[gmx-users] NVT Equilibration error

[Justin Lemkul]

On 5/5/15 12:18 PM, Agnivo Gosai wrote:
> Hi,
>
> 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
> angles
>            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
>    O
> ATOM   2430  CG2 THR H 229      23.066  40.670  37.642  1.00  6.21
>    C
> ATOM   2431  N      HIS H 230      25.280  38.177  39.029  1.00 10.19
>      N
>
> 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

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

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
http://mackerell.umaryland.edu/~jalemkul

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