[gmx-users] Re:gmx-users Digest, Vol 54, Issue 23
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 6 15:31:14 CEST 2008
dcip1101 wrote:
> Hi Justin,
>
> Thanks so much for your prompt response. If using AMBER force field, can
> one construct the parameters of non-standard molecules through
> ANTECHAMBER in AMBER package?
>
Yes. The parameter files can then be converted to Gromacs format using scripts
present in the User Contributions section of the Gromacs website.
-Justin
> Thanks in advance.
> Have a nice day.
>
> ---
> Jeffrey
>
> >Message: 3
> >Date: Mon, 06 Oct 2008 07:03:58 -0400
> >From: "Justin A. Lemkul"
> >Subject: Re: [gmx-users] some questions about gromacs
> >To: Discussion list for GROMACS users
> >Message-ID: <48E9F09E.7040308 at vt.edu>
> >Content-Type: text/plain; charset=UTF-8; format=flowed
> >
> >
> >
> >dcip1101 wrote:
> >> Dear all,
> >>
> >> I am a new user of Gromacs. To start my job, I am confused by several
> >> questions about GROMACS and requesting the answers.
> >>
> >> 1. Can one use amber force field in gromacs?
> >
> >Yes. See http://chemistry.csulb.edu/ffamber/ and follow the usage
> instructions
> >carefully.
> >
> >> 2. How to prepare parameters for a cofactor not included in the
> standard
> >> force fields?
> >
> >This is a very advanced topic. See here:
> >
> >http://wiki.gromacs.org/index.php/Parameterization
> >
> >> 3. Any further suggestions to a new user to use the package better?
> >>
> >
> >Depends on what you are doing. Read lots of tutorials and consult the
> mailing
> >list archive and wiki site (wiki.gromacs.org) if you have problems or
> are not
> >certain how to implement certain features.
> >
> >-Justin
> >
> >>
> >> Thanks so much for your time.
> >> Have a nice day.
> >>
> >> ----
> >> Jeffrey
> >>
> >>
>
>
> 在2008-10-06，gmx-users-request at gromacs.org 写道：
>>Send gmx-users mailing list submissions to
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>>When replying, please edit your Subject line so it is more specific
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>>
>>Today's Topics:
>>
>> 1. some questions about gromacs (dcip1101)
>> 2. RE: Heat Flux and Lambda (Berk Hess)
>> 3. Re: some questions about gromacs (Justin A. Lemkul)
>> 4. Re: Pull.pdo Columns (Thomas Schlesier)
>> 5. Re: steady (Justin A. Lemkul)
>> 6. questions about using GROMACS (dcip1101)
>>
>>
>>----------------------------------------------------------------------
>>
>>Message: 1
>>Date: Mon, 6 Oct 2008 17:52:45 +0800 (CST)
>>From: dcip1101
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>>> --
>>> David.
>>> ________________________________________________________________________
>>> David van der Spoel, PhD, Professor of Biology
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>>------------------------------
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>>Message: 3
>>Date: Mon, 06 Oct 2008 07:03:58 -0400
>>From: "Justin A. Lemkul"
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
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>>
>>--
>>========================================
>>
>>Justin A. Lemkul
>>Graduate Research Assistant
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu | (540) 231-9080
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>========================================
>>
>>
>>------------------------------
>>
>>Message: 4
>>Date: Mon, 6 Oct 2008 13:10:56 +0200
>>From: Thomas Schlesier
>
>
>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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