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 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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