AMBER Archive (2009)

Subject: Re: [AMBER] DMF solvent box

From: Jio M (jiomm_at_yahoo.com)
Date: Fri Sep 11 2009 - 10:00:40 CDT

Dear Amber users ;

(Abhishek PLEASE DONOT FOLLOW THIS PROCEDURE : SOME EXPERT SHOULD CHIME INTO THIS)

can we do like this ....

first we can minimise meoh and dmf seperately in some QM software (like
GAUSSIAN) then taking there output file  .out  file in
antechamber to give atom types and  charge.  also create the
frcmod files for meoh and dmf

then save them in some library say abc.lib  containing meoh and dmf

source leaprc.gaff

loadoff abc.lib

list

meoh dmf gaff

load the frcmod files also

solvateoct meoh dmf (selecting buffer such that only one residue is added that may be less than 12 )

edit meoh

meoh surrounded  by only one  dmf

solvateoct meoh meoh
12                
#####this meoh is meoh + dmf ######

 this should work

regards ,

JIomm
--- On Fri, 9/11/09, Abhishek Banerjee <a.banerjee_at_ymail.com> wrote:

From: Abhishek Banerjee <a.banerjee_at_ymail.com>
Subject: [AMBER] DMF solvent box
To: amber_at_ambermd.org
Date: Friday, September 11, 2009, 2:40 AM

Hi all,

I have started MD simulation for a month back. I want to create a DMF
and methanol mixture like binary mixture. Can some one give me some
advice how to go about it. I am using amber 9
thanks
abhishek

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