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.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.u.washington.edu
________________________________________________________________
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Received on Fri Oct 29 2004 - 17:53:00 PDT
