[gmx-users] Re:gmx-users Digest, Vol 54, Issue 23

[dcip1101]

 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? 
 
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：
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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
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
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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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