[gmx-users] ligand topology for opls.aa

Andrey Frolov andrey.i.frolov at mail.ru
Fri Jun 13 12:38:42 CEST 2014

-------- Пересылаемое сообщение --------
От кого: Andrey Frolov <andrey.i.frolov at mail.ru>
Кому: gromacs.org_gmx-users at maillist.sys.kth.se
Копия: samanshahriyari at yahoo.com
Дата: Fri, 13 Jun 2014 14:34:50 +0400
Тема: Re: gromacs.org_gmx-users Digest, Vol 122, Issue 61

Dear Saman,

You might want to consider OPLS-AA 2005 as implemented in the Shorodinger software. The Schrodinger Maestro is FREE for academia, after registering you can download it and use. There is an utility "ffld_server", which is able to automatically assign OPLS-AA 2005 to any ligand molecule. Once you have the output of ffld_server, you can convert this into gromacs topology format by a python program called "ffconv.py" (see  http://frolov-pchem.wikispaces.com/Downloads ). Also you can check if the conversion in your case was correct by "check_conversion.sh" script therein. This is well-documented and has real-life examples, so it is easy to start using this. See the documentation inside.

Please give me your feedback if you use this tool.

Kind regards,

Fri, 13 Jun 2014 12:00:02 +0200 от gromacs.org_gmx-users-request at maillist.sys.kth.se:
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>   1. ligand topology for opls.aa (Saman Shahriyari)
>Message: 1
>Date: Fri, 13 Jun 2014 01:32:46 -0700 (PDT)
>From: Saman Shahriyari < samanshahriyari at yahoo.com >
>To: Discussion list for GROMACS users < gmx-users at gromacs.org >
>Subject: [gmx-users] ligand topology for opls.aa
>< 1402648366.13559.YahooMailNeo at web163203.mail.gq1.yahoo.com >
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>Dear users
>i wanted to know if "Acpyte" generated topologies for a ligand are compatible with OPLS-AA.ff? i am searching for a reliable topology builder for OPLS-aa like ATP for gromos53a6.ff so that i can avoid manual approached like?using?"gaussian" .
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