[gmx-users] adding a new atom type

Justin Lemkul jalemkul at vt.edu
Wed Jul 25 14:07:20 CEST 2012

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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