AMBER: RESP procedure for DMPC monomer

From: Akshay Patny <>
Date: Wed, 20 Dec 2006 10:04:00 -0600

Dear Amber users

I am trying to perform membrane simulation of a GPCR using
DMPC bilayer. For that, I am trying to generate parameters
and partial atomic charges for a DMPC mononer using RESP
fitting integrated with antechamber.

DMPC momoner has a formal +1 (N atom) and -1 (P atom)
charge, and is thus overall neutral.

I generated the gaussian input file using antechamber, as

% antechamber –fi mol2 –i DMPC_mono_sybyl.mol2 –fo
gcrt –o

Then, using the generated input file, I ran a gaussian job,
as follows:

% g03sub –n 1

Then I used the gaussian output in antechamber to do the
2-stage RESP fitting as follows:

% antechamber -rn DMP -fi gout -i H1DMPC_mono.out -fo prepi
-o DMPC_mono_resp.prep -c resp -s 2

This gave me the prep file, which I checked using PARMCHK
utility, as follows:

% parmchk -i DMPC_mono_resp.prep -f prepi -o

The only warning I got in this frcmod was following:

c3-o -c -os 10.5 180.0 2.0
General improper torsional angle (2 general atom types)

QUESTION: I am new to gaussian calculations and RESP
fitting. Although, I tried to follow the suggestions
closely, and seemingly the jobs have gone towards

1. I am wondering if there are places where I should look
to make sure if everything is in order?
2. Does the improper warning seems okay?

I look forward to your suggestions. Thanks in advance.

-Akshay Patny (Olemiss)
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Received on Sun Dec 24 2006 - 06:07:10 PST
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