Re: [gmx-users] determining restraints for pulling

[Justin Lemkul]

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  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 > 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
> 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 > 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

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-requ...@gromacs.org
.
>
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-users

Re: [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  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 > > 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
>> > 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 > > 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
>> 
>> 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
>> > x-users> or
>> > send a mail to gmx-users-requ...@gromacs.org
>> .
>> >
>> --
>> 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
>> 

Re: [gmx-users] determining restraints for pulling

[Justin Lemkul]

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 > 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 > 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 > 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
 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-requ...@gromacs.org
.
>
--
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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 or
send a mail to gmx-users-requ...@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 

Re: [gmx-users] determining restraints for pulling

[abhisek Mondal]

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 
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  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 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-requ...@gromacs.org.
> >
> --
> 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-requ...@gromacs.org.
>



-- 
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 before posting!

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

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] determining restraints for pulling

[Mark Abraham]

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  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 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-requ...@gromacs.org.
>
-- 
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

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mail to gmx-users-requ...@gromacs.org.

[gmx-users] determining restraints for pulling

[abhisek Mondal]

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 before posting!

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

* For (un)subscribe requests visit
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