AMBER Archive (2006)

Subject: AMBER: cAMP ligand charge

From: Fenghui Fan (
Date: Mon Sep 11 2006 - 10:06:40 CDT

Dear all:

Here is the commands to get the ligand charge:

respgen -i -o sustiva.respin1 -f resp1
respgen -i -o sustiva.respin2 -f resp2
resp -o -i sustiva.respin1 -o sustiva.respout1 -e
sustiva.esp -t qout_stage1
resp -o -i sustiva.respin2 -o sustiva.respout2 -e
sustiva.esp -q qout-stage1 -t qout_stage2
antechamber -i -fi ac -o
-fo ac -c rc -cf qout_stage2.

I have the following questions:

Which output file is on the net charge of the sustiva?
That mean from which file I can know how much is the
net charge of the moleucle?

Seocndly, from the sustiva.pdb, how can we get the If the GAUSSION is needed for this, where
should we download it? I donot think AMBER has
GAUSSION as its component.

I am looking forward to getting your reply.

Best regards.

Fenghui Fan

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