AMBER Archive (2008)

Subject: AMBER: connectivity problem

From: rams rams (rams.crux_at_gmail.com)
Date: Wed Jan 09 2008 - 08:53:55 CST

Dear All,

I have the following connectivity problem:

I am using antechamber for generating .frcmod and .prep files for one of my
inhibitor. If I compare the NEWPDB file of the inhibitor generated in
antechamber and the original pdb file of the inhibitor which I extracted
from the crystal structure reported (protein with inhibitor), the
coordinates are exactly the same. But there is a connectivity lose between
P(H2PO3) and C (CF2) in the NEWPDB. Despite of the lose of this
connectivity, I continued doing LEaP and gas phase minimization, one of the
P got attached to C (out of two) but the second one still remains as an
isoloted species. Is there any way I can fix this problem I have the same
connectivity problem between C and Br atoms in another inhibitor. Is this a
common problem in using antechamber or any specific care has to be taken
while doing antechamber.

Thanks and Regards,
Ram.

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