AMBER Archive (2006)

Subject: Re: AMBER: RESP procedure for DMPC monomer

From: linfu (linfu3200_at_mail.sioc.ac.cn)
Date: Wed Dec 20 2006 - 18:54:43 CST

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!

BEST REGARDS
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
>follows:
>
>% antechamber –fi mol2 –i DMPC_mono_sybyl.mol2 –fo
>gcrt –o DMPC_mono.com
>
>Then, using the generated input file, I ran a gaussian job,
>as follows:
>
>% g03sub –n 1 DMPC_mono.com
>
>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
>DMPC_mono_frcmod
>
>The only warning I got in this frcmod was following:
>
>IMPROPER
>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
>completion.
>
>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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= = = = = = = = = = = = = = = = = = = =
                        

　　　　　　　　致
礼！
 
                                 
　　　　　　　　linfu
　　　　　　　　linfu3200_at_mail.sioc.ac.cn
　　　　　　　　　　2006-12-21

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