[gmx-users] adding a new atom type

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Jul 27 19:08:14 CEST 2012

Which parameter is supposed to be changed to get the sufficient minimized system? Would anyone guide me  please?

Thanks in advance


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, July 25, 2012 4:37 PM
Subject: Re: [gmx-users] adding a new atom type

On 7/25/12 7:58 AM, Shima Arasteh wrote:
>   Some time ago I defined a new residue and after running grompp I got an error as there are some interactions assigned multiple times. Then I decided to duplicate the atoms involved in that residue to avoid this error.

That error usually indicates your system is crashing and the DD algorithm is failing.  That means either the coordinates are insufficiently minimized, the topology is incorrect, or the .mdp settings are leading to instability.

> Next I renamed the atomtypes in atometypes.atp as below:
>   ZC    12.01100 ;    carbonyl C, peptide backbone
> ZCT1    12.01100 ;    aliphatic sp3 C for CH
> ZCT3    12.01100 ;    aliphatic sp3 C for CH3
> ZO    15.99900 ;    carbonyl oxygen
> ZHC    1.00800 ;    N-ter H
> ZNH1    14.00700 ;    peptide nitrogen
> ZH    1.00800 ;    polar H
> ZHB    1.00800 ;    backbone H
> ZHA    1.00800 ;    nonpolar H
> Then I wanted to modify the .itp file, got in to the trouble; I couldn't find the C atomtype in nonbonded.itp file. Actually I don't know what to do now!

Start over with a fresh set of force field files that you haven't experimented with and troubleshoot the stability of your system.  If you Google or search the mailing list archive for this error, tons of useful results show up.


-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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