[gmx-users] membrane protein simulation

Title: membrane protein simulation Hi gmx-users I am trying to set up an ED experiment with the low resolution structure of a membrane protein in the hope of generating NMR-like structures. >From what I have read until now, I know that I should either restrain the transmembrane domain of th

[gmx-users] binding free energy calculations on charged ligands

Hello all,   I'm still trying to get the binding free energy for my ligands, and I now think I will have to do another simulation, since my first one used PME and I didn't record velocities in my trajectory.   But first I need some advice, since I can't find a paper which describes unambiguously

RE : [gmx-users] *.xvg to jpeg/pdf/png

Hi Arindam To read *.xvg files you need the xmgrace software, which is distributed free of charge, sometimes as a rpm depending on your linux version. It is also available for Cygwin, but I have never managed to make it work. Once you have opened the *.xvg file in xmgrace (xmgrace *.xvg), you

RE: [gmx-users] Ligand binding energy using LIE with PME

one residue away from the active site ? -Original Message- From: [EMAIL PROTECTED] on behalf of Diane Fournier Sent: Wed 8/16/2006 10:10 AM To: gmx-users@gromacs.org Subject: [gmx-users] Ligand binding energy using LIE with PME Hi gmx-users I know that this has been discussed before

RE: [gmx-users] steroid topology

I am also working with steroids (but in my case, steroidal hybrid inhibitors) with the gmx force field. From my experience working with the PRODRG program, the topologies needed some modifications (for example the program assigns my phenol OH as a carbonyl and one aromatic bare carbon as a CH1)

[gmx-users] Ligand binding energy using LIE with PME

Title: Ligand binding energy using LIE with PME Hi gmx-users I know that this has been discussed before from consultation of the mail archive, but there is still confusion : I want to obtain the ligand binding energy from my 1ns PME simulation of a ligand-protein complex. I have made, as di

RE: [gmx-users] problem with ambconv

Diane, We have an in-house script called amb2gmx written in collaboration with the Pande group that works for this purpose, although it requires an installation of AMBER. Let me know if you would like it. Thanks, David On 8/4/06, Diane Fournier <[EMAIL PROTECTED]> wrote: > > >

[gmx-users] problem with ambconv

Title: problem with ambconv Hi I'm presently trying to use the ambconv program to convert amber topologies generated with antechamber v. 1.26 and tleap to gromacs format for use with the amber force field port. The problem is, I can't get the program to work. For example : $ ambconv -v -at

RE: [gmx-users] does gromos force field can explain pi-pi interaction

Yes, this looks like the force field application of the Hunter point-charge model (J. Am. Chem. Soc.; 1990; 112(14); 5525-5534). This force field could theoretically be used to model pi-stacking in proteins, as a more computationally economical procedure compared to QMMM. Unfortunately, I don

RE: [gmx-users] does gromos force field can explain pi-pi interaction

I have read a lot on this subject since I wanted to prove one such interaction myself (between inhibitor and enzyme). Generally, authors who talk of such interaction never give proof using simulation, but use a simple geometric criteria (benzene rings are superposed in T-shape or face-to-face s

[gmx-users] MPI gromacs usage

Hi gromacs users   I've already used gromacs single-processor version and I want to use the parallel version of gromacs on a SGI Altix 2700 with 32 processors. I'm wondering how to proceed, because this does not seem to be explained properly anywhere. Do I have to give special instructions in g

[gmx-users] prodrg and charge groups

Title: prodrg and charge groups I don't know if this has already been discussed, but I'm wondering how the charges and charge groups are assigned by PRODRG. I'm curious about this because I have been using it for a few similar ligands which all contain a steroid (estradiol) moiety. In the thr

RE : [gmx-users] Does Gromacs work on a molecule w hich is not protein

For molecules which are not amino acids, DNA or RNA, you have to write a topology yourself. There are some tools that can help you with that. If you plan to use the gromacs united-atom forcefield (ffgmx), you can try PRODRG, which is available on the Dundee server (http://davapc1.bioch.dundee.a

RE : [gmx-users] Fatal error: moleculetype S OL is redefined.

I had the same problem once, and it turned out that I had mistakenly put information about my ligand molecule in the "moleculetype" section of my enzyme topology file. That info is also given in the .itp files that are included into your peptide topology file (at the end of the file for ions and

RE: [gmx-users] ligand falling out of active site during EM

, Diane Fournier <[EMAIL PROTECTED]> wrote: > Still on the same problem, I made a pr run on the complex, and had the same > result (ligand is out of the active site at time = 0.000 ps. Then I ran the > same pr run, but with dt = 0.001 ps with all coordinates output for my > tr

RE: [gmx-users] ligand falling out of active site during EM

if my input coordinates have the ligand inside. What is happening ?? -Original Message- From: [EMAIL PROTECTED] on behalf of Diane Fournier Sent: Fri 5/5/2006 3:05 PM To: gmx-users@gromacs.org Subject: [gmx-users] ligand falling out of active site during EM Hello ! I'm trying to

[gmx-users] ligand falling out of active site during EM

Title: ligand falling out of active site during EM Hello ! I'm trying to run a molecular dynamics on a drug-enzyme complex. I did John Kerrigan's tutorial and everything worked fine. Now I'm trying with my system but I get a problem : the ligand keeps falling out of the active site during EM

RE : RE : [gmx-users] segmentation fault in mdrun when using PME

0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Diane Fournier wrote: De: [EMAIL PROTECTED] de la part de David van der Spoel Da

RE : [gmx-users] segmentation fault in mdrun when using PME

De: [EMAIL PROTECTED] de la part de David van der Spoel Date: lun. 2006-05-01 13:33 À: Discussion list for GROMACS users Objet : Re: [gmx-users] segmentation fault in mdrun when using PME Have you enabled fortran at the compilation stage? In that case try it

RE: [gmx-users] segmentation fault in mdrun when using PME

-Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Sat 4/29/2006 2:25 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] segmentation fault in mdrun when using PME Diane Fournier wrote: > Hi, I'm new to Gromacs and I'm tr

[gmx-users] segmentation fault in mdrun when using PME

Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex molecular dynamics simulation. I have tried doing John Kerrigan's Drug-Enzyme tutorial and mdrun crashes with segmentation fault and core dump at the steepest descents minimization step. However, mdrun works fine when using cu