[gmx-users] Re : NVT Equilibration error
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.
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
Grad Student, Iowa State University.
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