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: Thu Nov 30 2006 - 06:13:42 CST

appendix B in the Amber9 manual

a a wrote:

> Dear Carlos,
>
> Sorry to bother you again, do you mean I could use commands in xleap
> to define atoms to the same group and apply the force to the group?
> If yes, I will read the manual regarding leap. If I still
> misunderstand your reply, could you mind to let me know what "group
> syntax" are you talking about?
>
> Best regards,
>
> Annie
>
>
>
>
>
>> From: Carlos Simmerling <carlos_at_csb.sunysb.edu>
>> Reply-To: amber_at_scripps.edu
>> To: amber_at_scripps.edu
>> Subject: Re: AMBER: How to apply a force to some atom in a residues?
>> Date: Wed, 29 Nov 2006 07:26:19 -0500
>>
>>
>> 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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>
>
> _________________________________________________________________
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