[gmx-users] determining restraints for pulling
Justin Lemkul
jalemkul at vt.edu
Fri Apr 7 14:01:31 CEST 2017
On 4/7/17 1:43 AM, abhisek Mondal wrote:
> 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 ?
>
Yes, you can define a pull vector in the negative Z dimension (pull-coordN-vec =
0 0 -1 or whatever is appropriate).
-Justin
> 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*
>>> > --
>>> > Gromacs Users mailing list
>>> >
>>> > * Please search the archive at
>>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
>>> <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List>
>>> before
>>> > posting!
>>> >
>>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> <http://www.gromacs.org/Support/Mailing_Lists>
>>> >
>>> > * For (un)subscribe requests visit
>>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx
>>> -users
>>> <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gm
>>> x-users> or
>>> > send a mail to gmx-users-request at gromacs.org
>>> <mailto:gmx-users-request at gromacs.org>.
>>> >
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
>>> <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List>
>>> before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> <http://www.gromacs.org/Support/Mailing_Lists>
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx
>>> -users
>>> <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gm
>>> x-users> or
>>> send a mail to gmx-users-request at gromacs.org
>>> <mailto:gmx-users-request at gromacs.org>.
>>>
>>>
>>>
>>>
>>> --
>>> 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
>>
>> ==================================================
>>
>> --
>> 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
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>
--
==================================================
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
==================================================
More information about the gromacs.org_gmx-users
mailing list