Re: AMBER: RESP procedure for DMPC monomer

From: linfu <>
Date: Thu, 21 Dec 2006 08:54:43 +0800

Hi Akshay Patny!

DMPC momoner has a formal +1 (N atom) and -1 (P atom)
charge, and is thus overall neutral. do you check how
much charge on that N and P atom in DMPC_mono_resp.prep.
do the antechamber give the reasonable result for that charge!

it seems that you want to perform membrane simulation of a GPCR
in AMBER, do AMBER can do z-retrain to maintain stability of membrane!

Fu Lin

======= 2006-12-21 00:04:00 您在来信中写道:=======

>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)
>The AMBER Mail Reflector
>To post, send mail to
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Received on Sun Dec 24 2006 - 06:07:15 PST
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