[gmx-users] Re: Topology file

[Ankita naithani]

Is this because the topol_Protein_Chain_D.itp has a line of including
the position restraint file for chain D?



On Wed, Aug 15, 2012 at 2:05 PM, Ankita naithani
<ankitanaithani at gmail.com> wrote:
> Hi,
>
> I noticed that in my topology file, there is no inclusion of position
> restraint file for my protein. For instance, my topology file looks
> like this:
>
> ; Include forcefield parameters
> #include "gromos53a6.ff/forcefield.itp"
>
> ; Include chain topologies
> #include "topol_Protein_chain_D.itp"
> #include "topol_Protein_chain_E.itp"
> #include "topol_Protein_chain_F.itp"
> #include "topol_Protein_chain_G.itp"
>
> ;Include ligand topology
> #include "FDP_Dp.itp"
>
> ; Include water topology
> #include "gromos53a6.ff/spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
>
> ; Include topology for ions
> #include "gromos53a6.ff/ions.itp"
>
>
> But, after running pdb2gmx, I do get 4 posre files for all the
> individual chains. Do I need to add in them manually? Also, I am
> unable to understand as to why did it not get included in the first
> instance itself? I am using gromos53a6 force field.
>
>
> Best Wishes,
>
> --
> Ankita Naithani



-- 
Ankita Naithani