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