Re: [gmx-users] creating trajectory with ligand close to the protein

Hi David, If you use a structure file (.gro/.pdb) which corresponds to the starting structure and has the protein and ligand in the right place, you can do it with trjconv -pbc nojump. Cheers, Tsjerk On Sun, Feb 24, 2008 at 4:47 AM, David Osguthorpe <[EMAIL PROTECTED]> wrote: > On Sun, Feb 24,

Re: [gmx-users] creating trajectory with ligand close to the protein

On Sun, Feb 24, 2008 at 01:35:51PM +1100, Mark Abraham wrote: > > > >Ive been using trjconv but it seems to be failing for a case where the > >protein switches > >image in the trajectory but the ligand does not. > > Check out trjconv -h, and if none of the options works, please describe > why th

Re: [gmx-users] creating trajectory with ligand close to the protein

David Osguthorpe wrote: Hi, Can anybody tell me what is the best way to re-write a trajectory run with periodic boundary conditions such that a molecule (eg. the protein) is chosen as the reference and every other molecule in the system (eg. ligands) is transformed such that its periodic imag

Re: [gmx-users] problem with exchange probabilities in remd

OZGE ENGIN wrote: Hi all, I am performing a remd simulation of a peptide+water system. I have tried different temperature distributions. I am using an NVT ensemble. My temperature coupling constant is 0.1 ps. The problem is that upon increasing the temperature difference between the two repli

[gmx-users] creating trajectory with ligand close to the protein

Hi, Can anybody tell me what is the best way to re-write a trajectory run with periodic boundary conditions such that a molecule (eg. the protein) is chosen as the reference and every other molecule in the system (eg. ligands) is transformed such that its periodic image closest to the referenc

[gmx-users] problem with exchange probabilities in remd

Hi all, I am performing a remd simulation of a peptide+water system. I have tried different temperature distributions. I am using an NVT ensemble. My temperature coupling constant is 0.1 ps. The problem is that upon increasing the temperature difference between the two replicas more than two (

[gmx-users] Strange PDO output during umbrella sampling

Hi All, I am trying to do umbrella sampling and I am getting very strange PDO output. The PDO out put does not correspond to the distances between groups. Below is my pdo output my mdp and ppa info and log file info showing the distances. I compared the values with output from g_dist just to verif

[gmx-users] Re: Strange PDO output during umbrella sampling

Scratch my post. I need to learn to read the manual more closely. I thought the PDO output was the distance and not the deviation from the restrained position. Thanks, Ilya On Sat, Feb 23, 2008 at 1:04 PM, Ilya Chorny <[EMAIL PROTECTED]> wrote: > Hi All, > > I am trying to do umbrella sampling

Re: [gmx-users] which type of cysteine residue?

If you use pdb2gmx -ss you can interactively choose whether or not your cysteines are linked, and pdb2gmx will write the .top file with the correct designators. -Justin Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > Hi all, > > I want to make the cysteine residues of my peptide to make a disulphide

[gmx-users] which type of cysteine residue?

Hi all, I want to make the cysteine residues of my peptide to make a disulphide bridge with each other. So, what type of cysteine residue should I use? There are 4 possibilities. CYS, CYSH, CYS1, CYS2. The last two seems to be the same in respect of atomic charges, bond types but not parameters

Re: [gmx-users] error in coordinate file

s lal badshah wrote: Hi, I am new to GROMACS.Currently I am working on a protein.For minimization I prepare file and when I gave the command in the shell the following output comes: Fatal error: number of coordinates in coordinate file (2a5f_b4ion.pdb, 40183) does not match topolo

Re: [gmx-users] error in coordinate file

Carefully check the number of all the molecules listed in your topology file [ molecules ] section and verify if that corresponds exactly to the number of atoms in your coordinate file. You have added some extra atoms/molecules in the topology. Venky ~ Venky