Hi You Zou,<div><br></div><div>Complementing Justin's message, I would invite you to take a look at <a href="http://acpype.googlecode.com">acpype.googlecode.com</a>. It's my attempt to address problems like yours. There's also links to some options besides ACPYPE.</div>
<div><br></div><div>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.</div>
<div><br></div><div>Feel free to contact.</div><div><br></div><div>Best regards,</div><div><br></div><div>Alan<br><br><div class="gmail_quote">On Tue, May 18, 2010 at 01:28, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div id=":1al" class="ii gt">Message: 2<br>
Date: Mon, 17 May 2010 12:58:09 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] OPLS-AA/L force field<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4BF175A1.9040506@vt.edu">4BF175A1.9040506@vt.edu</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
<br>
<br>
you zou wrote:<br>
> Dear Users,<br>
><br>
> I have one question about Drug-Enzyme Complex,Similar to tutorial If I<br>
> want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug<br>
> but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg<br>
> Beta version" server too, or not?<br>
<br>
No. You can't use two different force fields in one simulation system.<br>
<br>
> If I can't use this server, how can I make .gro file and .itp file for<br>
> drug that remove from initial .pdb file?<br>
><br>
<br>
There are several programs in the User Contributions from the website, x2top<br>
(which is distributed with Gromacs), or you can build the topology by hand. No<br>
matter what you choose, you need a thorough understanding of the mechanics of<br>
your chosen force field, methods of validation, and of course Chapter 5 in the<br>
Gromacs manual.<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Parameterization" target="_blank">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>
<br>
-Justin<br></div></blockquote></div><br><br clear="all"><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</div>