[gmx-users] change atom type in ffbonded.itp

Justin Lemkul jalemkul at vt.edu
Tue Nov 1 13:18:40 CET 2016

On 11/1/16 8:10 AM, Mostafa Khedrinia wrote:
> hello
> I'm using Gromacs with
> charm27.ff force-field.I adding a new residue (NAG) in force field
> I have a problem with water molecules in my system: During
> minimization, I have this message:
> step X: Water molecule starting at atom XXX can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> My problem is related to protein structure.I changed angletypes part in
>  ffbonded.itp .  so not errors.
> my question:
> This change how much is true?

I don't know whether three different people are actually sending identical 
questions or if you're just posting repeatedly with different emails to try to 
get attention, but in any case I will reply here and hope all relevant parties 
see it.

There are a couple things that could be going wrong.  The first is that you are 
mixing protein and CGenFF atom types to try to hack together a topology.  Don't. 
  Build a suitable residue topology using available atom types from the protein 
and carbohydrate force fields.  You can use charges from CGenFF as initial 
guesses, but these should be cross-checked against existing chemical moieties.

Then you need to prove that this topology is reasonable.  If your whole protein 
system is crashing, de-complicate matters by simulating only the custom residue 
in vacuo, then in a box of water.  Then, if that works, verify that your protein 
minimization actually converged adequately.  There's no sense running dynamics 
if your system still has bad clashes/high forces.  If that's still crashing, 



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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