[gmx-users] Protein-ligand complex simulation

[Nivedita Rai]

Dear Gromacs User,

I am running *protein ligand complex* simulation by
following the Beven lab tutorial. while production run im getting two notes
such as:

NOTE 1 [file topol.top]:
  The largest charge group contains 11 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

Number of degrees of freedom in T-Coupling group Protein_UNK is 8298.87
Number of degrees of freedom in T-Coupling group Water_and_ions is 180606.12
Largest charge group radii for Van der Waals: 0.267, 0.265 nm
Largest charge group radii for Coulomb:   0.267, 0.265 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 84x84x84, spacing 0.118 0.118 0.118
Estimate for the relative computational load of the PME mesh part: 0.32

NOTE 2 [file md.mdp]:
  This run will generate roughly 5681 Mb of data

Is *note1* will create any trouble? if yes then how to rectify it?

-- 
Thanks and regards


Nivedita Rai
PhD in Bioinformatics
Centre for Bioinformatics
Pondicherry University, Pondicherry (605014), 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.

[gmx-users] Protein ligand complex simulation

[RAHUL SURESH]

I followed the complex simulation tutorial. Minimisation for 2ns

I used auto dock to dock ligand with protein. During simulation I find the
ligand out of protein. Is that usual?
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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.

Re: [gmx-users] Protein-ligand complex simulation

[Justin Lemkul]

On 1/9/17 1:58 AM, Nivedita Rai wrote:

Dear Gromacs User,

I am running *protein ligand complex* simulation by
following the Beven lab tutorial. while production run im getting two notes
such as:

NOTE 1 [file topol.top]:
  The largest charge group contains 11 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

Number of degrees of freedom in T-Coupling group Protein_UNK is 8298.87
Number of degrees of freedom in T-Coupling group Water_and_ions is 180606.12
Largest charge group radii for Van der Waals: 0.267, 0.265 nm
Largest charge group radii for Coulomb:   0.267, 0.265 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 84x84x84, spacing 0.118 0.118 0.118
Estimate for the relative computational load of the PME mesh part: 0.32

NOTE 2 [file md.mdp]:
  This run will generate roughly 5681 Mb of data

Is *note1* will create any trouble? if yes then how to rectify it?



I answered this last week:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-January/110245.html

-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

* 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.

Re: [gmx-users] Protein ligand complex simulation

[RAHUL SURESH]

I mean the ligand is not bonded with the protein.


On Sat, 1 Apr 2017 at 6:29 PM, RAHUL SURESH  wrote:

> I followed the complex simulation tutorial. Minimisation for 2ns
>
> I used auto dock to dock ligand with protein. During simulation I find the
> ligand out of protein. Is that usual?
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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.

Re: [gmx-users] Protein ligand complex simulation

[Justin Lemkul]

On 4/1/17 8:59 AM, RAHUL SURESH wrote:

I followed the complex simulation tutorial. Minimisation for 2ns



FYI there is no time during energy minimization, so you did not do "2 ns" of 
minimization.



I used auto dock to dock ligand with protein. During simulation I find the
ligand out of protein. Is that usual?



This is probably a periodicity effect.  There's no way during the course of 
minimization that a ligand-protein complex can completely dissociate.  Use 
trjconv to make sure you've properly re-imaged the system.  A simple recentering 
should do it.


-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

* 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.

Re: [gmx-users] Protein ligand complex simulation

[RAHUL SURESH]

Dear Justin

First I apologise for the error I had made in my previous mail. It's during
production.

I have recentered it. The ligand is out of the protein. The ligand is not
in position where I docked.


On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul  wrote:

>
>
> On 4/1/17 8:59 AM, RAHUL SURESH wrote:
> > I followed the complex simulation tutorial. Minimisation for 2ns
> >
>
> FYI there is no time during energy minimization, so you did not do "2 ns"
> of
> minimization.
>
> > I used auto dock to dock ligand with protein. During simulation I find
> the
> > ligand out of protein. Is that usual?
> >
>
> This is probably a periodicity effect.  There's no way during the course of
> minimization that a ligand-protein complex can completely dissociate.  Use
> trjconv to make sure you've properly re-imaged the system.  A simple
> recentering
> should do it.
>
> -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
>
> * 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.
>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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.

Re: [gmx-users] Protein ligand complex simulation

[Justin Lemkul]

On 4/3/17 7:56 AM, RAHUL SURESH wrote:

Dear Justin

First I apologise for the error I had made in my previous mail. It's during
production.

I have recentered it. The ligand is out of the protein. The ligand is not
in position where I docked.



Then watch the recentered trajectory to see what happened.  Dissociation should 
be apparent, and smooth if the PBC effects have been correctly accounted for. 
If the dissociation is real, either the initial position was unfavorable 
(docking is sometimes incorrect!) or the topology of the ligand was inadequate 
and thus you got a poor model of the interactions.


-Justin



On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul  wrote:




On 4/1/17 8:59 AM, RAHUL SURESH wrote:

I followed the complex simulation tutorial. Minimisation for 2ns



FYI there is no time during energy minimization, so you did not do "2 ns"
of
minimization.


I used auto dock to dock ligand with protein. During simulation I find

the

ligand out of protein. Is that usual?



This is probably a periodicity effect.  There's no way during the course of
minimization that a ligand-protein complex can completely dissociate.  Use
trjconv to make sure you've properly re-imaged the system.  A simple
recentering
should do it.

-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

* 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.



--
==

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

* 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.

Re: [gmx-users] Protein ligand complex simulation

[RAHUL SURESH]

The ligand is out of protein in the very first frame of production run.
 Then that should be my docking error.?

On Mon, 3 Apr 2017 at 5:30 PM, Justin Lemkul  wrote:

>
>
> On 4/3/17 7:56 AM, RAHUL SURESH wrote:
> > Dear Justin
> >
> > First I apologise for the error I had made in my previous mail. It's
> during
> > production.
> >
> > I have recentered it. The ligand is out of the protein. The ligand is not
> > in position where I docked.
> >
>
> Then watch the recentered trajectory to see what happened.  Dissociation
> should
> be apparent, and smooth if the PBC effects have been correctly accounted
> for.
> If the dissociation is real, either the initial position was unfavorable
> (docking is sometimes incorrect!) or the topology of the ligand was
> inadequate
> and thus you got a poor model of the interactions.
>
> -Justin
>
> >
> > On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 4/1/17 8:59 AM, RAHUL SURESH wrote:
> >>> I followed the complex simulation tutorial. Minimisation for 2ns
> >>>
> >>
> >> FYI there is no time during energy minimization, so you did not do "2
> ns"
> >> of
> >> minimization.
> >>
> >>> I used auto dock to dock ligand with protein. During simulation I find
> >> the
> >>> ligand out of protein. Is that usual?
> >>>
> >>
> >> This is probably a periodicity effect.  There's no way during the
> course of
> >> minimization that a ligand-protein complex can completely dissociate.
> Use
> >> trjconv to make sure you've properly re-imaged the system.  A simple
> >> recentering
> >> should do it.
> >>
> >> -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
> >>
> >> * 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.
> >>
>
> --
> ==
>
> 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
>
> * 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.
>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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.

Re: [gmx-users] Protein ligand complex simulation

[Justin Lemkul]

On 4/3/17 8:05 AM, RAHUL SURESH wrote:

The ligand is out of protein in the very first frame of production run.
 Then that should be my docking error.?



It sounds like your starting configuration was prepared incorrectly (however you 
manipulated it to prepare the system) or this is a PBC effect.


-Justin


On Mon, 3 Apr 2017 at 5:30 PM, Justin Lemkul  wrote:




On 4/3/17 7:56 AM, RAHUL SURESH wrote:

Dear Justin

First I apologise for the error I had made in my previous mail. It's

during

production.

I have recentered it. The ligand is out of the protein. The ligand is not
in position where I docked.



Then watch the recentered trajectory to see what happened.  Dissociation
should
be apparent, and smooth if the PBC effects have been correctly accounted
for.
If the dissociation is real, either the initial position was unfavorable
(docking is sometimes incorrect!) or the topology of the ligand was
inadequate
and thus you got a poor model of the interactions.

-Justin



On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul  wrote:




On 4/1/17 8:59 AM, RAHUL SURESH wrote:

I followed the complex simulation tutorial. Minimisation for 2ns



FYI there is no time during energy minimization, so you did not do "2

ns"

of
minimization.


I used auto dock to dock ligand with protein. During simulation I find

the

ligand out of protein. Is that usual?



This is probably a periodicity effect.  There's no way during the

course of

minimization that a ligand-protein complex can completely dissociate.

Use

trjconv to make sure you've properly re-imaged the system.  A simple
recentering
should do it.

-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

* 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.



--
==

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

* 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.



--
==

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

* 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.

Re: [gmx-users] Protein ligand complex simulation

[Mark Abraham]

Hi,

Look at your docking result before you use it for something else. (Same
goes for any computed result from any software.)

Mark

On Mon, 3 Apr 2017 14:06 RAHUL SURESH  wrote:

> The ligand is out of protein in the very first frame of production run.
>  Then that should be my docking error.?
>
> On Mon, 3 Apr 2017 at 5:30 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 4/3/17 7:56 AM, RAHUL SURESH wrote:
> > > Dear Justin
> > >
> > > First I apologise for the error I had made in my previous mail. It's
> > during
> > > production.
> > >
> > > I have recentered it. The ligand is out of the protein. The ligand is
> not
> > > in position where I docked.
> > >
> >
> > Then watch the recentered trajectory to see what happened.  Dissociation
> > should
> > be apparent, and smooth if the PBC effects have been correctly accounted
> > for.
> > If the dissociation is real, either the initial position was unfavorable
> > (docking is sometimes incorrect!) or the topology of the ligand was
> > inadequate
> > and thus you got a poor model of the interactions.
> >
> > -Justin
> >
> > >
> > > On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul  wrote:
> > >
> > >>
> > >>
> > >> On 4/1/17 8:59 AM, RAHUL SURESH wrote:
> > >>> I followed the complex simulation tutorial. Minimisation for 2ns
> > >>>
> > >>
> > >> FYI there is no time during energy minimization, so you did not do "2
> > ns"
> > >> of
> > >> minimization.
> > >>
> > >>> I used auto dock to dock ligand with protein. During simulation I
> find
> > >> the
> > >>> ligand out of protein. Is that usual?
> > >>>
> > >>
> > >> This is probably a periodicity effect.  There's no way during the
> > course of
> > >> minimization that a ligand-protein complex can completely dissociate.
> > Use
> > >> trjconv to make sure you've properly re-imaged the system.  A simple
> > >> recentering
> > >> should do it.
> > >>
> > >> -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
> > >>
> > >> * 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.
> > >>
> >
> > --
> > ==
> >
> > 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
> >
> > * 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.
> >
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> 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.

[gmx-users] Protein-ligand complex simulation and ATBserver file

[Sri Prasanth Ghanta, Doctoral Research Scholar, Biosciences, SSSIHL]

Dear all,

I have started following the new tutorial
 and the old tutorial

to carryout the simulation of JZ4 with Lysozyme.
I was unable to run the cgenff script as I am not aware of setting up
microenvironment in Ubuntu to run older python version, which is essential
in running the script required for creation of ligand topology.

>From a bit of reading, I understood that ATBserver is preferred over PRODRG
as the topology created is more accurate.
I had followed the tutorial to build the complex (complex.gro) by
incorporating jz4.gro (from ATBserver) in the 3htb_processed.gro. I had
also incorporated the ligand topolgy (jz4.itp) into the topol.top as
instructed.
I was successful in building the box and solvating. However, when i try to
run
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
I get an error in line 1345 stating,
-

*Fatal error:*
*Atomtype CAro not found*

*--*
I am assuming it's something to do with the representation of the carbon
(aromatic) in the topology of the ligand (jz4.itp), which reads like this..
-
[ moleculetype ]
; Name   nrexcl
WX56 3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemass
1   CH31WX56 C11   -0.011  15.0350
2   CH21WX56 C220.028  14.0270
3   CH21WX56 C330.113  14.0270
4  CAro1WX56 C44   -0.194  12.0110
5  CAro1WX56 C950.338  12.0110
6  OAlc1WX56 O16   -0.588  15.9994
7  HS141WX56H1270.428   1.0080
8  CAro1WX56 C88   -0.268  12.0110
9HC1WX56H1190.167   1.0080
   10  CAro1WX56 C7   10   -0.100  12.0110
   11HC1WX56H10   110.131   1.0080
   12  CAro1WX56 C6   12   -0.201  12.0110
   13HC1WX56 H9   130.136   1.0080
   14  CAro1WX56 C5   14   -0.124  12.0110
   15HC1WX56 H8   150.145   1.0080
; total charge of the molecule:  -0.000


However, I am not sure, which code I need to use in the place of CAro, OAlc
and HS14. Can you please help me in this regard?
P.S: I am trying to use GROMOS96 54a7 forcefield for this purpose.

-- 
Regards,
Prasanth.
-- 
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.

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

[Justin Lemkul]

On Tue, Dec 18, 2018 at 12:17 AM Sri Prasanth Ghanta, Doctoral Research
Scholar, Biosciences, SSSIHL  wrote:

> Dear all,
>
> I have started following the new tutorial
>  and the old tutorial
> <
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html
> >
> to carryout the simulation of JZ4 with Lysozyme.
> I was unable to run the cgenff script as I am not aware of setting up
> microenvironment in Ubuntu to run older python version, which is essential
> in running the script required for creation of ligand topology.
>
> From a bit of reading, I understood that ATBserver is preferred over PRODRG
> as the topology created is more accurate.
> I had followed the tutorial to build the complex (complex.gro) by
> incorporating jz4.gro (from ATBserver) in the 3htb_processed.gro. I had
> also incorporated the ligand topolgy (jz4.itp) into the topol.top as
> instructed.
> I was successful in building the box and solvating. However, when i try to
> run
> gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
> I get an error in line 1345 stating,
> -
>
> *Fatal error:*
> *Atomtype CAro not found*
>
> *--*
> I am assuming it's something to do with the representation of the carbon
> (aromatic) in the topology of the ligand (jz4.itp), which reads like this..
> -
> [ moleculetype ]
> ; Name   nrexcl
> WX56 3
> [ atoms ]
> ;  nr  type  resnr  resid  atom  cgnr  chargemass
> 1   CH31WX56 C11   -0.011  15.0350
> 2   CH21WX56 C220.028  14.0270
> 3   CH21WX56 C330.113  14.0270
> 4  CAro1WX56 C44   -0.194  12.0110
> 5  CAro1WX56 C950.338  12.0110
> 6  OAlc1WX56 O16   -0.588  15.9994
> 7  HS141WX56H1270.428   1.0080
> 8  CAro1WX56 C88   -0.268  12.0110
> 9HC1WX56H1190.167   1.0080
>10  CAro1WX56 C7   10   -0.100  12.0110
>11HC1WX56H10   110.131   1.0080
>12  CAro1WX56 C6   12   -0.201  12.0110
>13HC1WX56 H9   130.136   1.0080
>14  CAro1WX56 C5   14   -0.124  12.0110
>15HC1WX56 H8   150.145   1.0080
> ; total charge of the molecule:  -0.000
> 
>
> However, I am not sure, which code I need to use in the place of CAro, OAlc
> and HS14. Can you please help me in this regard?
> P.S: I am trying to use GROMOS96 54a7 forcefield for this purpose.
>
>
Are you trying to combine this ligand topology with the CHARMM protein
topology generated in the tutorial? If so, that's fundamentally incorrect
and you can never make that work.

If you're doing things entirely within the context of GROMOS, then you
likely need additional files from the ATB server that provide parameters
for the "unknown" atom types.

-Justin
-- 

==

Justin A. Lemkul, Ph.D.

Assistant Professor

Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com


==
-- 
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.

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

[Prasanth G, Research Scholar]

Dear Sir,

I am running GROMACS 5.1.4 on a server.
I had converted the protein(pdb2gro) using the latest GROMOS forcefield.
As per your suggestion, I had downloaded the parameter files from ATB
server. As per the readme file from the server (in the parameters folder),
i had updated my topol.top like this and also included the extracted folder
to the working directory on the server.
---
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include ligand topology
#include "jz4.itp"

; Include force field parameters
#include "home/bio1/PG/gromos54a7_atb.ff/forcefield.itp"

; Include topology for ions
#include "home/bio1/PG/gromos54a7_atb.ff/ions.itp"

; Include water topology
#include "home/bio1/PG/gromos54a7_atb.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

[ system ]
; Name
LYSOZYME

[ molecules ]
; Compound#mols
Protein_chain_A 1
JZ4 1

However, when i try to execute the grompp to add ions, the error still
persists-

*Fatal error:*

*Atomtype CAro not found *

Could you please tell me, if i have to change the way this  has to be done.
Here is the list of parameter files obtained from the ATBserver.
link- https://atb.uq.edu.au/molecule.py?molid=342699#panel-md
---
aminoacids.c.tdb, aminoacids.hbd, amonoacids.n.tbb, aminoacids.r2b,
aminoacids.rtp, aminoacids.vsd, atomtypes.atp, dppc.itp, ffbonded.itp,
ffdum.itp, ffnonbonded.itp, forcefield.doc, forcefield.itp, ions.itp,
popc.itp, README.md, spc.itp, spce.itp, tip3.itp, tip4.itp, tmcl.itp,
watermodels.dat
---

Thanks in advance,
Prasanth.

Are you trying to combine this ligand topology with the CHARMM protein
topology generated in the tutorial? If so, that's fundamentally incorrect
and you can never make that work.

If you're doing things entirely within the context of GROMOS, then you
likely need additional files from the ATB server that provide parameters
for the "unknown" atom types.

-Justin
-- 

==

Justin A. Lemkul, Ph.D.

Assistant Professor

Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com


==


--

On Tue, Dec 18, 2018 at 10:49 AM Sri Prasanth Ghanta, Doctoral Research
Scholar, Biosciences, SSSIHL  wrote:

> Dear all,
>
> I have started following the new tutorial
>  and the old tutorial
> 
> to carryout the simulation of JZ4 with Lysozyme.
> I was unable to run the cgenff script as I am not aware of setting up
> microenvironment in Ubuntu to run older python version, which is essential
> in running the script required for creation of ligand topology.
>
> From a bit of reading, I understood that ATBserver is preferred over
> PRODRG as the topology created is more accurate.
> I had followed the tutorial to build the complex (complex.gro) by
> incorporating jz4.gro (from ATBserver) in the 3htb_processed.gro. I had
> also incorporated the ligand topolgy (jz4.itp) into the topol.top as
> instructed.
> I was successful in building the box and solvating. However, when i try to
> run
> gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
> I get an error in line 1345 stating,
> -
>
> *Fatal error:*
> *Atomtype CAro not found*
>
> *--*
> I am assuming it's something to do with the representation of the carbon
> (aromatic) in the topology of the ligand (jz4.itp), which reads like this..
> -
> [ moleculetype ]
> ; Name   nrexcl
> WX56 3
> [ atoms ]
> ;  nr  type  resnr  resid  atom  cgnr  chargemass
> 1   CH31WX56 C11   -0.011  15.0350
> 2   CH21WX56 C220.028  14.0270
> 3   CH21WX56 C330.113  14.0270
> 4  CAro1WX56 C44   -0.194  12.0110
> 5  CAro1WX56 C950.338  12.0110
> 6  OAlc1WX56 O16   -0.588  15.9994
> 7  HS141WX56H1270.428   1.0080
> 8  CAro1WX56 C88   -0.268  12.0110
> 9HC1WX56H1190.167   1.0080
>10  CAro1WX56 C7   10   -0.100  12.0110
>11HC1WX56H10   110.131   1.0080
>12  CAro1WX56 C6   12   -0.201  12.0110
>13HC1WX56 H9   130.136   1.0080
>14  CAro1WX56 C5   14   -0.124  12.0110
>15HC1WX56 H8   150.145   1.0080
> ; total charge of the molecule:  -0.000
> 
>
> However, I am not sure, which 

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

[Justin Lemkul]

On Wed, Dec 19, 2018 at 4:34 AM Prasanth G, Research Scholar <
prasanthgha...@sssihl.edu.in> wrote:

> Dear Sir,
>
> I am running GROMACS 5.1.4 on a server.
> I had converted the protein(pdb2gro) using the latest GROMOS forcefield.
> As per your suggestion, I had downloaded the parameter files from ATB
> server. As per the readme file from the server (in the parameters folder),
> i had updated my topol.top like this and also included the extracted folder
> to the working directory on the server.
> ---
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include ligand topology
> #include "jz4.itp"
>
> ; Include force field parameters
> #include "home/bio1/PG/gromos54a7_atb.ff/forcefield.itp"
>
>
Your #include statements are out of order. The #include statement for the
parent force field (the line above) should appear before anything else in
the topology, as it defines the atom types. The ffnonbonded.itp file does,
in fact, define CAro, which is a nonstandard type from ATB. I also suspect
that your specified PATH is lacking an initial / - note that full PATH
information is not necessary if the force field subdirectory is in $GMXLIB
or in the working directory.

-Justin

-- 

==

Justin A. Lemkul, Ph.D.

Assistant Professor

Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com


==
-- 
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.

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

[Prasanth G, Research Scholar]

Dear Sir,

Thanks a lot for the inputs. I tried incorporating the forcefield
parameters (directory) obtained from the atbserver in the working
directory. When i was trying to convert the protein.pdb to .gro, I noticed
that the forcefield showed up in the menu as one included in local
directory, just as it does for cgenff in the tutorial.
I chose it to prepare the protein.gro file and then incorporated the
jz4.itp into the topology file of protein.
I was able to overcome the issues and complete npt and nvt equilibration.
Will proceed with the mdrun tomorrow morning.
Can you please suggest a solution for resuming the mdrun, in case there is
an interruption in the connectivity with the server. As i am running the
simulation from a laptop, I might not be able to leave it on through out.
Thank you once again.

---
Your #include statements are out of order. The #include statement for the
parent force field (the line above) should appear before anything else in
the topology, as it defines the atom types. The ffnonbonded.itp file does,
in fact, define CAro, which is a nonstandard type from ATB. I also suspect
that your specified PATH is lacking an initial / - note that full PATH
information is not necessary if the force field subdirectory is in $GMXLIB
or in the working directory.

-Justin

-- 

==

Justin A. Lemkul, Ph.D.

Assistant Professor

Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com


==

On Wed, Dec 19, 2018 at 3:05 PM Prasanth G, Research Scholar <
prasanthgha...@sssihl.edu.in> wrote:

> Dear Sir,
>
> I am running GROMACS 5.1.4 on a server.
> I had converted the protein(pdb2gro) using the latest GROMOS forcefield.
> As per your suggestion, I had downloaded the parameter files from ATB
> server. As per the readme file from the server (in the parameters folder),
> i had updated my topol.top like this and also included the extracted folder
> to the working directory on the server.
> ---
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include ligand topology
> #include "jz4.itp"
>
> ; Include force field parameters
> #include "home/bio1/PG/gromos54a7_atb.ff/forcefield.itp"
>
> ; Include topology for ions
> #include "home/bio1/PG/gromos54a7_atb.ff/ions.itp"
>
> ; Include water topology
> #include "home/bio1/PG/gromos54a7_atb.ff/spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct   fcxfcyfcz
>11   1000   1000   1000
> #endif
>
> [ system ]
> ; Name
> LYSOZYME
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_A 1
> JZ4 1
> 
> However, when i try to execute the grompp to add ions, the error still
> persists-
>
> *Fatal error:*
>
> *Atomtype CAro not found *
>
> Could you please tell me, if i have to change the way this  has to be
> done. Here is the list of parameter files obtained from the ATBserver.
> link- https://atb.uq.edu.au/molecule.py?molid=342699#panel-md
> ---
> aminoacids.c.tdb, aminoacids.hbd, amonoacids.n.tbb, aminoacids.r2b,
> aminoacids.rtp, aminoacids.vsd, atomtypes.atp, dppc.itp, ffbonded.itp,
> ffdum.itp, ffnonbonded.itp, forcefield.doc, forcefield.itp, ions.itp,
> popc.itp, README.md, spc.itp, spce.itp, tip3.itp, tip4.itp, tmcl.itp,
> watermodels.dat
> ---
>
> Thanks in advance,
> Prasanth.
>
> 
> Are you trying to combine this ligand topology with the CHARMM protein
> topology generated in the tutorial? If so, that's fundamentally incorrect
> and you can never make that work.
>
> If you're doing things entirely within the context of GROMOS, then you
> likely need additional files from the ATB server that provide parameters
> for the "unknown" atom types.
>
> -Justin
> --
>
> ==
>
> Justin A. Lemkul, Ph.D.
>
> Assistant Professor
>
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
>
> ==
>
>
> --
>
> On Tue, Dec 18, 2018 at 10:49 AM Sri Prasanth Ghanta, Doctoral Research
> Scholar, Biosciences, SSSIHL  wrote:
>
>> Dear all,
>>
>> I have started following the new tutorial
>>  and the old tutorial
>> 
>> to carryout the simulation of JZ4 with Lysozyme.
>> I was unable to run the cgenff script as I am not aware of setting up
>> microenvironment in Ubuntu to run older python version, which is essential
>>

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

[Justin Lemkul]

On Thu, Dec 20, 2018 at 10:05 AM Prasanth G, Research Scholar <
prasanthgha...@sssihl.edu.in> wrote:

> Dear Sir,
>
> Thanks a lot for the inputs. I tried incorporating the forcefield
> parameters (directory) obtained from the atbserver in the working
> directory. When i was trying to convert the protein.pdb to .gro, I noticed
> that the forcefield showed up in the menu as one included in local
> directory, just as it does for cgenff in the tutorial.
> I chose it to prepare the protein.gro file and then incorporated the
> jz4.itp into the topology file of protein.
> I was able to overcome the issues and complete npt and nvt equilibration.
> Will proceed with the mdrun tomorrow morning.
> Can you please suggest a solution for resuming the mdrun, in case there is
> an interruption in the connectivity with the server. As i am running the
> simulation from a laptop, I might not be able to leave it on through out.
>

http://www.gromacs.org/Documentation/How-tos/Doing_Restarts

Checkpointing makes continuing a simulation seamless.

-Justin

-- 

==

Justin A. Lemkul, Ph.D.

Assistant Professor

Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com


==
-- 
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.