[gmx-users] Re: OPLS-AA/L force field

[Alan]

Hi You Zou,

Complementing Justin's message, I would invite you to take a look at
acpype.googlecode.com. It's my attempt to address problems like yours.
There's also links to some options besides ACPYPE.

Bear in mind that you should know what you're doing. I would suggest you to
read the Wiki's there as well as several references also indicated there.
ACPYPE is far from being perfect but it can be very helpful. I have my own
methodology where it would require using RED Server for accurate partial
charge calculations (ACPYPE may use SQM, which is semi-empirical, via
Antechamber), then ACPYPE (which is mostly designed for Amber FF) and then
MKTOP for getting the oplsaa atom types.

Feel free to contact.

Best regards,

Alan

On Tue, May 18, 2010 at 01:28, <gmx-users-request at gromacs.org> wrote:

> Message: 2
> Date: Mon, 17 May 2010 12:58:09 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] OPLS-AA/L force field
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4BF175A1.9040506 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> you zou wrote:
> > Dear Users,
> >
> > I have one question about Drug-Enzyme Complex,Similar to tutorial If I
> > want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug
> > but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg
> > Beta version" server too, or not?
>
> No.  You can't use two different force fields in one simulation system.
>
> > If I can't use this server, how can I make .gro file and .itp file for
> > drug that remove from initial .pdb file?
> >
>
> There are several programs in the User Contributions from the website,
> x2top
> (which is distributed with Gromacs), or you can build the topology by hand.
>  No
> matter what you choose, you need a thorough understanding of the mechanics
> of
> your chosen force field, methods of validation, and of course Chapter 5 in
> the
> Gromacs manual.
>
> http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> -Justin
>



-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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