[gmx-users] positional restraint

[Xavier Periole]

Alok wrote:

> hello gmx uers,
>                        I have a problem concerning positional 
> restraint . I am constraining a residue from my protein during 
> minimization and consequently during the early  stage of my dynamics. 
> I have consequently constructed an ".itp file" for the purpose of 
> positional restraint of the residue which i then add to the ".top file".
>
> The  .itp file is as shown below:
>
> ; In this topology include file, you will find position restraint
> ; entries for all the heavy atoms in your original pdb file.
> ; This means that all the protons which were added by pdb2gmx are
> ; not restrained.
>
> [ position_restraints ]
> ; atom  type      fx      fy      fz
>   691     1      100000  100000  100000
>   692     1      100000  100000  100000
>   693     1      100000  100000  100000
>   694     1      100000  100000  100000
>   695     1      100000  100000  100000
>   696     1      100000  100000  100000
>   697     1      100000  100000  100000
>   698     1      100000  100000  100000
>   699     1      100000  100000  100000
>   700     1      100000  100000  100000
>   701     1      100000  100000  100000
>
> The output data that i get after preprocessing my input files for 
> minimization is as follows:
>
> processing coordinates...
> double-checking input for internal consistency...
> Reading position restraint coords from out2sxl.gro
> renumbering atomtypes...
> converting bonded parameters...
> #      BONDS:   39330
> #   G96BONDS:   2817
> #     ANGLES:   26220
> #  G96ANGLES:   5464
> #      PDIHS:   2470
> #      IDIHS:   2285
> #       LJ14:   4581
> #     POSRES:   22


Position restrains have to be assigned on the atom number of the 
molecule not the
number in the gro file !!
Just in case you you did not do.
XAvier

-- 
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   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole
   
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