[gmx-users] Simulatimg two proteins in water system

radhika jaswal jaswalradhika at yahoo.co.in
Tue Jun 29 08:30:26 CEST 2010

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

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


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



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