[gmx-users] NVT Equilibration error

Agnivo Gosai agnivogromacs14 at gmail.com
Tue May 5 19:59:12 CEST 2015


As per my previous mails I checked the atoms mentioned in the long bond
warning and the residues involved for different pdb entries ( the protein
in question is thrombin and I looked at different pdb files available to
see if my structure is missing any residue or atoms).

I found that the structure used by me is not missing any atoms for the
residues in question. So , I am confused as to why this long bond warning
is coming. Should I do something to stop this bond from happening ?

The bond takes place between 2429 and 2431 as per pdb2gmx warning

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

I am attaching two images.

1st image is when the molecule is put inside the box
2nd image is after energy minimization

3rd image is close up of the structure after energy minimization


For the 1st image VMD did not show the secondary structures of the protein
as a STRIDE warning and error came. However the energy minimized structure
did not show such warnings.

Any suggestions ????

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

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