[gmx-users] Re: Topology file

[Justin Lemkul]

On 8/15/12 9:12 AM, Ankita naithani wrote:
> Is this because the topol_Protein_Chain_D.itp has a line of including
> the position restraint file for chain D?
>

Yes, #include statements for position restraint files are contained in each 
chain topology.

-Justin

>
>
> 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
>
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================