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 <jalem...@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.m...@gmail.com
<mailto:abhisek.m...@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.abra...@gmail.com
<mailto:mark.j.abra...@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.m...@gmail.com
<mailto:abhisek.m...@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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/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
/
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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
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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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