[gmx-users] error in coordinate file

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 topology (2a5f.top, 40612) Ple

[gmx-users] GTPgammaS topology

Dear all, I am writing to enquire if anyone has a gromos96 topology file for GTPgammaS and GDP. I trying to perform simulations on a G-protein. Also, I would like to know if anyone has ever tried to replace a GTPgammaS with GTP in a G-protein. If so, I woud like to know the procedure for converting

Re: [gmx-users] Temparature and density

Hi Chandu > Because I am using NPT ensemble will it automatically adjust to that > density? (because box size will increase under high temperature and > constant pressure therefore density will be decreased) Yes. But don't expect to get right on with the density (or viscosity/diffusion/...).

Re: [gmx-users] twin range and switched cutoffs energy differences

On Thu, Feb 21, 2008 at 02:16:39PM +1100, Mark Abraham wrote: > David Osguthorpe wrote: > >Hi, > > > >I am having a problem understanding the GROMACS implementation of cutoffs > >and switching functions - at least Im getting results I cant make sense of. > > Have you read manual sections 4.1.5 and

[gmx-users] Temparature and density

Hi all, I have one small doubt regarding high temperature simulation. Because I am simulating at high temperature,for instance at 498 K, the density is different (0.828 gram/cc at 498 K) from 300 K. I have generated a water box whose density is around 1 gram/cc. My question is ... should I change

Re: [gmx-users] gmx_alltoall

Anna Marabotti wrote: Dear GMX-developers (in particular dear Carsten Kutzner), to overcome problems in making parallel runs with GROMACS on a Linux cluster with Gigabit Ethernet interconnection, I downloaded the package gmx_all-to-all to speed up the processes. In the instructions, however, th

Re: [gmx-users] Re: Dose the GROMOS FF favour beta-sheets?

Hi, On Friday, 22. February 2008 14:51, [EMAIL PROTECTED] wrote: > > Thank you very much for your answer! I use the 43a1 force field. Here are > two references of comparative force field studies that suggest that > gromos-g96 favours beta sheets. I would be interested in any other study > with sim

[gmx-users] problem regarding pr.mdp file of protein embedded in popc

Dear gmx-users, I have inserted my protein into membrane. I did energy minimisation with Steepest descent, that output used for input of position restrain, this "EM out.gro" structure is fine . When I do Position restrain, this step goes fine but, popc structure of " PR out.gro " looks tilted.

[gmx-users] Re: Dose the GROMOS FF favour beta-sheets?

Hi Tsjerk, Thank you very much for your answer! I use the 43a1 force field. Here are two references of comparative force field studies that suggest that gromos-g96 favours beta sheets. I would be interested in any other study with similar or different conclusions. Yoda, T.; Sugita, Y. & Okamoto,

[gmx-users] gmx_alltoall

Dear GMX-developers (in particular dear Carsten Kutzner), to overcome problems in making parallel runs with GROMACS on a Linux cluster with Gigabit Ethernet interconnection, I downloaded the package gmx_all-to-all to speed up the processes. In the instructions, however, this package is indicated

Re: [gmx-users] problem about position restrain

On Feb 21, 2008, at 13:27, Justin A. Lemkul wrote: Quoting sudheer babu <[EMAIL PROTECTED]>: Hi gmx users, I am trying to run position restrain step for protein embedded in popc. is it possible to do position restrain at a time for both popc and protein like below mentioned here? in " .t

Re: [gmx-users]build topology file for a molecule define with new residues

HI Tsjerk, Well i found i didn't find much in the litterature, some publications give some informations about structures (angles, bonds, dihedrals) but it's theoretical calculation using PM3 method. So i really don't know about how to handle the problem of force field. I now need to get and gather

Re: [gmx-users] Selection of multiple residues

Hi, index files contain groups of atoms represented by their atom number. Just check an index file how it is constructed. By default, there are several groups (System, Protein, Protein-H, etc.). So if you want to work with a range of residues (e.g. 1-300) just create a new group and copy the at

Re: [gmx-users] Selection of multiple residues

Berk Hess wrote: You don't specity what you want exactly. make_ndx can select residue on number and name, can select multiple residues with one command and can select residue sequences. make_ndx can also select chains, if the input is a pdb or tpr file. Berk. Or they can do it by hand if they

RE: [gmx-users] Selection of multiple residues

You don't specity what you want exactly. make_ndx can select residue on number and name, can select multiple residues with one command and can select residue sequences. make_ndx can also select chains, if the input is a pdb or tpr file. Berk. > > Hello, > > I want to select 300 residues out o

Re: [gmx-users] Selection of multiple residues

"to select and copy the indices from an existing index-file to create a new group" I am sorry I did not understand the meaning of the above ? I will have the first atom number and the last atom number, and then ? How do I copy the indices ... On Fri, Feb 22, 2008 at 10:58 AM, Bjoern Windshuegel <

Re: [gmx-users] Selection of multiple residues

Hi, I assume you want to select a range of residues, not some scattered amino acids.. So just check from your gro-file the atom numbers of begin and end of the region you need and use the information to select and copy the indices from an existing index-file to create a new group. Best regard

[gmx-users] Selection of multiple residues

Hello, I want to select 300 residues out of my 1000 residue protein and make an index out of it. make_ndx does not seem to have a simple method to do this. These are all residues in the same chain. How does one do this ? Sincerely -Maria -- Maria G. Technical University of Denmark Copenhagen _

RE: [gmx-users] Free energy for charged molecules with PME

> Date: Thu, 21 Feb 2008 16:32:45 -0700 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] Free energy for charged molecules with PME > > dear gmx users > > Any rigorous approach available currently to solve the problems mentioned in

Re: [gmx-users]build topology file for a molecule define with new residues

Hi Justin (and Geraldine), I think that cross-referring people asking about building topologies to the exotic species wiki page by default is a bit too much. It's Parameterization they need to read (and chapter 5 of the manual). Exotic species are those weird atoms you sometimes encounter in ligan