VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Mar 17 2011 - 02:27:23 CDT

Hello:
Having had no reply to my question, I understand there is no interest
in VMD dealing with pdbqt files. However, I believe that docking can
hardly have any physical significance (if it has any at the current
state of the art, with docking "in vacuo" for a rigid-backbone
protein) without properly equilibrating the protein. To this concern,
I came across

> well, but it is a field required by the PDB standard.
> if you check the definition of ATOM records in the PDB
> standard format documentation, only charge and sequence
> entries are named optional.
That's a good point. But, many modeling programs, including psfgen,
leaves the chain column blank by default.
I just think it would be more convenient if VMD didn't do anything to
PDB files except the things that I specifically tell it to do.
Sanghyun (year 2007)

I was unable to trace any further comment on that. Therefore, may I
ask, after 4 years have elapsed, if vmd/namd-charmm.ff could be harmed
by conserving the subunit ID when preparing psf files? I was now using
namd/charmm.ff equilibrated pdf for autodock-vina and had to
reconstruct the chain ids to get pdbqt files.

Autodock is of widespread use (perhaps too much for what it can do).
At any event, pdbdatabank has stopped to support segid, although
luckily it has not used its columns.

thanks
francesco pietra