From: Axel Kohlmeyer (
Date: Wed Jan 09 2008 - 10:09:35 CST

On Wed, 9 Jan 2008, rams rams wrote:

RR> Dear All,
RR> I have the following connectivity problem:
RR> I am using antechamber for generating .frcmod and .prep files for one of my
RR> inhibitor. If I compare the NEWPDB file of the inhibitor generated in
RR> antechamber and the original pdb file of the inhibitor which I extracted
RR> from the crystal structure reported (protein with inhibitor), the
RR> coordinates are exactly the same. But there is a connectivity lose between
RR> P(H2PO3) and C (CF2) in the NEWPDB. Despite of the lose of this

dear ram,

PDB files (usually) don't contain any connectivity information.
whatever VMD displays as bonds is based on a (crude?) heuristic
guess and that may or may not be correct for your system at hand.
VMD has _no_ real knowledge of chemistry.

if you want to see the proper connectivity you'll have to (first)
load a matching _topology_ file (with recent amber this is file
type parm7). then you should see exactly the bonds, that amber uses
in its calculations.

RR> connectivity, I continued doing LEaP and gas phase minimization, one of the
RR> P got attached to C (out of two) but the second one still remains as an
RR> isoloted species. Is there any way I can fix this problem I have the same
RR> connectivity problem between C and Br atoms in another inhibitor. Is this a
RR> common problem in using antechamber or any specific care has to be taken
RR> while doing antechamber.

no, this is simply a problem of you not giving VMD the full information.


RR> Thanks and Regards,
RR> Ram.

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.