[gmx-users] NVT Equilibration error

Agnivo Gosai agnivogromacs14 at gmail.com
Tue May 5 18:18:50 CEST 2015


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 was my pdb2gmx command :

pdb2gmx_467 -f input.pdb -o complex.gro -p topol.top

and I use AMBER99SB ( with parmbsc0 for the DNA part ) , TIP3P water.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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