Re: [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  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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu *
* Skype: parash.khan2*
*Cell: +12085967165*
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Re: [gmx-users] energy minization mdp

[Justin Lemkul]

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] energy minization mdp

[Mohammad Zahidul Hossain Khan]

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.

-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu *
* Skype: parash.khan2*
*Cell: +12085967165*
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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