[gmx-users] Selection of residues in one of the chains of heterodimer

[Dallas Warren]

So, what is the difference between the 2 PDB files?  What information
was in the original PDB file, that was then lost when converted to the
GRO file, then was not recovered when that was converted to a PDB?

Load the files with a text editor, you will see what information is
contained in each and the differences.

http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM

http://manual.gromacs.org/documentation/2018/user-guide/file-formats.html#gro

BTW, no reason to convert from a .gro to .pdb then load into vmd, .gro
will work just fine, unless you are going to then add more information
into the .pdb file that the .gro can't hold.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
On Mon, 29 Oct 2018 at 19:46, Raag Saluja <saluja.raag at gmail.com> wrote:
>
> Hi!
>
> I simulated a heterodimer and converted the md.gro file into a pdb file.
> This pdb file I visualised in vmd. I wish to select residues (first 50,
> then next 50 and so on), so that I can correlate the structure with the
> graphs obtained by structure analysis.
> If I give the command resid 1 to 50 and protein, the first 50 residues of
> both chains are selected.
> If I give the command resid 1 to 50 and protein and chain A, it works with
> the original file obtained from protein data bank. However, with the
> simulated protein’s pdb file, the area just gets deselected.
> Can you please help?
> Thank you in advance!
> Regards,
> Raag
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