[gmx-users] required topology stuff modification for GBSA

Dear GROMACS users: This is self-reply to resolve the following error I'd met. > Then I believe the error > > "Fatal error: > > Cannot find length for atoms 1-3 involved in angle". > occurs with some side-effects from the implicit solvent setting. I'd found that the topology stuff should be more

[gmx-users] Re: About the %SS values in the output of do_dssp

Ok Thank you Justin for this clarification > > > > sa wrote: > > Dear All, > > > > I have simulated 6 peptides (with 7 AA each capped in N and C termini) > > in water and trehalose. During all the simulation time, the six peptides > > have b-sheet conformations. I would like to calculate the a

[gmx-users] R: gmx-users Digest, Vol 86, Issue 183

Dear Tsjerk, dear all, thank you very much for suggestion. One of the main reasons why I never used the rhombic dodecahedron box for my simulations is the fact that it is really hard to visualize the results with programs such as VMD or Pymol, and therefore I cannot check easily during the setting

[gmx-users] about periodic image violations

Sorry, I forgot to change the subject of my previous mail. Anna -Messaggio originale- Da: Anna Marabotti [mailto:anna.marabo...@isa.cnr.it] Inviato: martedì 28 giugno 2011 12.09 A: 'gmx-users@gromacs.org' Oggetto: R: gmx-users Digest, Vol 86, Issue 183 Dear Tsjerk, dear all, thank you v

[gmx-users] Broken protein chain.

Dear users, Has anyone done simulation with a broken crystal structure? I know that it can be modeled before simulating. But I just wanted to know whether any one had done with the crystal structure having breakage as such without modelling. Thanking you Respectfully M. Kavyashree -- gmx-users m

[gmx-users] Tabulated potential for metal-oxide

Dear All, I've just started using GROMACS, I've read the manual and searched the mailing list but still confused. I'm trying to simulate metal oxidation with GROMACS. As a first step, I'm trying to tabulate the EAM (Embedded atom potential), which in addition to residual pair-pair repulsion includ

Re: [gmx-users] about periodic image violations

Anna Marabotti wrote: Sorry, I forgot to change the subject of my previous mail. Anna -Messaggio originale- Da: Anna Marabotti [mailto:anna.marabo...@isa.cnr.it] Inviato: martedì 28 giugno 2011 12.09 A: 'gmx-users@gromacs.org' Oggetto: R: gmx-users Digest, Vol 86, Issue 183 Dear T

Re: [gmx-users] Broken protein chain.

Kavyashree M wrote: Dear users, Has anyone done simulation with a broken crystal structure? I know that it can be modeled before simulating. But I just wanted to know whether any one had done with the crystal structure having breakage as such without modelling. You need an intact starting s

Re: [gmx-users] Broken protein chain.

Sir, Ok Thanks. With Regards M. Kavyashree On Tue, Jun 28, 2011 at 4:25 PM, Justin A. Lemkul wrote: > > > Kavyashree M wrote: > >> Dear users, >> >> Has anyone done simulation with a broken crystal structure? >> I know that it can be modeled before simulating. But I just wanted >> to know whet

[gmx-users] force on protein by solvent

Dear all, I want to calculate the force on each protein atom induced by the SPC solvent. Therefore I use the mdrun -rerun option and add to the .mdp file the line energygrps = Protein SOL If I compare afterwards the total force and the force of the solvent written to the trr file I get

Re: [gmx-users] Tabulated potential for metal-oxide

On 28/06/2011 8:49 PM, manana koberidze wrote: Dear All, I've just started using GROMACS, I've read the manual and searched the mailing list but still confused. I'm trying to simulate metal oxidation with GROMACS. As a first step, I'm trying to tabulate the EAM (Embedded atom potential), whic

Re: [gmx-users] gromacs 2.1

On Sun, Jun 26, 2011 at 14:09, wrote: > /bin/sh: line 0: cd: include: No such file or directory There's a mistake in the Makefile: include is one level higher, but is treated as if it would be in the current level and a "cd .." is done afterwards. You can move include into src, or just add a lin

[gmx-users] reg ionic strngth

Dear justin,    Thank you for your Previous Reply. Now I am studying The effect of ionic strength on the disassociation of My protein using  steered MD . I would like to explain my result of  pullf.xvg  force profile variation for different concentration of ions .  my Question is

[gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27

Dear gromacs users, I constructed a small *.pdb file comprised of only lipids (POPE bilayer). If I try to convert this pdb file with pdb2gmx (gromacs 4.5.4) and the included charmm27 forcefield, I get warnings for "missing hydrogen atoms" and "Long Bond" warnings. In other threads, the lipid

[gmx-users] How to protonate a gmx trajectory?

Hi there, I am using GROMACS4.5.4 and the GROMOS 53A6 united-atom force field to do MD with my protein-ligand system. I was trying to add aliphatic hydrogens to the .gro and .trr or .xtc trajectory file with g_protonate, but the Fatal error was: Library file in current dir nor not found ffgmx

Re: [gmx-users] reg ionic strngth

vidhya sankar wrote: Dear justin, Thank you for your Previous Reply. Now I am studying The effect of ionic strength on the disassociation of My protein using steered MD . I would like to explain my result of pullf.xvg force profile variation for different concentration o

Re: [gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27

kalav...@gmx.net wrote: Dear gromacs users, I constructed a small *.pdb file comprised of only lipids (POPE bilayer). If I try to convert this pdb file with pdb2gmx (gromacs 4.5.4) and the included charmm27 forcefield, I get warnings for "missing hydrogen atoms" and "Long Bond" warnings.

Re: [gmx-users] How to protonate a gmx trajectory?

Yun Shi wrote: Hi there, I am using GROMACS4.5.4 and the GROMOS 53A6 united-atom force field to do MD with my protein-ligand system. I was trying to add aliphatic hydrogens to the .gro and .trr or .xtc trajectory file with g_protonate, but the Fatal error was: Library file in current dir n

[gmx-users] building a new molecule which does not exist in gmx data base

Dear Justin and other gmx-users, As per the journal article, Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies, PRODRG 2.5 server does not assign charges compatible with GROMOS force field. PRODRG 2.5, however, assigns the correct atom types and bonded parameters.

Re: [gmx-users] building a new molecule which does not exist in gmx data base

shivangi nangia wrote: Dear Justin and other gmx-users, As per the journal article, Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies, PRODRG 2.5 server does not assign charges compatible with GROMOS force field. PRODRG 2.5, however, assigns the correct atom

[gmx-users] Directional Thermostat in GROMACS

Hi, I want to implement a directional thermostat in GROMACS. But I am not sure which files I will need to modify. Can anyone help me with this. I am using GROMACS 4.5.1. Thanks. Apoorv -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please s

Re: [gmx-users] Directional Thermostat in GROMACS

On 29/06/2011 5:49 AM, Apoorv Kalyankar wrote: Hi, I want to implement a directional thermostat in GROMACS. But I am not sure which files I will need to modify. Can anyone help me with this. I am using GROMACS 4.5.1. You'll have to look at how the existing T-coupling regimes work. src/mdlib/c

Re: [gmx-users] R: gmx-users Digest, Vol 86, Issue 183

On 28/06/2011 8:09 PM, Anna Marabotti wrote: Dear Tsjerk, dear all, thank you very much for suggestion. One of the main reasons why I never used the rhombic dodecahedron box for my simulations is the fact that it is really hard to visualize the results with programs such as VMD or Pymol, and ther

[gmx-users] trjorder and index

Hi, I am trying to use trjorder command to generate a sorted trajectory where all the water molecules are certain distance away. I can use the trjorder command to generate the sorted trajectory where all waters are sorted based on distance but I am looking for method for creating a index fil

Re: [gmx-users] trjorder and index

Sanku M wrote: Hi, I am trying to use trjorder command to generate a sorted trajectory where all the water molecules are certain distance away. I can use the trjorder command to generate the sorted trajectory where all waters are sorted based on distance but I am looking for method for cre

[gmx-users] converting psf file to gromacs .itp file

Hi, Is there any way to convert NAMD generated psf file to GROMACS .itp file as I have generated the parameters for my compound using NAMD.. -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.

Re: [gmx-users] converting psf file to gromacs .itp file

bharat gupta wrote: Hi, Is there any way to convert NAMD generated psf file to GROMACS .itp file as I have generated the parameters for my compound using NAMD.. Both are just text files; use your favorite scripting language to convert between the two. There is a program called top2psf.p

[gmx-users] Running Lyz in water

Dear all, I have been running lyz in water. I have 20 ps pre-equilibrated NVT and 200 ps NPT configuration of spce216 water. I am following the instruction from gromacs tutorial. This is the link for the tutorial, http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/l