Re: [gmx-users] Regarding umbrella sampling simulations along H-bonds

Dear Neeru Sharma, I know off hand from years of work with Mg-GTP sites, they are realativly rigid/staritforward. If the bonds arn't present with occupied GTP, or Mg at the beggining, you should equilabrate your starting structures more. Unless your looking at the GTP binding to Mg in which c

[gmx-users] Force constant - units

Dear Gmx Users, How to recalculate the force constant from the harmonic potential: 1 [pN/A] into [kJ/mol nm2] ? Where is the [mol] here? Thanks, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed

[gmx-users] editconf do not center protein

Hi everybody, I want to put my protein in a box with the command: editconf -f 3m71.gro -o 3m71_box.gro -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut and add solvent afterwards with: genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro 2>>logErr 1>>logOut But when I look at it I

Re: [gmx-users] Berger lipid

Hi Shima, The lipids.rtp file in the charmm36.ff folder has many different entries for lipids. All you need to do is to run pdb2gmx with just one of your lipids of interest. This will produce a .top for this one lipid which is trivial to convert into an .itp (see Chapter 5 of the manual). Ch

Re: [gmx-users] Berger lipid

Dear Thomas, It's a good idea. Thanks :)   Sincerely, Shima - Original Message - From: Thomas Piggot To: Discussion list for GROMACS users Cc: Sent: Friday, June 29, 2012 1:39 PM Subject: Re: [gmx-users] Berger lipid Hi Shima, The lipids.rtp file in the charmm36.ff folder has many d

[gmx-users] no SOL in topology file after genbox command

Hi everybody, I wanted to add water in the box where I put the protein with the command genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro 2>>logErr 1>>logOut The result is that I have indeed water (SOL) in the protein file (3m71_water.gro). But there is a problem in the topolog

[gmx-users] Structure optimization failure

Hello I use a CHARMM27 force field and my system is lumiflavin in water. I use the spc216 water model, a dodecahedral box with 1.3 nm. I want to make a structure minimization. I made a file pr.mdp. Could you please tell me, what I could do better in this file, or what is wrong? I guess there ha

Re: [gmx-users] no SOL in topology file after genbox command

Make sure your top file #include ff/spc.itp On 2012-06-29 11:35:24AM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: > Hi everybody, > I wanted to add water in the box where I put the protein with the command > > genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro > 2

Re: [gmx-users] editconf do not center protein

On 6/29/12 4:48 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to put my protein in a box with the command: editconf -f 3m71.gro -o 3m71_box.gro -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut and add solvent afterwards with: genbox -cp 3m71_box.gro -cs spc216.gr

Re: [gmx-users] Structure optimization failure

On 6/29/12 6:01 AM, Lara Bunte wrote: Hello I use a CHARMM27 force field and my system is lumiflavin in water. I use the spc216 water model, a dodecahedral box with 1.3 nm. I want to make a CHARMM27 should be combined with TIP3P, not SPC. structure minimization. I made a file pr.mdp. Could

Re: [gmx-users] Berger lipid

yes http://www.frontiersin.org/Bioinformatics_and_Computational_Biology/10.3389/fgene.2012.00061/abstract The files are here: http://uab.hyperfine.info/~pcl/files/popc36/ On 2012-06-28 09:58:26PM -0700, Shima Arasteh wrote: > Yes, I remember now...you are right :) But I didn't kno

Re: [gmx-users] Berger lipid

Dear Peter, Thanks a lot :)   Sincerely, Shima - Original Message - From: Peter C. Lai To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Friday, June 29, 2012 2:54 PM Subject: Re: [gmx-users] Berger lipid yes http://www.frontiersin.org/Bioinformatics_and_Computational

[gmx-users] problem with git/4.6

hi as suggested in: http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6 i do: prompt> git clone git://git.gromacs.org/gromacs.git Cloning into 'gromacs'... remote: Counting objects: 119131, done. remote: Compressing objects: 100% (21428/21428), done. remote: Total 119131 (delta 100642), re

AW: [gmx-users] Structure optimization failure

Hi Lara, with the .mdp you sent you are NOT going to perform a minimization, but a NPT equilibration run (i.e. a MD simulation, as stated in the first line). So check a tutorial of your choice to get a proper .mdp for a simple energy minimization. Greetings Felix -Ursprüngliche Nachricht--

Re: [gmx-users] problem with git/4.6

On 6/29/12 6:27 AM, Michael Brunsteiner wrote: hi as suggested in: http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6 i do: prompt> git clone git://git.gromacs.org/gromacs.git Cloning into 'gromacs'... remote: Counting objects: 119131, done. remote: Compressing objects: 100% (21428/21

Re: [gmx-users] Structure optimization failure

Hi Thank you for the fast answer :-) I use a tip3p water model. I wrote spc216 because this is what I am using with genbox. My mistake. Now I used the equilibrating file out of this tutorial: http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html I got the s

Re: [gmx-users] Structure optimization failure

On 6/29/12 8:04 AM, Lara Bunte wrote: Hi Thank you for the fast answer :-) I use a tip3p water model. I wrote spc216 because this is what I am using with genbox. My mistake. Now I used the equilibrating file out of this tutorial: http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tuto

[gmx-users] error with grompp

Hi everybody, I added ions to the solvent around my structure with the command: genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA+ -nname CL- and then I select the 13 (SOL) Now I have in my topology file [ molecules ] ; Compound#mols Protein_chain_

[gmx-users] COM Pulling

HI , I have been performing SMD after reading bevan lab tutorial. The tutorial was very informative in basic aspects. Now I have my ligand inside the protein and I wan to pull it out in a specific direction. I applied force separately along the X, Y and Z axis . In which none of the pull seems to b

Re: [gmx-users] error with grompp

Hi, Check out the order of sections which you have included in your .top file. I always got this error because of the wrong orders of sections. Cheers, Shima From: "reising...@rostlab.informatik.tu-muenchen.de" To: gmx-users@gromacs.org Sent: Friday, Ju

Re: [gmx-users] error with grompp

On 6/29/12 8:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I added ions to the solvent around my structure with the command: genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA+ -nname CL- and then I select the 13 (SOL) Now I ha

Re: [gmx-users] error with grompp

On 6/29/12 9:04 AM, Shima Arasteh wrote: Hi, Check out the order of sections which you have included in your .top file. I always got this error because of the wrong orders of sections. Incorrect order will lead to a series of "non-matching atom names" in the grompp output. In this case

Re: [gmx-users] COM Pulling

On 6/29/12 9:03 AM, Raj wrote: HI , I have been performing SMD after reading bevan lab tutorial. The tutorial was very informative in basic aspects. Now I have my ligand inside the protein and I wan to pull it out in a specific direction. I applied force separately along the X, Y and Z axis . I

Re: [gmx-users] Structure optimization failure

On 6/29/12 9:04 AM, massimo sandal wrote: On 29 Jun 2012 14:08, "Justin A. Lemkul" mailto:jalem...@vt.edu>> > > The settings in my tutorial are for use with OPLS-AA and are thus not suitable for a simulation with CHARMM. Cutoffs and other aspects will be different. This is interesting. In

Re: [gmx-users] error with grompp

So just entering the -pname NA and -nname CL !   Sincerely, Shima - Original Message - From: Justin A. Lemkul To: Discussion list for GROMACS users Cc: Sent: Friday, June 29, 2012 5:36 PM Subject: Re: [gmx-users] error with grompp On 6/29/12 8:54 AM, reising...@rostlab.informatik.t

Re: [gmx-users] error with grompp

Hi Justin, thank you for your answer. So you mean that I should only name NA and CL like this: genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA -nname CL But when I now want to run the alraedy mentioned grompp command I get the error: No such moleculetyp

Re: [gmx-users] error with grompp

Thank you for your answer. I tried it only with NA and CL and it also didn't work. Now I have the same error with NA Bests Eva > > > Hi, > > Check out the order of sections which you have included in your .top file. > I always got this error because of the wrong orders of sections. > > > > > Chee

Re: [gmx-users] error with grompp

On 6/29/12 9:18 AM, Shima Arasteh wrote: So just entering the -pname NA and -nname CL ! Precisely, as genion -h instructs. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.

Re: [gmx-users] error with grompp

On 6/29/12 9:20 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, thank you for your answer. So you mean that I should only name NA and CL like this: genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA -nname CL This is a correct comm

[gmx-users] Re: COM Pulling

Thanks for your reply Justin. >From your umbrella tutorial I thought the reference group should be the protein. Now from your reply i think I can specify any amino acid residue in the protein and I can drive the ligand towards the residue. where I need to specify the group If i'm using the pull c

Re: [gmx-users] Re: COM Pulling

On 6/29/12 9:38 AM, Raj wrote: Thanks for your reply Justin. From your umbrella tutorial I thought the reference group should be the protein. Now from your reply i think I can specify any amino acid residue in the protein and I can drive the ligand towards the residue. where I need to specif

Re: [gmx-users] problem with git/4.6

> You should have it.  In CMakeLists.txt, PROJECT_VERSION should be set to > "4.6-dev" so you can check that. ithat what i looks like ... i now get: prompt> mdrun_d [...] :-)  VERSION 4.6-dev-20120629-9c6be1c  (-: [...] which gives me: g_bar_d -f mdv*.xvg -b 100 [...] tot

Re: [gmx-users] problem with git/4.6

On 6/29/12 11:08 AM, Michael Brunsteiner wrote: You should have it. In CMakeLists.txt, PROJECT_VERSION should be set to "4.6-dev" so you can check that. ithat what i looks like ... i now get: prompt> mdrun_d [...] :-) VERSION 4.6-dev-20120629-9c6be1c (-: [...] which give

Re: [gmx-users] Structure optimization failure

On 6/29/12 11:10 AM, massimo sandal wrote: On 29 Jun 2012 15:09, "Justin A. Lemkul" mailto:jalem...@vt.edu>> wrote: > > > > On 6/29/12 9:04 AM, massimo sandal wrote: >> >> >> On 29 Jun 2012 14:08, "Justin A. Lemkul" mailto:jalem...@vt.edu>

Re: [gmx-users] Force constant - units

Hi Steven, How much is 1 [pN/A] in [kJ/nm2] (without the mol)? And why would anyone want to use force-constants in the 10^-23 ? So why not define a force-constant for 1 mol of bonds instead of a sole bond? I think you can see where I'm going. Oliver On Fri, Jun 29, 2012 at 2:32 AM, Steven Neu

[gmx-users] pdb file of polymer

Hi, I am trying to do polymer simulation with gromacs. I am new to gromacs and trying to construct topology for a system of polymer chains. My problem is that i am facing difficulties to creat pdb file for polymer chain containing 1000 monomers. I have used PRODRG server but it gives me a pdb and t

[gmx-users] BAR gives different result than TI

Hi, we've been trying to do free energy calculations for solvation of two small molecules in water, n-butylamine (NBA) and diethyl-ether (DEE). For one of them the result with BAR (using Justin's tutorial) is significantly different from TI: BAR TI Exper. (kJ/mol) NBA -11.1

Re: [gmx-users] pdb file of polymer

On 6/29/12 2:21 PM, Parvez khan wrote: Hi, I am trying to do polymer simulation with gromacs. I am new to gromacs and trying to construct topology for a system of polymer chains. My problem is that i am facing difficulties to creat pdb file for polymer chain containing 1000 monomers. I have use

Re: [gmx-users] pdb file of polymer

thanx a lot Justin for reply Regards parvez On Fri, Jun 29, 2012 at 2:27 PM, Justin A. Lemkul wrote: > > > On 6/29/12 2:21 PM, Parvez khan wrote: >> >> Hi, I am trying to do polymer simulation with gromacs. I am new to >> gromacs and trying to construct topology for a system of polymer >> chains

[gmx-users] .top file incoherent with the values in the ffbonded.itp file

Hello My A.gro file is: 1PvB CB1 3.109 2.784 0.803 0. 0. 0. 1PvBHB12 3.156 2.880 0.843 0. 0. 0. 1PvBHB23 2.997 2.797 0.819 0. 0. 0. 1PvBHB34 3.129 2.765 0.693 0. 0. 0.

Re: [gmx-users] .top file incoherent with the values in the ffbonded.itp file

On 6/29/12 3:55 PM, sreeta.g wrote: Hello My A.gro file is: 1PvB CB1 3.109 2.784 0.803 0. 0. 0. 1PvBHB12 3.156 2.880 0.843 0. 0. 0. 1PvBHB23 2.997 2.797 0.819 0. 0. 0. 1PvBHB34 3.12

[gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file

Hi Justin Thank you for your reply. However, when I am using the grompp command, the topol.tpr file is not being formed due to a fatal error. This fatal error is the cumulative of ' No default Ryckaert-Bell.' types for many atoms in the polymer chain. Also, regarding the comment on the atom types a

Re: [gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file

On 6/29/12 4:44 PM, sreeta.g wrote: Hi Justin Thank you for your reply. However, when I am using the grompp command, the topol.tpr file is not being formed due to a fatal error. This fatal error is the cumulative of ' No default Ryckaert-Bell.' types for many atoms in the polymer chain. And a

Re: [gmx-users] error with grompp

Hi Justin, yes I removed all the old resulting files and did everything again. So now there is the topology and coordinate file with only NA and CL and not NA+ or CL-. I also checked whether the molecules are listed in the same order as in the .gro file and it is the case. So that is also correct.

Re: [gmx-users] error with grompp

On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, yes I removed all the old resulting files and did everything again. So now there is the topology and coordinate file with only NA and CL and not NA+ or CL-. I also checked whether the molecules are listed in the

[gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file

Hi Justin I have changed all the force field parameters as below, (I have already shown my ffbonded.itp file) ffnonbonded.itp ; name bond_typemasscharge ptype sigma epsilon opls_966 CA612.01100 0.240 A3.5000e-01 3.3600e-01 opls_967 CA6

Re: [gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file

On 6/29/12 6:10 PM, sreeta.g wrote: Hi Justin I have changed all the force field parameters as below, (I have already shown my ffbonded.itp file) ffnonbonded.itp ; name bond_typemasscharge ptype sigma epsilon opls_966 CA612.01100 0.240 A3.500

[gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file

Hi Justin I read through the beastly error file and did as you said. It worked! Just missed a few lines in the ffbonded.itp. Thank you -- View this message in context: http://gromacs.5086.n6.nabble.com/top-file-incoherent-with-the-values-in-the-ffbonded-itp-file-tp4998966p4998975.html Sent from