AMBER Archive (2006)

Subject: Re: AMBER: How to apply a force to some atom in a residues?

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Nov 29 2006 - 06:26:19 CST

the Amber manual has a section for the GROUP syntax that shows how
to specify atoms.

a a wrote:

>
>
>
>> From: "a a" <patd_2_at_hotmail.com>
>> Reply-To: amber_at_scripps.edu
>> To: amber_at_scripps.edu
>> Subject: Re: AMBER: nmode output with ptraj
>> Date: Wed, 29 Nov 2006 11:18:32 +0800
>>
>> Dear Sir/Madam,
>>
>> Could you mind to teach me how to assign a force to some of the atoms
>> in a residue for MIN and MD calculations?
>>
>> I know if I have to apply a force to a residue, I need "RES 1 4" in
>> the in file. like this?
>> ----------------------------
>> Keep DNA fix
>> 10.0
>> RES 1 4
>> ----------------------------
>>
>> How about if I just want to fix the C1, C2, C3 and C4 atoms in the
>> RES 1? What can I do?
>>
>> Best regards,
>>
>> Annie
>>
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>
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