Re: AMBER: files in Amber directory ( to Junmei Wang )

From: John Bennett <john.bennett.ymail.com>
Date: Fri, 18 Jul 2008 04:25:38 -0700 (PDT)

Dear  Wang,

 

First of all, I want to thank you
for  all useful information. After I read
your mail and my Amber notes and manuals on this issue I had some new questions
that I wanted to learn the answers. So I want to ask these questions. If  I do these operations based on GAFF ( AA
force field ) Will I have used OPLS-UA for 
my structure? Or Should I call this force field like AMBER/OPLS or  modified GAFF ? My second questions is If I
can use OPLS-UA with the operations you mentioned Can I also use TraPPE-UA force field with the same procedure?

 

Thanks


 

Kind
regards



--- On Thu, 7/17/08, Junmei Wang <junmwang.gmail.com> wrote:
From: Junmei Wang <junmwang.gmail.com>
Subject: Re: AMBER: files in Amber directory ( to Junmei Wang )
To: amber.scripps.edu
Date: Thursday, July 17, 2008, 2:56 PM

Hi, John,
Antechamber is designed to work with molecules having no open valence. But if no atom type and bond type assignments and charge calculations are involved, antechamber can be used to to handle molecules with open valences. For your molecules, you could generate mol2 or ac files, manually assign atom types, and generate prepi files using antechamber if you want to. For the force field parameters, you may run parmchk to find the missing parameters and print out all the force field parameters using the "-a" flag. If you want to use OPLS-UA, you need to assign atom types based on the atom type definitions of OPLS-UA and loading the OPLS-UA parmameter file with the "-p" flag when running parmchk (the default is gaff.dat). You cannot change the functional form for the current Amber packages. 


Best

Junmei


2008/7/15 John Bennett <john.bennett.ymail.com>:


Dear  Wang,
I'm using Amber 9 v.  I'm interested in  n-alkanes and  evaluating thermophysical and structural properties of n- alkanes  and  binary mixtures  of n-alkanes. I examined all the files in Amber directory and saw some files called OPLS. And I am planning  to modify gaff and use OPLS-UA force fields for  my  molecular  structure. I wonder if I can use  OPLS-UA force field using Antechamber. So I need to know some extra information about this issue  and need some expert advice and suggestions. I thought that you can help and also lead me to do the right thing. As you know GAFF and OPLS-UA have different functional forms and force constants. I can edit charge info and use my own force field parameters. I think it is also need to use the right functional forms and force constants . Am I right? How can I change and edit the functional forms and force constants of GAFF force field ?  Where are the functional forms and force constants information of
 force fields in Amber directory? .   In this sense, I'm waiting for your contributions.

 
 Sincerely,
 


      



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Received on Sun Jul 20 2008 - 06:07:40 PDT
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