VMD-L Mailing List

From: Nicholas Musolino (musolino_at_mit.edu)
Date: Tue Oct 19 2010 - 12:10:51 CDT

On Oct 19, 2010, at 11:36 AM, Joyce Tan wrote:

> Hi.
>
> I have my 5000 frames .xtc and .gro loaded into vmd.
>
> And I was trying to convert one of the frames into pdb through this:
>
> set A [atomselect top protein frame 4998]
> $A writepdb xx.pdb
>
> When I load xx.pdb into the vmd, one atom from one residue is connected to another atom from another residue. This particular bonding was not found in the trajectory file. I really don't understand why is this happening. Can someone help?
> Thanks.
>

Hi Joyce,

Do you understand how those bonds are drawn? I am guessing your PDB has no bond information, just the spatial positions of the atoms. If you look at the contents (text) of the PDB, this is the case, no?

VMD will then draw bonds between atoms according to the heuristic rule described here:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node26.html

Hope this helps.

Nicholas Musolino
---------------------------------------------------------------------------
Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT
musolino_at_mit.edu | 617-253-6675 | Room E19-528