[gmx-users] NVT Equilibration error

[Justin Lemkul]

On 5/5/15 1:59 PM, Agnivo Gosai wrote:
> 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>
> ​

None of those images is informative.

>
> 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.
>

OK, so you had a bad structure, then it's a less bad structure.

> Any suggestions ????
>

What is the PDB code of the structure you are using?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================