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: Fri Dec 01 2006 - 04:26:51 CST

Dear Carlos,

Thank you very much. I just learn to fix the position of some of the atoms.
  Thank you very much for your help again.

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: Thu, 30 Nov 2006 07:13:42 -0500
>
>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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