[gmx-users] Simulatimg two proteins in water system

Mark Abraham mark.abraham at anu.edu.au
Tue Jun 29 08:35:07 CEST 2010

----- Original Message -----
From: radhika jaswal <jaswalradhika at yahoo.co.in>
Date: Tuesday, June 29, 2010 16:30
Subject: [gmx-users] Simulatimg two proteins in water system
To: gmx-users at gromacs.org

| > Hiiii Everybody ther,
>  I am simulating two already docked proteins which are in a single .pdb file to study the aggregation behavior. Doing for the first time, I have tried with and without TER option too. There are 28 residues and 240 atoms in first chain A and same number of atoms in chain B. But while using pdb2gmx command following error is coming..
>  Processing chain 1 'A' (199 atoms, 28 residues)
>  There are 32 donors and 36 acceptors
>  There are 39 hydrogen bonds
>  -------------------------------------------------------
>  Program pdb2gmx, VERSION 3.3.1

I hope there's a good scientific reason to be using a version more than 3 years old. Faster performance and more fixed bugs is only a download away...

>  Source code file: pdb2gmx.c, line: 393
>  Fatal error:
>  Atom S in residue MET 21 not found in rtp entry with 9 atoms
>               while sorting atoms
>  ..

Look at atom S in residue MET 21 and see why it doesn't match the .rtp entry for methionine. Then cope with that :-)

>  All Suggestions are welcome. And why it is showing only chain 1 A.

Maybe it died before reaching the second chain.


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