AMBER Archive (2004)

Subject: Re: AMBER: Settings about frozen atoms in sander

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Mon Nov 29 2004 - 10:54:10 CST

Hi,

You can use ambmask to determine the residues not within 16A of you
inhibitor:

ambmask -p [prmtop file] -c [coordinate file] -find ":[resnum Inh.]
>:16" -out short

This will produce a list of the residue numbers like:

:1-3 :5-7 :102 .......

You will simply need to replace the ":" by "RES " and get rid of all
"-". (Please see documentation on the GROUP specification in the
appendix of the amber manual).

But note:
o if you want to use belly you need to specify the residues that MOVE
o you may use restraints instead of belly. Then you need to specify the
restraint group

Best,
Oliver

Xiao He wrote:
> Dear Amber users,
> If I want to froze the atoms beyond 16 Angstrom of the inhibitor during MD simulation,
> As I know now ,I have to use ibelly=1 command,then give sander each frozen groups by human observation.
> Is there any easier way?
> Thanks in advance!
>
> 　　　　　　　　Xiao He
> 　　　　　　　　hx_at_itcc.nju.edu.cn
> 　　　　　　　　　　2004-10-29
>
>
>
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-- 
________________________________________________________________

Oliver Hucke, Dr.
Biomolecular Structure Center   Health Sciences Building - K418C
Dept. of Biochemistry           1959 NE Pacific St.
University of Washington        phone: (206) 685 7046
Box 357742                      fax  : (206) 685 7002
Seattle, WA 98195-7742          email: ohucke_at_u.washington.edu
________________________________________________________________

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