[gmx-users] energy minization mdp

[Mohammad Zahidul Hossain Khan]

Dear Sir

Thank you very much. It is working now.



On Fri, Jul 28, 2017 at 4:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/28/17 2:54 PM, Mohammad Zahidul Hossain Khan wrote:
>
>> Dear User
>>
>> I have protein-ligand system. I have basic idea for energy
>> minimization.mdp
>> parameter.
>> ;
>> integrator = steep
>> emtol = 10.0
>> emstep = 0.01
>> nsteps = 500
>> energygrps = Protein OAI
>> ;
>> nstlist    = 1
>> cutoff-scheme = Verlet
>> ns_type    = grid
>> rlist    = 1.0
>> coulombtype    = PME
>> rcoulomb    = 1.0
>> rvdw    = 1.0
>> pbc        = xyz
>>
>> but I have not idea how to write the parameter *where all the backbone
>> heavy atoms of the protein have to be constrained with an elastic constant
>> of 50 kcal /mol Å -2 and the other atoms should be free.*
>>
>> Does anyone know how to write elastic constant parameter in energy
>> minimization mdp file.
>>
>>
> Restraints are a topological construct, not one that is (directly)
> specified in the .mdp file.  Run your protein coordinates (only) through
> gmx genrestr and choose the backbone as the output group.  Specify the
> desired force constant on the command line (make sure to convert your value
> to kJ mol^-1 nm^-2).  Save the new position restraint file to something
> like "posre_bb.itp" and #include it in the topology in the protein's
> [moleculetype] section, e.g.
>
> #ifdef POSRES_BB
> #include "posre_bb.itp"
> #endif
>
> Then specify "define = -DPOSRES_BB" in the .mdp file.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5121 at vandals.uidaho.edu <khan5121 at vandals.uidaho.edu>*
* Skype: parash.khan2*
*Cell: +12085967165*