[gmx-users] determining restraints for pulling

[abhisek Mondal]

Is it possible to pull (distance pull) along negative of Z axis (for
example, I'm saying Z) ? Do I need to mention -Z in pull code or the
program improvises if I say Z axis distance pull in .mdp ?

On Wed, Apr 5, 2017 at 5:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
> Please keep the discussion on the mailing list.
>
> On 4/5/17 8:04 AM, abhisek Mondal wrote:
>
>> Hello Justin,
>>
>> Can you provide some direction to this approach I'm using for performing
>> umbrella sampling of a protein-ligand complex ?
>>
>> I had restrained it during the equilibration of the molecule. As advised
>> in the
>> Protein-ligand simulation tutorial. But I'm unsure regarding what kind of
>> treatment I'm supposed to give the complex while targeting for umbrella
>> sampling. Do I need to restrain the ligand during equilibration ?
>>
>> I have solved the crystal structure of the complex and want to determine
>> if I
>> pull out the ligand then how the side chains reorient according to the
>> ligand
>> withdrawal. That's the goal.
>>
>> Some suggestions regarding the issue will be highly appreciated.
>>
>>
> What does your examination of the literature for similar systems suggest
> as an appropriate protocol?
>
> -Justin
>
> Thank you
>>
>> On Wed, Apr 5, 2017 at 3:51 PM, abhisek Mondal <abhisek.mndl at gmail.com
>> <mailto:abhisek.mndl at gmail.com>> wrote:
>>
>>     I had restrained it during the equilibration of the molecule. As
>> advised in
>>     the Protein-ligand simulation tutorial. But I'm unsure regarding what
>> kind
>>     of treatment I'm supposed to give the complex while targeting for
>> umbrella
>>     sampling. Do I need to restrain the ligand during equilibration ?
>>
>>     I have solved the crystal structure of the complex and want to
>> determine if
>>     I pull out the ligand then how the side chains reorient according to
>> the
>>     ligand withdrawal. That's the goal.
>>
>>     On Wed, Apr 5, 2017 at 3:09 PM, Mark Abraham <
>> mark.j.abraham at gmail.com
>>     <mailto:mark.j.abraham at gmail.com>> wrote:
>>
>>         Hi,
>>
>>         Why are you trying to keep the ligand in place (by restraining
>> it) and pull
>>         it out?
>>
>>         Mark
>>
>>         On Wed, 5 Apr 2017 09:51 abhisek Mondal <abhisek.mndl at gmail.com
>>         <mailto:abhisek.mndl at gmail.com>> wrote:
>>
>>         > Hi,
>>         >
>>         > I'm trying to pull a ligand from a protein-ligand complex. As
>> per the
>>         > ligand-protein tutorial, I have restrained the ligand in
>> topology file and
>>         > it looks like:
>>         >
>>         > ; Include Position restraint file
>>         > #ifdef POSRES
>>         > #include "posre.itp"
>>         > #endif
>>         >
>>         > ; Include ligand topology
>>         > #include "drg.itp"
>>         >
>>         > ; Include position restraints
>>         > #ifdef POSRES_LIG
>>         > #include "posre_ACO.itp"
>>         > #endif
>>         >
>>         > ; Include water topology
>>         > #include "gromos43a1.ff/spc.itp"
>>         >
>>         > In the md_pull.mdp, I'm using:
>>         >
>>         > title       = Umbrella pulling simulation
>>         > define      = -DPOSRES
>>         > ; Run parameters
>>         > integrator  = md        ;applying leap frog algorithm
>>         >
>>         > So, is it proper for pulling ligand (ACO) from the protein or
>> I'm doing
>>         > something wrong ? I'm really lost here, please help me out.
>>         >
>>         > Thank you.
>>         >
>>         >
>>         > --
>>         > Abhisek Mondal
>>         >
>>         > *Senior Research Fellow*
>>         >
>>         > *Structural Biology and Bioinformatics Division*
>>         > *CSIR-Indian Institute of Chemical Biology*
>>         >
>>         > *Kolkata 700032*
>>         >
>>         > *INDIA*
>>         > --
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>>
>>
>>     --
>>     Abhisek Mondal
>>     /Senior Research Fellow
>>     /
>>     /Structural Biology and Bioinformatics Division
>>     /
>>     /CSIR-Indian Institute of Chemical Biology/
>>     /Kolkata 700032
>>     /
>>     /INDIA
>>     /
>>
>>
>>
>>
>> --
>> Abhisek Mondal
>> /Senior Research Fellow
>> /
>> /Structural Biology and Bioinformatics Division
>> /
>> /CSIR-Indian Institute of Chemical Biology/
>> /Kolkata 700032
>> /
>> /INDIA
>> /
>>
>
> --
> ==================================================
>
> 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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-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*