AMBER Archive (2006)

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

From: a a (patd_2_at_hotmail.com)
Date: Thu Nov 30 2006 - 00:45:04 CST

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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