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: <[EMAIL PROTECTED]>
>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
>>
>>
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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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Message: 3
Date: Mon, 06 Oct 2008 07:03:58 -0400
From: "Justin A. Lemkul"
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========================================
Justin A. Lemkul
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Department of Biochemistry
Virginia Tech
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========================================
------------------------------
Message: 4
Date: Mon, 6 Oct 2008 13:10:56 +0200
From: Thomas Schlesier
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========================================
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Virginia Tech
Blacksburg, VA
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