Hungie Hungie wrote:
>
> Dear Amber users,
>
> I am trying to minimize H positions and fix heavy atoms (no solvent) with
> input file
>
> ---------------------------------------
> minimization to fix up hydrogen positions
> &cntrl
> imin = 1,
> maxcyc = 6000,
> ncyc = 3000,
> ntr = 1,
> ntb = 0,
> igb = 2,
> &end
> Restrain the heavy atoms I
> 5000.0
> FIND
> * CT * *
> * C * *
> * CA * *
> * CM * *
> * CC * *
> * CW * *
> * CR * *
> * CB * *
> * CN * *
> SEARCH
> RES 1 198
> END
> Restrain the heavy atoms II
> 5000.0
> FIND
> * O2 * *
> * OH * *
> * O * *
> * NA * *
> * N* * *
> * N2 * *
> * N3 * *
> * NA * *
> * S * *
> END
> SEARCH
> RES 1 198
> Restrain the heavy atoms III
> 5000.0
> FIND
> * SH * *
> END
> END
> ------------------------
>
> I got error message as
>
> | Reading &cntrl namelist w/ machine lib
>
> This seems that amber doesn't recognize some input parameter. I am using
> amber4.1 and as I read in manual, variable IGB is no longer support. Could
> anyone please tell me how to set parameter instead of IGB?
>
> Thank you very much in advance.
>
> Hungie
>
> _________________________________________________________________
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You cannot do a belly restraint with GB solvation model.
Instead, you must use in vacuo for the electrostatics, e.g. do
not use IGB< instead use something like IDIEL=0, DIELC=4, and of
course, IBELLY=1.
Hope this helps
Stef
--
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*
Teletchea Stephane - CNRS UMR 8601
Lab. de chimie et biochimie pharmacologiques et toxicologiques
45 rue des Saints-Peres 75270 Paris cedex 06
tel : (33) - 1 42 86 20 86 - fax : (33) - 1 42 86 83 87
mel : steletch_at_biomedicale.univ-paris5.fr
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Received on Mon Sep 10 2001 - 05:17:45 PDT
