[gmx-users] Re : NVT Equilibration error

Mark Abraham mark.j.abraham at gmail.com
Tue May 5 20:30:19 CEST 2015


If 2429 is named OG1, then it is a substituent on the gamma carbon CG of
threonine and has no business being bonded to the backbone nitrogen 2431 of
histidine. You need to look at your input file and see what has become of
the threonine backbone O that should form that bond.


On Tue, 5 May 2015 18:16 Agnivo Gosai <agnivogromacs14 at gmail.com> 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 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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