[gmx-users] NVT Equilibration error
jalemkul at vt.edu
Tue May 5 18:26:32 CEST 2015
On 5/5/15 12:18 PM, Agnivo Gosai wrote:
> This is the warning message I received while preparing the topology. It
> occurred for one chain of the protein.
> Making bonds...
> Warning: Long Bond (2429-2431 = 0.80585 nm)
> Number of bonds was 4137, now 4136
> Generating angles, dihedrals and pairs...
> Before cleaning: 10853 pairs
> Before cleaning: 10993 dihedrals
> Keeping all generated dihedrals
> Making cmap torsions...There are 10993 dihedrals, 841 impropers, 7477
> 10769 pairs, 4136 bonds and 0 virtual sites
> Total mass 29166.760 a.m.u.
> Total charge 5.000 e
> I checked the two atoms mentioned in the warning part and found that they
> are in two residues of the protein chain in question. I am not sure if in
> physiological pH they bond with each other or not.
> This is the raw data from the pdb file :
> ATOM 2429 OG1 THR H 229 24.393 41.044 35.727 1.00 2.93
> ATOM 2430 CG2 THR H 229 23.066 40.670 37.642 1.00 6.21
> ATOM 2431 N HIS H 230 25.280 38.177 39.029 1.00 10.19
> Should I stop this bond making by somehow ? Below the warning it is written
> : Number of bonds was 4137, now 4136 , so did pdb2gmx remove this bond ?
This comes from merging termini and .rtp entries; it's not relevant to your problem.
An 8-Angstrom separation is massive. Either there are missing residues
(checking for obvious MISSING lines in the .pdb file) or the assigned geometry
is really bad. There's probably some residue missing. Never overlook long and
short bond warnings. They usually indicate trouble.
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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