[gmx-users] NVT Equilibration error

[Agnivo Gosai]

Hi,

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
  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

I am attaching two images.

1st image is when the molecule is put inside the box
​
 box.png
<https://docs.google.com/file/d/0B-U8uULVZjfRTVVILXhRSVcyT1E/edit?usp=drive_web>
​
2nd image is after energy minimization

​
 em.png
<https://docs.google.com/file/d/0B-U8uULVZjfRdWhVUEZpMmoxcVE/edit?usp=drive_web>
​
3rd image is close up of the structure after energy minimization

​
 structurezoom.png
<https://docs.google.com/file/d/0B-U8uULVZjfRQ0JzdVZlcG1YWjQ/edit?usp=drive_web>
​

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.