 15 that will give you the combination of the two groups (if 14 is SOL and 15 is CL-) > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] merger ligand and protein to constriant
Hi all I already look in the turorial however that is not the thing that I try to look for. I would like to merge the ligand into the protein and then make the contrain between two atoms, one from the liagand and one from the protein. However, as far as I know, I can do the constraint or restraint just in the one chain. I cant do that with the different chain. So that i try to merge ligand chain and protein chain. I tried to do that with pdb2gmx but it is not work. So that i would like to know is there any way to merge the ligand chain with the protein chain. Thanks for all your suggstionsBest RegardKanin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re:[gmx-users] merger ligand and protein to constriant
What about merging the ligand the the protein by DeepView? In your mail: >From: "kanin wichapong" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: gmx-users@gromacs.org >Subject: [gmx-users] merger ligand and protein to constriant >Date:Tue, 12 Sep 2006 13:40:59 +0200 > >Hi all > I already look in the turorial however that is not the thing that I try to >look for. I would like to merge the ligand into the protein and then make >the contrain between two atoms, one from the liagand and one from the >protein. However, as far as I know, I can do the constraint or restraint >just in the one chain. I cant do that with the different chain. So that i >try to merge ligand chain and protein chain. I tried to do that with pdb2gmx >but it is not work. So that i would like to know is there any way to merge >the ligand chain with the protein chain. >Thanks for all your suggstions > >Best Regard >Kanin >___ >gmx-users mailing listgmx-users@gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to [EMAIL PROTECTED] >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 don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] merger ligand and protein to constriant
Hi, you can also have different chains (Protein and Ligand) and constrain them. Using the -merge option you can merge the ligand into the protein but for that you need the topology for the ligand (as rtf, not from prodrg). If you use Prodrg-topology you first set up the protein without ligand. Then you include the topology for the ligand into the protein topology (#include XXX.top) and also the coordinates in the protein-gro-file. Then you can proceed with adding water, ions, etc. Then you can also apply position-restraints. By the way, as far as I know Sonja Schlimme has used a similar kind of setup in her MD simulations. So you could also ask her. Best regards, Björn > Hi all > I already look in the turorial however that is not the thing that I try > to look for. I would like to merge the ligand into the protein and then > make the contrain between two atoms, one from the liagand and one from the > protein. However, as far as I know, I can do the constraint or restraint > just in the one chain. I cant do that with the different chain. So that i > try to merge ligand chain and protein chain. I tried to do that with > pdb2gmx but it is not work. So that i would like to know is there any way > to merge the ligand chain with the protein chain. > Thanks for all your suggstions > > Best Regard > Kanin -- Björn Windshügel Department of Pharmaceutical Chemistry University of Kuopio Harjulantie 1 70211 Kuopio, FINLAND Phone: (+358) 17 162463 Fax: (+358) 17 162456 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] cross terms!!
hello,gmx-users yes! thanks david!! where and how the cross terms, like bond-bond and bond-angle cross potential terms, designated in the parameter file. the mannual had these potential functions but i don't know how to switch it off, so as to make the parameter for my system the same with those in literature. regards! thanks! Rongliang Wu [EMAIL PROTECTED] 2006-09-12 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] cross terms!!
Rongliang Wu wrote: hello,gmx-users yes! thanks david!! where and how the cross terms, like bond-bond and bond-angle cross potential terms, designated in the parameter file. the mannual had these potential functions but i don't know how to switch it off, so as to make the parameter for my system the same with those in literature. not sure I understand what you mean. best thing to try is to write a topology file, run grompp and then with gmxdump -s topol.tpr | less you check whether the parameters are interpreted correctly by grompp. these functions have not been excessively tested, so please compare results carefully! regards! thanks! Rongliang Wu [EMAIL PROTECTED] 2006-09-12 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RB dihedral potential query in OPLS
hello gmx users, First of all thanks to Chris for his response to my previous mail.But I still have a doubt regarding RB potential which I would like to get clarified about. I would be very thankfull if you can go through my post (patiently) and comment on it. ___ Gromacs 3.2 manual states " The use of RB potential implies exclusion of LJ interactions between the first and the last atom of the dihedral..." I also searched the mailing list and came accross a response from David to one of the queries which is as follows: "The original Ryckaert Bellemans potential is for carbon tails only (e.g. decane, or lipids). The same potential is used in OPLS but with different parameters in which the(scaled) pair interaction is part of the parameterization" http://www.gromacs.org/pipermail/gmx-users/2004-May/010500.html Gromacs 3.3 manual along with the above mentioned statement in manual 3.2 also states that: "Ryckaert-Bellemans potentials are also used in e.g. the OPLS force field in combination with 1-4 interactions. You should therefore not modify topologies generated by pdb2gmx in this case". I presently ran a MD simulaiton of a protein solvated in water using gromacs 3.2.1 and OPLS-AA force filed.A energy output in the log file looks like: Bond AngleProper Dih. Ryckaert-Bell. LJ-14 1.15231e+032.92374e+031.73760e+021.32334e+031.86599e+03 Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) 5.03326e+031.39004e+05 -1.66722e+03 -9.54632e+05 -5.37046e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -8.58528e+051.57277e+05 -7.01250e+053.04174e+02 -4.80269e+01 So I have a Ryckaert-Bell. energy term for Proper dihedral potential. I also have a 14 terms for LJ and Coulomd energy. My initial impression was that once we use the RB dihedral term,we may actually not get the 14 term in my energy profile (Manual 3.2) But after going through the manual 3.3 and also Divid's post,I suppose that the parameters in OPLS-AA are so defined that RB potential along with the 14 interactions (scaled) are calculated seperately. Is this the case? PS: Chris suggested me to check the [pairs] and [dihedral] entry in the *.top (*.itp) file which I did and I found identical atoms in both the entries which according to Chris should not be the case...So I am more confused. Regards. Alok Jain. > >>In manual (chapter 4 page no 62) it was written The use of RB potential >>implies exclusion of LJ interaction between first and the last atom of >> the >>dihedral (mean 1-4 interaction).So why I am getting LJ-14 and Coulomb-14 >>energy in my log file (see below) is there is any problem in this >>simulation or it is normal? > > Only the 1-4 interactions spanning RB potentials should be excluded from > LJ-14 > and coulomb-14. For example, lipid headgroups may be treated without RB's > and > the acyl chains treated with RB's. If you want to see where things are > coming > from, make an index file and then use enerygrps in your .mdp so that > g_energy > can give you some useful output for further testing. Look at your [ pairs > ] > section in your .itp file. Those are the source of the LJ-14 and > Coulomb-14 > energies. > >>and what I understood from articles on OPLS force field that it scale >> down >>the LJ-14 and Coulomb-14 energy my a factor of two? as it is specify in >>ffoplsaa.itp file >>what about GROMOS96 force field, it is mention in manual (Chapter 4 page >>no 75) it also scale down the LJ-14 repulsion term . >>what I understood by manual that It uses separate parameter for LJ-14 >>interaction Is it is correct? If yes then It uses separate parameters >> only >>for LJ repulsive term or all the non bonded terms i.e. LJ repulsive,LJ >>attractive and for coulomb term? > > The .itp file for your molecules will have the information that you are > after. > 1. The [ pairs ] section is a list that defines what 1-4 interactions > exist. If > a 1-4 pair is not in the [ pairs ] section, LJ-14 and Coulomb-14 > interactions > will not be included in the energies. > > **That's a good test for you right there. Remove all entries from the [ > pairs ] > section and your 1-4 energies should drop to zero. > > 2. The charges for 1-4 interactions are the normal ones, and FudgeQQ will > be > applied. > 3. The LJ sigma / epsilon parameters will be taken from [ pairs ] if they > are > there, or (second in hiearchy) from [ pairtypes ] if they are there, or > (third > in hiearchy) generated from the regular non-bonded parameters if > gen-pairs=yes. > In this third case, FudgeLJ is applied. > > Each force-field has its own rules (e.g. gen-pairs and FudgeLJ/QQ), but > these > apply to the information outlined above. For example, gen-pairs does NOT > mean > "generate a [ pairs ] sectio
[gmx-users] re: RB dihedral potential query in OPLS
Those OPLS-AA "Ryckaert Bellemans" terms are intended to work with [ pairs ]. They are not the same as the real RB terms. Here is a good explaination: http://www.gromacs.org/pipermail/gmx-users/2004-May/010500.html "The original Ryckaert Bellemans potential is for carbon tails only (e.g. decane, or lipids). The same potential is used in OPLS but with different parameters in which the (scaled) pair interaction is part of the parameterization." My appologies for leading you astray earlier, I thought you were refering to RB terms in lipid tails. Chris. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] CVS password
Hi, I executed this command : cvs -z3 -d :ext:@cvs.gromacs.org:/home/gmx/cvs co gmx But I don't have the password. What is the password? Thanks. ALVARO FERNANDEZ ``` GRUPO DE QUÍMICA TEÓRICA: /\\ PROCESOS DINÁMICOS EN QUÍMICA |()|| \// Facultad de Ciencias - ULA La Hechicera, Mérida-5101 - Vlza. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fatal error: Force field inconsistency
Hello, I had this error while trying to run a simulation for a small molecule without water and bilayer, I have included in the topol.top its parameters taken from OPLS and its topology, since I did not created the topology with the pdb2gmx I did not included the ffoplsa.itp in the topol, however after grompp -norenum debug, and mdrun I got the following message Fatal error: Force field inconsistency: 1-4 interaction parameters for atoms 9-10 not the same as for other atoms with the same atom type. I already checked the [pairs] and found that for the same type of atoms the parameters are the same . so why is giving me this error?. It doesn't make sense. I read in the GROMACS mailing list that including -norenum with grompp, it make work but it did not, so what I did was to commented out the 9-10 pair interaction from [pairs], but still the same error, then I comented out [pairs] and all the 1-4 interactions defined in [pairs] in my molecule.itp, and after grompp and mdrun the system did not complain. The thing is that now it is calculating the 1-4 interactions from the molecule parameters in molecule.itp [which has the parameters and topology], with :[ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 yes 1.0 0.5 because the explicit [pairs ] were comented out due to the Fatal error: Force field inconsistency. Can somebody give an advice, some people had this problem posted on the web, but I couldn't find the solution for my eventhought we all get the same error. Thanks, Sandra ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] running CPMD with GROMACS interface in SGI irix 6.5
Hi I got some trouble in running CPMD with GROMACS interface in SGI irix 6.5. Thanks in advance the error is [PEAK NUMBER 116] PEAK MEMORY 14169180 = 113.4 MBytes [ALL. NUMBER 116] TOTAL MEMORY 13983696 = 111.9 MBytes == PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK| CORRUPTED MEMORY [PROC= 8] EIGV 390897072 CORRUPTED 390994624 CORRUPTED 12193 SC0 390994640 CORRUPTED 391254032 CORRUPTED 32423 PME 391254048 CORRUPTED 391513440 CORRUPTED 32423 GDE 391513456 CORRUPTED 391772848 CORRUPTED 32423 HGPOT 391860984 CORRUPTED 392180992 CORRUPTED 4 HIPZ 392181008 CORRUPTED 394741016 CORRUPTED 32 NZFFP 394741032 CORRUPTED 396297320 CORRUPTED 194535 NZFSP 396297336 CORRUPTED 396987776 CORRUPTED 86304 396987792 CORRUPTED 403238296 CORRUPTED 781312 403238312 CORRUPTED 416826464 CORRUPTED 1698518 -- [PEAK NUMBER 116] PEAK MEMORY 14169180 = 113.4 MBytes [ALL. NUMBER 116] TOTAL MEMORY 13983696 = 111.9 MBytes == PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK| CORRUPTED MEMORY [PROC= 9] [PEAK NUMBER 116] PEAK MEMORY 14169180 = 113.4 MBytes [ALL. NUMBER 116] TOTAL MEMORY 13983696 = 111.9 MBytes == PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK| CORRUPTED MEMORY [PROC= 10]PC: 0xb18ca40 MPI_SGI_stacktraceback in /usr/lib64/libmpi.soPC: 0xb1b5e30 PMPI_Abort in /usr/lib64/libmpi.soPC: 0xb1e84b8 pmpi_abort_ in /usr/lib64/libmpi.so PC: 0x10624edc stopgm in /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.xPC: 0x1049884c memory_check in /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.xPC: 0x1051866c testex in /home/irix/meen/jzhang/qmmm/CPMD- 3.11.1/SOURCE/cpmd.xPC: 0x10447cd4 updwf in /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.xPC: 0x10399770 interface in /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.xPC: 0x10633614 interpt in /home/irix/meen/jzhang/qmmm/CPMD- 3.11.1/SOURCE/cpmd.xPC: 0x10698438 cpmd in /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.xPC: 0x10698510 cpmd_stuttgart in /home/irix/meen/jzhang/qmmm/CPMD-3.11.1/SOURCE/cpmd.xPC: 0x291fc34 main in /usr/lib64/libftn.so -- Sincerely yours,James jianzhangDepartment of Mechanical and Chemical Engineering North Carolina Agricultural and Technical State University 1601 East Market Street Greensboro, NC 27411 -- Sincerely yours,James jianzhangDepartment of Mechanical and Chemical Engineering North Carolina Agricultural and Technical State University 1601 East Market Street Greensboro, NC 27411 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] CHARMM force field implementation in Gromacs : conversion of periodic into Ryckaert-Bellemans parameters.
Hello, I have noticed that both in the Yuguang Mu's and the Mark Abraham's work, the periodic parameters of dihedral angles have been converted into Ryckaert-Bellemans ones. I have tried to find more info about this in the CHARMM and Gromacs documentations but I have not found much. Why exactly this conversion should be done since the periodic potential is implemented in both force fields? My problem is that several dihedral angles cannot be easily converted in RB parameters since their multiplicities is equal to 6 and the RB potential implemetation is limited to 5 constants. Thanks Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University Dr. NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] CHARMM force field implementation in Gromacs : retrieval of bonded/non-bonded parameters
Hello, I'm trying to use an implementation of the CHARMM force fields in Gromacs and I'm still a little bit confused about how Gromacs retrieves the bonded/non-bonded parameters when the .top file is created. Concretely, I have : 1. a ffcharmmnb.itp where I have defined specific 1-4 LJ parameters in the [pairtypes] section 2. a ffcharmmbon.itp where I have defined bonded parameters 3. a ffcharmm.rtp where I have defined the topology of amimo acids, etc. Since the [bonds], [angles], [dihedral] sections are optional in the .rtp file, I haven't defined them. How all these parameters are taken into account when I generate the .top file with pdb2gmx? When I look in the .top file, I see an [atoms] section but no [bonds] or [pairs] etc. and the charmm ff doesn't seem to be included with an #include command. So, are all my specific 1-4 parameters really taken into account in this case? In fact, I have tried to add somd bonds and improper but that generates a chunk of warnings when I use grompp. Sorry for this basic question but I'm still new in Gromacs... Thanks Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University Dr. NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CHARMM force field implementation in Gromacs : conversion of periodic into Ryckaert-Bellemans parameters.
> Hello, > > I have noticed that both in the Yuguang Mu's and the Mark Abraham's work, > the periodic parameters of dihedral angles have been converted into > Ryckaert-Bellemans ones. I have tried to find more info about this in the > CHARMM and Gromacs documentations but I have not found much. Why exactly > this conversion should be done since the periodic potential is implemented > in both force fields? My problem is that several dihedral angles cannot be > easily converted in RB parameters since their multiplicities is equal to 6 > and the RB potential implemetation is limited to 5 constants. To quote my own code comment, "# We need some elaborate functionality to convert the CHARMM dihedral type # of k * (1 + cos(n * xi - delta ) ) functions summed over n into something # GROMACS can implement. While the above functional form exists in # GROMACS, you can't have more than one function of this type, and # CHARMM has a number of dihedral interactions that require more than # one such function. However for delta = 0 or pi and n <= 5, then the above # cosine function can be expanded in powers of cos xi, and the coefficients # of the expansion can be summed in this conversion and presented to # GROMACS as a ready-made Ryckaert-Bellemans dihedral. In practice, this # works because CHARMM only uses such delta and n values for atom type # combinations that need multiple functions of the above form. Warnings # are issued when delta is some other value, and the algorithm dies if # n is > 6. In order to simplify GROMACS logfile output so that it only # has to report one sort of dihedral term for most simulations, all # dihedral terms with n <= 5 are expressed as R-B, even when not necessary. # Dihedrals with n=6 are left in periodic form, since it is not possible # to convert these to R-B form when the summation is limited to the # fifth power of cos xi." So if you have a single dihedral over a set of atoms that has n>=6 then you can leave it in periodic form and the only cost is that you have to remember that the output will likely have both periodic and R-B dihedrals. If you have one such a dihedral in combination with others n<6 then you can use a combination of periodic and R-B. If you have multiple dihedrals with n>=6 you will need to hack the source code, except in some trivial cases, perhaps. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CHARMM force field implementation in Gromacs : retrieval of bonded/non-bonded parameters
> Hello, > > I'm trying to use an implementation of the CHARMM force fields in Gromacs > and I'm still a little bit confused about how Gromacs retrieves the > bonded/non-bonded parameters when the .top file is created. Concretely, > I have : > 1. a ffcharmmnb.itp where I have defined specific 1-4 LJ parameters in the > [pairtypes] section > > 2. a ffcharmmbon.itp where I have defined bonded parameters > > 3. a ffcharmm.rtp where I have defined the topology of amimo acids, etc. > Since the [bonds], [angles], [dihedral] sections are optional in the .rtp > file, I haven't defined them. > > How all these parameters are taken into account when I generate the .top > file with pdb2gmx? Section 5.5.1 of the manual describes the behaviour of pdb2gmx in interpreting the contentes of the .rtp file in conjunction with the .itp files. > When I look in the .top file, I see an [atoms] section > but no [bonds] or [pairs] etc. In particular, you will read there that angles are automatically generated. Perhaps that should be amened to include the proviso that they are automatically generated only between pairs of bonds. Since you have defined no bonds, you will get nothing else. > and the charmm ff doesn't seem to be > included with an #include command. So, are all my specific 1-4 parameters > really taken into account in this case? In fact, I have tried to add somd > bonds and improper but that generates a chunk of warnings when I use > grompp. Go back and try adding bonds to your .rtp and see how you go. Cheers, Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] A method to scale Coulombic 1-4 interactions seperately
There is a recent publication about combining the Berger lipids with OPLS-AA and getting the correct 1-4 scaling factor. New dihedrals were developed because it is possible to set special 1-4 parameters for LJ, but not coulomb. However, there is another workaround to this that should be generally applicable to 1-4 coulombic scaling. The lipids.itp file has already defined [ pairtypes ] so the LJ 1-4 is scaled correctly (FudgeLJ will not be applied to the values in [ pairtypes ]). The problem now is that OPLS-AA requires a FudgeQQ of 0.5 and the Berger lipids desire a FudgeQQ of one. The solution comes in two parts: 1. Divide the epsilon entries in the [ pairtypes ] of lipid.itp by 2.0. Now the LJ and coulombic 1-4 interactions are both exactly half of what they should be. 2. Every entry in the [ pairs ] section of pope.itp should appear twice. Now the LJ and coulombic 1-4 interactions are both exactly what they should be. This solution should work for an arbitrary 1-4 scaling problem, just make sure that you get the ratios correct. A detailed method is outlined below and that is followed by the method that I used to test this procedure. I have also run a 0.5ns simulation and the system "looks" fine (when I say looks fine I mean by visual inspection or by g_density). 0.5ns is not nearly long enough to properly evaluate area per lipid, but for what it's worth I get 0.53nm^2 per lipid with regular combination rules and 0.52nm^2 per lipid with the half-epsilon-double-pair method outlined here. Perhaps the Gromacs crew could tell us whether a double [ pairs ] entry might run into problems in any special situations? # Method to change your files: 1. I assume that OPLS-AA + Berger lipid users have done something similar to this: http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html 2. copy ffoplsaa.itp to ffoplsaa_mod.itp and edit the new file to contain entries like this: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 #include "/dir/ffoplsaanb_mod.itp" #include "/dir/ffoplsaabon.itp" 3. copy ffoplsaanb.itp to ffoplsaanb_mod.itp and edit the new file to contain entries like this: ;Here are the unmodified atomtypes from lipid.itp LO LO 115.9994 0.000 A2.96000e-01 8.87864e-01 ;carbonyl O, OPLS LOM LOM 115.9994 0.000 A2.96000e-01 8.87864e-01 ;carbonyl O, OPLS ;... ;Here are the original parameters from lipid.itp that have been moved directly to this file. Note that these parameters are commented out and could be removed. ;[ pairtypes ] ; i j funct sigma epsilon ; LO LO 1 2.96E-011.10E-01 ; LO LOM 1 2.96E-011.10E-01 ; ;Here are the parameters from above where epsilon has been divided by 2.0 [ pairtypes ] ; i j funct sigma epsilon LO LO 1 2.96E-015.50E-02 LO LOM 1 2.96E-015.50E-02 ; 4. Copy your lipid topology file (e.g. pope.itp) and, in the new version, copy the [ pairs ] section to right underneath itself (without the [ pairs ] header) If it looked like this first (pope.itp): [ pairs ] 4 7 1 5 8 1 6 9 1 It should look like this after (pope_mod.itp): [ pairs ] ;Here is the first copy 4 7 1 5 8 1 6 9 1 ; Here is the second copy. Only use this with the modified LJ-14 epsilon values 4 7 1 5 8 1 6 9 1 5. Your run .top file should look like this: ; Include forcefield parameters #include "/dir/ffoplsaa_mod.itp" ; Include topologies #include "/dir/pope_mod.itp" [ system ] ... # TESTING: Use a system with a protein inserted into a membrane and solvated. OPLS-AA rules. 1. Do a run with nsteps=0 for the original setup and for the new setup 2. gmxdump the .trr file 3. diff the two gmxdumps The only differences are in the forces section and they only apply to atoms in the [ pairs ] section that have been intentionally modified. For example, in pope.itp I get different forces for all atoms except: H1,H2,H3, C17, C20-C31, C36, C39-CA2 There is no difference for some of these because they are not in the [ pairs ] list at all: H1,H2,H3,C20-C23,C25-C31,C39-CA2 There is no difference for some others because one of the parteners in the pair has a charge of zero: C17 in [ pair ] 13 17 (LH1 LP2; LP2 has zero charge) C36 in [ pair ] 32 36 (LC2 LP2; LP2 has zero charge) C24 in [ pair ] 24 27 (LP2 LH1; LP2 has zero charge) C25 in [ pair ] 22 25 (LH1 LP2; LP2 has zero charge) Remember that the LJepsilon was divided by 2 so with double inclusion the Lj portion is not changed at all. This is a decent internal test also because if we had accidentally modified the effecti
[gmx-users] wham question
hi all does anyone have an example/tutorial of how to do umbrella sampling using gromacs & wham? i'm about to try to calculate free energies of binding using this method. i can find no information whatsoever about 'wham.gct', which is an optional input mentioned in the mdrun online reference page. what is this file supposed to contain? i've yet to actually try it, but setting up the other input files seems relatively straightforward. i'm hoping to benefit from others' experience to figure out how to choose and vary the harmonic force constants for the different umbrella runs. any advice would be greatly appreciated. cheers mo __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Simulation problem with extended membrane system!
If I solvate my GPCR into the DPPC128 system using genbox, there are only about 50 lipids left, which I think are too few, so I want a larger starting structure.According to your note, when I did step 3, loaded my DPPC183 system to VMD, I found the edges lined up poorly, there is are gaps between two periodic cells. I also try other system like DPPC200, DPPC150, but only the original dppc128 system, I've equilibrated it for 2ns, have no gap between two periodic cells. So, I will try another starting structure, like POPC, DMPC or your POPE. But I still can't figure out why there are gaps when using genbox to extend the DPPC system.On 9/9/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: >According to your suggestion, I did a energy minimization and then a MDS>with "freezegrps=SOL, freezedim=N, N, Y", the rest of the system were>simulated with no constraint. This time I use semiisotropic pressure >coupling with tau_p=5. The system will be equilibrated with water>constrained for 1ns, do you think it's enough?It will be more than enough. Use vmd to watch the trajectory. It's importantactually look at the structures. >The reason why I want to extend the system is because that I've got a GPCR,>and I want to simulate it in a DPPC membrane environment, but the z>dimension of the membrane, downloaded from Dr. Tielman's websit, was not >large enough, when I align the protein to the z axis of the membrane I find>the two ends of the protein are poking out of both water layers.In this case you may not need to extend the lipid. Why not just use editconf to increase the z dimension while keeping the x and y constant. Then insert yourprotein, re-solvate, re-equilibrate, and your into production. If your lipidtakes up a maximum amout of space D in the xy-plane, then x and y need only be equal to [D + 2*max(LJ cutoff, Coulombic real-space cutoff) + some extra amountin case the protein fluctuations make it larger during the simulation].>Back to the previous question, after solvate the lipids in water, can I >remove the water placed in the membrane with excel instead of script? Cause>with editconf we can know the z dimension of the lipids_only system, let's>say 6, so if I center the whole system with 0 0 0, the water molecules with >z coordinates below 3 and above -3 will be excluded. If I'm right, I think>excel can do it too, or the scripts have some advantages?Sure you can use excel, but I am not sure how that is going to affect your formatting or how gromacs responds to formatting (i.e. spaces / tabs / thenumber of each) So scrips have 2 advantages: 1)formatting is easily maintained,2)if you need to do it a second time you just type one command. After using excel (or a script) make sure to update you topology file to indicate the numberof waters.___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].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 don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Simulation problem with extended membrane system!
>If I solvate my GPCR into the DPPC128 system using genbox, there are only >about 50 lipids left, which I think are too few, so I want a larger starting >structure. >According to your note, when I did step 3, loaded my DPPC183 system to VMD, >I found the edges lined up poorly, there is are gaps between two periodic >cells. I also try other system like DPPC200, DPPC150, but only the original >dppc128 system, I've equilibrated it for 2ns, have no gap between two >periodic cells. >So, I will try another starting structure, like POPC, DMPC or your POPE. But >I still can't figure out why there are gaps when using genbox to extend the >DPPC system. It's because any overlap causes an entire lipid to be removed. If you don't want to equilibrate, try exactly doubling your system size in x and y. That should work perfectly. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to write a annealing .mdp
hello everyone i want to anneal my system,but i don't konw how to wrote a right annealing-mdp! could anyone give me a moldel? tanks in advaced! 3G 时 代 来 临 了，坚 决 对 传 统 邮 箱 说 不 ！ 新 一 代 极 速 3G 邮 箱 闪 亮 登 场 ，280 兆 网 盘 免 费 送 ！ 点 击 此 处 注 册 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] does the conformation cause this error?
hi all i have a problem:when i did the mdrun ,it stopped early for error:Maximum force = 9.0996275e+09 on atom 606 Norm of force = 2.8519283e+08 does this cause by the conformation?and how to resolve it? 3G 时 代 来 临 了，坚 决 对 传 统 邮 箱 说 不 ！ 新 一 代 极 速 3G 邮 箱 闪 亮 登 场 ，280 兆 网 盘 免 费 送 ！ 点 击 此 处 注 册 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] does the conformation cause this error?
zzhwise1 wrote: > hi all > i have a problem:when i did the mdrun ,it stopped early for > error:Maximum force = 9.0996275e+09 on atom 606 > Norm of force = 2.8519283e+08 > > does this cause by the conformation?and how to resolve it? Yes. You are probably simulating with a structure that is either non-physical, or not energy-minimized before equilibration. If you haven't tried working through some tutorial material, now might be a good time to consider doing that. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
