[gmx-users] OPLS3 forcefield

[Neha Gupta]

Hi gromacs users,

How to generate OPLS3 force field parameters for an organic molecule?

I want to build an automated topology file using OPLS3 force field. How to
proceed?

Thanks,
Neha
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Re: [gmx-users] RESTARTING THE CALCULATION

[Neha Gupta]

Hi,

I gave

gmx mdrun -s md.tpr -cpi md_step17960400.cpt

It says, Checkpoint file corrupted or truncated or you are out of disk
space?

I have deleted files of higher MB. Why the problem persists?

Thanks,
Neha

On Sun, Mar 11, 2018 at 10:55 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Exactly as you ran the original simulation, plus pass the name of the
> latest checkpoint file to -cpi. Back up your files first.
>
> Mark
>
> On Sun, Mar 11, 2018 at 6:18 PM Neha Gupta <nehaphysic...@gmail.com>
> wrote:
>
> > Hi gromacs users,
> >
> > I wanted to do simulations fro 50 ns.
> >
> > But, due to lack of disk space, it abruptly stopped.
> >
> >
> > I have md.xtc, md.cpt, md.log, md_step17960400.cpt, md_prev.cpt.
> >
> > How to restart the calculation and complete it successfully?
> >
> > Thanks,
> > Neha
> > --
> > Gromacs Users mailing list
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[gmx-users] RESTARTING THE CALCULATION

[Neha Gupta]

Hi gromacs users,

I wanted to do simulations fro 50 ns.

But, due to lack of disk space, it abruptly stopped.


I have md.xtc, md.cpt, md.log, md_step17960400.cpt, md_prev.cpt.

How to restart the calculation and complete it successfully?

Thanks,
Neha
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[gmx-users] Installing DSSP

[Neha Gupta]

Hi,

I use gromacs version 5.1.4 through cygwin

Please let me know how to install DSSP?

Which version of DSSP would be compatible with the above version of gromacs?

Thanks,
Neha
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[gmx-users] MOVIE.pdb

[Neha Gupta]

Hi Justin,

I followed your protein-ligand complex tutorials to do the simulation.

I intend to run the simulation for 50 ns.

In the final md run section, can we modify the command like this

nstxout-compressed  = 50  ; write .xtc trajectory every 1000.0 ps


You have written the .xtc trajectory every 10 ps.

How would the above command change the o/p?


Thanks,
Neha
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[gmx-users] regarding rdf

[Neha Gupta]

Hi,

I take the following steps to perform rdf calculation for my organic
molecule.

min, min2, eql, eql2 and prd.

In order to check, whether my molecule is intact, I generate .pdb of the
entire system after each step.

Till eql step, my molecule remains intact.

After eql2, the molecule breaks.


I make use of the following code for eql :

integrator   = md
dt   = 0.002 ; 2 fs
nsteps   = 50; 1.0 ns

nstenergy= 200
nstlog   = 2000
nstxout-compressed   = 1

continuation = yes
constraint-algorithm = lincs
constraints  = h-bonds

cutoff-scheme= Verlet

coulombtype  = PME
rcoulomb = 1.0

vdwtype  = Cut-off
rvdw = 1.0
DispCorr = EnerPres

tcoupl   = Nose-Hoover
tc-grps  = LIG  Water
tau-t= 2.0   2.0
ref-t= 298.15   298.15
nhchainlength= 1

pcoupl   = Parrinello-Rahman
tau_p= 2.0
compressibility  = 4.46e-5
ref_p= 1.0


How to fix it?

Thanks,
Neha
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[gmx-users] RADIAL DISTRIBUTION FUNCTION

[Neha Gupta]

Hi,

I want to calculate radial distribution function for my organic molecule.

How to proceed?

How to write codes for RDF?

Thanks,
Neha
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Re: [gmx-users] PROTEIN FOLDING

[Neha Gupta]

At first, I gave,
gmx trjconv -pbc whole -s prd.tpr -f prd.xtc -o trajwhole.xtc
 I selected "system" for output

It says
Program gmx trjconv, VERSION 5.1.4
Source code file:
/cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/gmx_trjconv.c,
line: 1322

Fatal error:
Index[6376] 6377 is larger than the number of atoms in the
trajectory file (6376). There is a mismatch in the contents
of your -f, -s and/or -n files.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Which index number should I select for all the three commands mentioned
above?

Thanks,
Neha



On Sat, Dec 30, 2017 at 9:42 PM, Justin Lemkul  wrote:

>
>
> On 12/30/17 10:47 AM, Alexandr Nasedkin wrote:
>
>> gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc nojump -o trajclust.xtc -n
>> index.ndx -center
>>
>>
> Removing jumps and centering simultaneously should be considered mutually
> exclusive. One usually needs a few rounds of trjconv, e.g.
>
> gmx trjconv -pbc whole
> gmx trjconv -pbc nojump
> gmx trjconv -pbc mol -center
>
> Almost always does the trick for simple systems.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
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Re: [gmx-users] PROTEIN FOLDING

[Neha Gupta]

Hi Justin,

Can you please let me know the exact commands?

None of the commands which I tried are working...

Thanks,
Neha




On Thu, Dec 28, 2017 at 7:04 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 12/28/17 8:33 AM, Neha Gupta wrote:
>
>> Hi,
>>
>> I tried this one
>>
>> gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc cluster -o trajclust.xtc -n
>> index.ndx
>>
>> This asks me to select a group fro clustering and then select a group for
>> output..
>>
>> What should I select first and then next?
>>
>
> Clustering isn't relevant. Your situation is much simpler than it's being
> made out to be.
>
> 1. Make molecules whole
> 2. Remove jumps
> 3. Center
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
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Re: [gmx-users] PROTEIN FOLDING

[Neha Gupta]

Hi,

I tried this one

gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc cluster -o trajclust.xtc -n
index.ndx

This asks me to select a group fro clustering and then select a group for
output..

What should I select first and then next?

Thanks,
Neha

On Thu, Dec 28, 2017 at 5:44 PM, Lakshman Ji Verma <lakshmanji...@gmail.com>
wrote:

> Do it multiple times by center the ligand first and then protein in the
> other step,while using pbc. Use -pbc mol option in one of the step to get
> the whole molecule.
>
> Thanks
>
> On Thu, Dec 28, 2017 at 6:26 AM Neha Gupta <nehaphysic...@gmail.com>
> wrote:
>
> > I gave
> >
> > gmx trjconv -pbc nojump -s  prd.gro -f prd.xtc -e 5.0 -n index.ndx -o
> > PRD.pdb
> >
> > Is there any other alternate command?
> >
> > Thanks,
> > Neha
> >
> > On Thu, Dec 28, 2017 at 11:30 AM, RAHUL SURESH <drrahulsur...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > migh be visualization error
> > >
> > > Apply pbc
> > >
> > > On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta <nehaphysic...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > I tried running the simulations for 50 ns.
> > > >
> > > > The protein breaks (but ligand remains in the active site of the
> > protein
> > > > and it is stable throughout )
> > > >
> > > > How to fix it?
> > > >
> > > > Thanks,
> > > > Neha
> > > >
> > > > On Wed, Dec 20, 2017 at 6:28 PM, João Henriques <
> > > > joao.m.a.henriq...@gmail.com> wrote:
> > > >
> > > > > Depends. If you're interested in local folding and there are SS
> > motifs
> > > in
> > > > > the region you're interested, then yes. If not, no. In terms of
> > overall
> > > > > folding of the entire protein, yes it surely can be an important
> > > > analysis.
> > > > >
> > > > > J
> > > > >
> > > > > On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta <
> nehaphysic...@gmail.com
> > >
> > > > > wrote:
> > > > >
> > > > > > Thank you Joao and Aman.
> > > > > >
> > > > > > I have noted the points you have suggested.
> > > > > >
> > > > > > Do you think analyzing DSSP would help?
> > > > > >
> > > > > > Thanks,
> > > > > > Neha
> > > > > >
> > > > > > On Wed, Dec 20, 2017 at 4:03 PM, João Henriques <
> > > > > > joao.m.a.henriq...@gmail.com> wrote:
> > > > > >
> > > > > > > "You can use various supporting tools from R language to debug
> > your
> > > > > > > trajectory but most third party software support NAMD and
> charmm
> > > > > format.
> > > > > > > You can use VMD to convert the trajectory to dcd and use R
> > language
> > > > > based
> > > > > > > packages to read your trajectory"
> > > > > > >
> > > > > > > What? How is this useful or helpful? At most it confuses the OP
> > > even
> > > > > > more.
> > > > > > >
> > > > > > > Also, the clustering analysis is unlikely to be what you want
> or
> > > need
> > > > > at
> > > > > > > this stage. Why overcomplicate? One of the simplest ways to
> check
> > > > that
> > > > > > > there are conformational changes on a given set of atoms is by
> > > doing
> > > > a
> > > > > > RMSD
> > > > > > > analysis using the folded structure as the reference. The RMSD
> is
> > > > > > somewhat
> > > > > > > degenerate, but should suffice for this purpose. You can use an
> > > index
> > > > > > file
> > > > > > > to restrict the RMSD analysis to a particular subset of your
> > system
> > > > > (the
> > > > > > > docking site, for example).
> > > > > > >
> > > > > > > You could look at the radius of gyration as well, Rg, as Aman
> > Deep
> > > > also
> > > > > > > suggests. This can either be calculated on a subset of atoms or
> > on
> >

Re: [gmx-users] PROTEIN FOLDING

[Neha Gupta]

I gave

gmx trjconv -pbc nojump -s  prd.gro -f prd.xtc -e 5.0 -n index.ndx -o
PRD.pdb

Is there any other alternate command?

Thanks,
Neha

On Thu, Dec 28, 2017 at 11:30 AM, RAHUL SURESH <drrahulsur...@gmail.com>
wrote:

> Hi,
>
> migh be visualization error
>
> Apply pbc
>
> On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta <nehaphysic...@gmail.com>
> wrote:
>
> > Hi,
> >
> > I tried running the simulations for 50 ns.
> >
> > The protein breaks (but ligand remains in the active site of the protein
> > and it is stable throughout )
> >
> > How to fix it?
> >
> > Thanks,
> > Neha
> >
> > On Wed, Dec 20, 2017 at 6:28 PM, João Henriques <
> > joao.m.a.henriq...@gmail.com> wrote:
> >
> > > Depends. If you're interested in local folding and there are SS motifs
> in
> > > the region you're interested, then yes. If not, no. In terms of overall
> > > folding of the entire protein, yes it surely can be an important
> > analysis.
> > >
> > > J
> > >
> > > On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta <nehaphysic...@gmail.com>
> > > wrote:
> > >
> > > > Thank you Joao and Aman.
> > > >
> > > > I have noted the points you have suggested.
> > > >
> > > > Do you think analyzing DSSP would help?
> > > >
> > > > Thanks,
> > > > Neha
> > > >
> > > > On Wed, Dec 20, 2017 at 4:03 PM, João Henriques <
> > > > joao.m.a.henriq...@gmail.com> wrote:
> > > >
> > > > > "You can use various supporting tools from R language to debug your
> > > > > trajectory but most third party software support NAMD and charmm
> > > format.
> > > > > You can use VMD to convert the trajectory to dcd and use R language
> > > based
> > > > > packages to read your trajectory"
> > > > >
> > > > > What? How is this useful or helpful? At most it confuses the OP
> even
> > > > more.
> > > > >
> > > > > Also, the clustering analysis is unlikely to be what you want or
> need
> > > at
> > > > > this stage. Why overcomplicate? One of the simplest ways to check
> > that
> > > > > there are conformational changes on a given set of atoms is by
> doing
> > a
> > > > RMSD
> > > > > analysis using the folded structure as the reference. The RMSD is
> > > > somewhat
> > > > > degenerate, but should suffice for this purpose. You can use an
> index
> > > > file
> > > > > to restrict the RMSD analysis to a particular subset of your system
> > > (the
> > > > > docking site, for example).
> > > > >
> > > > > You could look at the radius of gyration as well, Rg, as Aman Deep
> > also
> > > > > suggests. This can either be calculated on a subset of atoms or on
> > the
> > > > > entire protein. The latter could potentially be used to compare
> with
> > > the
> > > > > experimental reference obtained by SAXS, for example. Or you could
> > > > > calculate the SAXS curve and get a better understanding of size and
> > > shape
> > > > > differences between your protein and the reference, but that's more
> > > > > advanced stuff.
> > > > >
> > > > > J
> > > > >
> > > > > On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH <
> > drrahulsur...@gmail.com
> > > >
> > > > > wrote:
> > > > >
> > > > > > Also you must know, a lot analysis are available over the entire
> > > manual
> > > > > of
> > > > > > Gromacs where all cannot be performed. Gromacs always provide you
> > all
> > > > > > necessary analysis but to choose which one is always your choice
> > that
> > > > > suits
> > > > > > your simulation purpose.
> > > > > >
> > > > > >
> > > > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta <
> > nehaphysic...@gmail.com>
> > > > > > wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > >
> > > > > > > Thank you for your prompt reply.
> > > > > > >
> > > > > > > By clustering analysis, are 

Re: [gmx-users] PROTEIN FOLDING

[Neha Gupta]

Hi,

I tried running the simulations for 50 ns.

The protein breaks (but ligand remains in the active site of the protein
and it is stable throughout )

How to fix it?

Thanks,
Neha

On Wed, Dec 20, 2017 at 6:28 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Depends. If you're interested in local folding and there are SS motifs in
> the region you're interested, then yes. If not, no. In terms of overall
> folding of the entire protein, yes it surely can be an important analysis.
>
> J
>
> On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta <nehaphysic...@gmail.com>
> wrote:
>
> > Thank you Joao and Aman.
> >
> > I have noted the points you have suggested.
> >
> > Do you think analyzing DSSP would help?
> >
> > Thanks,
> > Neha
> >
> > On Wed, Dec 20, 2017 at 4:03 PM, João Henriques <
> > joao.m.a.henriq...@gmail.com> wrote:
> >
> > > "You can use various supporting tools from R language to debug your
> > > trajectory but most third party software support NAMD and charmm
> format.
> > > You can use VMD to convert the trajectory to dcd and use R language
> based
> > > packages to read your trajectory"
> > >
> > > What? How is this useful or helpful? At most it confuses the OP even
> > more.
> > >
> > > Also, the clustering analysis is unlikely to be what you want or need
> at
> > > this stage. Why overcomplicate? One of the simplest ways to check that
> > > there are conformational changes on a given set of atoms is by doing a
> > RMSD
> > > analysis using the folded structure as the reference. The RMSD is
> > somewhat
> > > degenerate, but should suffice for this purpose. You can use an index
> > file
> > > to restrict the RMSD analysis to a particular subset of your system
> (the
> > > docking site, for example).
> > >
> > > You could look at the radius of gyration as well, Rg, as Aman Deep also
> > > suggests. This can either be calculated on a subset of atoms or on the
> > > entire protein. The latter could potentially be used to compare with
> the
> > > experimental reference obtained by SAXS, for example. Or you could
> > > calculate the SAXS curve and get a better understanding of size and
> shape
> > > differences between your protein and the reference, but that's more
> > > advanced stuff.
> > >
> > > J
> > >
> > > On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH <drrahulsur...@gmail.com
> >
> > > wrote:
> > >
> > > > Also you must know, a lot analysis are available over the entire
> manual
> > > of
> > > > Gromacs where all cannot be performed. Gromacs always provide you all
> > > > necessary analysis but to choose which one is always your choice that
> > > suits
> > > > your simulation purpose.
> > > >
> > > >
> > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta <nehaphysic...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > >
> > > > > Thank you for your prompt reply.
> > > > >
> > > > > By clustering analysis, are you talking about gmx cluster command?
> > > > >
> > > > > "over particular PC sub space"
> > > > >
> > > > > Could you please elaborate a bit?
> > > > >
> > > > > Thanks a lot once again.
> > > > >
> > > > > Thanks,
> > > > > Neha
> > > > >
> > > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH <
> > drrahulsur...@gmail.com
> > > >
> > > > > wrote:
> > > > >
> > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta <
> > nehaphysic...@gmail.com
> > > >
> > > > > > wrote:
> > > > > >
> > > > > > > Hi gromacs users,
> > > > > > >
> > > > > > > After MD simulation of protein-ligand complex for 5ns, can we
> > view
> > > > > > protein
> > > > > > > folding?
> > > > > > >
> > > > > > > How to do it?
> > > > > > >
> > > > > > > I want to ascertain if there is any conformation change in
> > protein
> > > > > where
> > > > > > > the ligand binds. Is it possible?
> > > > > > >
> > 

Re: [gmx-users] PROTEIN FOLDING

[Neha Gupta]

Thank you Joao and Aman.

I have noted the points you have suggested.

Do you think analyzing DSSP would help?

Thanks,
Neha

On Wed, Dec 20, 2017 at 4:03 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> "You can use various supporting tools from R language to debug your
> trajectory but most third party software support NAMD and charmm format.
> You can use VMD to convert the trajectory to dcd and use R language based
> packages to read your trajectory"
>
> What? How is this useful or helpful? At most it confuses the OP even more.
>
> Also, the clustering analysis is unlikely to be what you want or need at
> this stage. Why overcomplicate? One of the simplest ways to check that
> there are conformational changes on a given set of atoms is by doing a RMSD
> analysis using the folded structure as the reference. The RMSD is somewhat
> degenerate, but should suffice for this purpose. You can use an index file
> to restrict the RMSD analysis to a particular subset of your system (the
> docking site, for example).
>
> You could look at the radius of gyration as well, Rg, as Aman Deep also
> suggests. This can either be calculated on a subset of atoms or on the
> entire protein. The latter could potentially be used to compare with the
> experimental reference obtained by SAXS, for example. Or you could
> calculate the SAXS curve and get a better understanding of size and shape
> differences between your protein and the reference, but that's more
> advanced stuff.
>
> J
>
> On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH <drrahulsur...@gmail.com>
> wrote:
>
> > Also you must know, a lot analysis are available over the entire manual
> of
> > Gromacs where all cannot be performed. Gromacs always provide you all
> > necessary analysis but to choose which one is always your choice that
> suits
> > your simulation purpose.
> >
> >
> > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta <nehaphysic...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > >
> > > Thank you for your prompt reply.
> > >
> > > By clustering analysis, are you talking about gmx cluster command?
> > >
> > > "over particular PC sub space"
> > >
> > > Could you please elaborate a bit?
> > >
> > > Thanks a lot once again.
> > >
> > > Thanks,
> > > Neha
> > >
> > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH <drrahulsur...@gmail.com
> >
> > > wrote:
> > >
> > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta <nehaphysic...@gmail.com
> >
> > > > wrote:
> > > >
> > > > > Hi gromacs users,
> > > > >
> > > > > After MD simulation of protein-ligand complex for 5ns, can we view
> > > > protein
> > > > > folding?
> > > > >
> > > > > How to do it?
> > > > >
> > > > > I want to ascertain if there is any conformation change in protein
> > > where
> > > > > the ligand binds. Is it possible?
> > > > >
> > > > > We observe hydrogen bonds through molecular docking. Hence, I want
> to
> > > > make
> > > > > observation through MD simulation which is not obtained through
> > > docking.
> > > >
> > > >
> > > > You can perform Clustering analysis over particular PC sub space to
> > > measure
> > > > the structural changes.
> > > >
> > > > >
> > > > >
> > > > > Can someone help me regarding this?
> > > > >
> > > > > Thank you very much in advance.
> > > > >
> > > > > Thanks,
> > > > > Neha
> > > > > --
> > > > > 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*
> > > > *Coimbat

Re: [gmx-users] PROTEIN FOLDING

[Neha Gupta]

Ok..Thank you..

I'll extend my simulation upto 50 ns.

Thanks,
Neha

On Tue, Dec 19, 2017 at 12:44 PM, Nikhil Maroli  wrote:

> After MD simulation of protein-ligand complex for 5ns, can we view protein
> folding?
>
> mostly, NO
>
> Search what time range 'protein folding' is happening.
>
> How to do it?
>
> I want to ascertain if there is any conformation change in protein where
> the ligand binds. Is it possible?
>
>
> You might want to do PCA, RMSD and DSSP
>
> We observe hydrogen bonds through molecular docking. Hence, I want to make
> observation through MD simulation which is not obtained through docking.
>
>
> gmx hbond
>
> Can someone help me regarding this?
>
>
> i really wondering what is possible in 5 ns simulation time, you may
> try to extend it up to 100 ns or atleast a 50 ns.
>
> Thank you very much in advance.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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>
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Re: [gmx-users] PROTEIN FOLDING

[Neha Gupta]

Hi,


Thank you for your prompt reply.

By clustering analysis, are you talking about gmx cluster command?

"over particular PC sub space"

Could you please elaborate a bit?

Thanks a lot once again.

Thanks,
Neha

On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH <drrahulsur...@gmail.com>
wrote:

> On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta <nehaphysic...@gmail.com>
> wrote:
>
> > Hi gromacs users,
> >
> > After MD simulation of protein-ligand complex for 5ns, can we view
> protein
> > folding?
> >
> > How to do it?
> >
> > I want to ascertain if there is any conformation change in protein where
> > the ligand binds. Is it possible?
> >
> > We observe hydrogen bonds through molecular docking. Hence, I want to
> make
> > observation through MD simulation which is not obtained through docking.
>
>
> You can perform Clustering analysis over particular PC sub space to measure
> the structural changes.
>
> >
> >
> > Can someone help me regarding this?
> >
> > Thank you very much in advance.
> >
> > Thanks,
> > Neha
> > --
> > 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/
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[gmx-users] PROTEIN FOLDING

[Neha Gupta]

Hi gromacs users,

After MD simulation of protein-ligand complex for 5ns, can we view protein
folding?

How to do it?

I want to ascertain if there is any conformation change in protein where
the ligand binds. Is it possible?

We observe hydrogen bonds through molecular docking. Hence, I want to make
observation through MD simulation which is not obtained through docking.

Can someone help me regarding this?

Thank you very much in advance.

Thanks,
Neha
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[gmx-users] RADIAL DISTRIBUTION FUNTION

[Neha Gupta]

Hi gromacs users,

Through my RDF graph, I want to ascertain that my molecule of interest is a
solid. How to observe that?

I get r (nm) in X-aix and g(r) in Y-axis.

But, in some graphs, I observe r/sigma along X-axis.

Which is correct?

Thanks,
Neha
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[gmx-users] libgomp: Thread creation failed: Cannot allocate memory

[Neha Gupta]

Hi,

When I give this command

gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm min


I get this error
libgomp: Thread creation failed: Cannot allocate memory


What is the reason?

Thanks,
Neha
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Re: [gmx-users] gromacs error

[Neha Gupta]

Hi Vytautas,

Thank you for your response..

I did as you told and got this message at the command prompt

libfftw3f: /usr/local/lib/libfftw3f.la /usr/local/lib/libfftw3f.a

But the error tells me :

gmx: error while loading shared libraries: libfftw3f.so.3: cannot open
shared object file: No such file or directory

Even when I go to that location, namely, /usr/local/lib. I do not find "
libfftw3f.so.3."

What is the next step?

Thanks,
Neha

On Mon, Aug 28, 2017 at 12:33 PM, Vytautas Rakeviius <vytautas1...@yahoo.com
> wrote:

>
> Make sure you have libfftw3f installed properly. In such case
> command:whereis libfftw3fshould give you location of that file which gmx is
> unable to find.
> On Saturday, August 26, 2017, 1:13:38 PM GMT+3, Neha Gupta <
> nehaphysic...@gmail.com> wrote:
>
> Hi gromacs users,
>
> How to fix this error?
>
> gmx: error while loading shared libraries: libfftw3f.so.3: cannot open
> shared object file: No such file or directory
>
> PATH=$PATH:"/usr/local/gromacs/bin/"
>
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/usr/local/gromacs/share/gromacs/top"
>
>
>
> Thanks,
> Neha
> --
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Re: [gmx-users] ERROR IN EXECUTION ---GMX

[Neha Gupta]

Hi,

I gave these commands initially

PATH=$PATH:"/usr/local/gromacs/bin/"  (this mentions path to gmx)

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/usr/local/gromacs/share/gromacs/top"

For that, I got the response,

gmx: error while loading shared libraries: libfftw3f.so.3: cannot open
shared object file: No such file or directory

I went through "lib" folder (had mentioned its contents above)  and lib64
which contains libgromacs.so.0.0.0


Thanks,
Neha
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Re: [gmx-users] ERROR IN EXECUTION ---GMX

[Neha Gupta]

Hi,

Thank you very much for the reply.

I went to the lib files..

They contain

libmd.la
libmd.a
libgmxpreprocess.la
libgmxpreprocess.a
libgmxana.la
libgmxana.a
libgmx.la
libgmx.a

Nowhere, libfftw3f.so.3 was found.

Hence, I am confused.


Can someone please help me?

Thanks,
Neha

On Mon, Aug 28, 2017 at 10:47 AM, Nikhil Maroli  wrote:

> Hi,
>
> You need to provide path for the lib files
> Open the folders and find the locations for these files and add it to
> .bashrc.
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[gmx-users] gromacs error

[Neha Gupta]

Hi gromacs users,

How to fix this error?

gmx: error while loading shared libraries: libfftw3f.so.3: cannot open
shared object file: No such file or directory

PATH=$PATH:"/usr/local/gromacs/bin/"

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/usr/local/gromacs/share/gromacs/top"



Thanks,
Neha
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[gmx-users] PBC ISSUES IN GROMACS

[Neha Gupta]

Hi gromacs users,

After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc

However, in the movie file, I witnessed bizarre long bonds...

How to fix it?

Any suggestions please?


Thanks,
Neha
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[gmx-users] QSUB commands

[Neha Gupta]

Hi gromacs users,

I use cygwin terminal in windows 7, 64 bit computer.

How to use qsub commands and thereby do gromacs simulations in a cluster?



Can anyone tell me clearly?

Thanks,
Neha
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[gmx-users] dssp installation using cygwin

[Neha Gupta]

Hi gromacs users,

 I am using gromacs in windows  through cygwin

How to install dssp through cygwin?

Can anyone help?

Thanks,
Neha
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[gmx-users] FLUCTUATION IN DISTANCE

[Neha Gupta]

Hi gromacs users,

How to examine the fluctuation in distance in protein ligand binding,
between protein residue and the ligand?

What is the exact command ?

Thanks,
Neha
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Re: [gmx-users] POTENTIAL ENERGY SURFACE SCAN

[Neha Gupta]

Thank you for the reply.

I am given to understand that, we are supposed to run em.mdp and md.mdp
file for the organic molecule of interest.

After that, we are supposed to run

mdrun -s md.tpr -rerun configuration.pdb

What are the factors should we take care of while running md.mdp?

How do we mention the dihedral angle of our interest?

Could you please elucidate?


Thanks,
Neha







On Fri, Jun 16, 2017 at 2:39 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Generate your configurations with some other tool, put them in a trajectory
> file, and use
> http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
>
> Mark
>
> On Fri, 16 Jun 2017 11:13 Neha Gupta <nehaphysic...@gmail.com> wrote:
>
> > Hi gromacs users,
> >
> > How to do potential energy surface scan for organic molecule using
> Gromacs?
> >
> > What are the steps?
> >
> > Thanks,
> > Neha
> > --
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[gmx-users] POTENTIAL ENERGY SURFACE SCAN

[Neha Gupta]

Hi gromacs users,

How to do potential energy surface scan for organic molecule using Gromacs?

What are the steps?

Thanks,
Neha
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[gmx-users] DIHEDRAL SCAN

[Neha Gupta]

Hi,

How to run potential energy surface scan for a molecule using gromacs?.

What are the steps?

Thanks,
Neha
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[gmx-users] RDF OF PROTEIN - LIGAND

[Neha Gupta]

Hi,

After simulations, can we plot the rdf of protein and ligand interaction?
How to refine the analysis?

Can anyone suggest suitable books / papers to interpret protein ligand
radial distribution funtion?

Thanks,
Neha
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[gmx-users] GROMACS INPUT FILE

[Neha Gupta]

Hi gromacs users,

I want to calculate RDF for my molecule using OPLS parameters.

I used topolbuild and got the required output file.

How to develop the files further to use as input file for gromacs?


Thanks,
Neha
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[gmx-users] Dihedral angles Vs time (in ps)

[Neha Gupta]

Hi gromacs users,

After protein ligand simulation for 1 ns, I want to study the orientation
of the ligand molecule.

I want to plot time in ps (x-axis) and dihedral angle (of ligand) in
(y-axis) and view the corresponding structure of the ligand too.

How to do this?

Thanks,
Neha
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[gmx-users] BOND DISSOCIATION ENERGY STUDY USING GROMACS

[Neha Gupta]

Hi gromacs users,

I want to calculate bond dissociation energy of a particular bond in my
organic compound.

How to proceed further?

Can anyone let me know?

Thanks,
Neha
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[gmx-users] PROTEIN FOLDING

[Neha Gupta]

Hi gromacs users,


I have run 2ns simulation of protein ligand complex using NVT ensemble
(after equilibration).


I want to know whether there is a structural/conformational change in the
protein especially in the active site where, the ligand forms hydrogen
bonds with the protein during simulation.


Can we visualize it? Is it possible?

Please let me know.


Thanks,
Neha
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Re: [gmx-users] Hydrogen bond occupancy

[Neha Gupta]

Hi,

Thank you for the reply.

However, I don't get the same bonds as obtained through docking.  Those
hydrogen bonds have vanished, I presume during the simulation duration of
2ns.

The bonding takes place with different protein residues. One donor -
acceptor has higher percentage (29%)  and the other has very less
percentage (0.05%)

Can someone tell me what does it mean?

Thanks,
Neha





On Wed, Apr 5, 2017 at 1:34 PM, Erik Marklund <erik.markl...@kemi.uu.se>
wrote:

> Dear Neha,
>
> What fraction of the time the ligand hydrogen bonds to whatever it
> interacts with.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>
>
> On 5 Apr 2017, at 10:00, Neha Gupta <nehaphysic...@gmail.com nehaphysic...@gmail.com>> wrote:
>
> Hi gromacs users,
>
> What is meant by Hydrogen bond occupancy in protein ligand simulations?
>
> What information do we extract from % of hydrogen bond occupancy?
>
> Thanks,
> Neha
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[gmx-users] Hydrogen bond occupancy

[Neha Gupta]

Hi gromacs users,

What is meant by Hydrogen bond occupancy in protein ligand simulations?

What information do we extract from % of hydrogen bond occupancy?

Thanks,
Neha
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[gmx-users] gmx mdrun

[Neha Gupta]

Hi gromacs users,


I am using Gromacs 5.1.1 in windows cygwin.

When I run long calculations my CPU switches off automatically (just before
writing the coordinate file .gro) . How to prevent this and ensure
longevity of CPU?

Running on 1 node with total 8 logical cores
Hardware detected:
  CPU info:
Vendor: AuthenticAMD
Brand:  AMD FX-8370E Eight-Core Processor
Family: 21  model:  2  stepping:  0



I also observed these in log file


SIMD instructions most likely to fit this hardware: AVX_128_FMA
 SIMD instructions selected at GROMACS compile time: SSE4.1


Binary not matching hardware - you might be losing performance.
SIMD instructions most likely to fit this hardware: AVX_128_FMA
SIMD instructions selected at GROMACS compile time: SSE4.1


The current CPU can measure timings more accurately than the code in gmx
was configured to use. This might affect your simulation speed as accurate
timings are needed for load-balancing.
Please consider rebuilding gmx with the GMX_USE_RDTSCP=ON CMake option.



Thanks,
Neha
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Re: [gmx-users] HYDROGEN BOND EXISTENCE MAP

[Neha Gupta]

Thanks.

On Sat, Apr 1, 2017 at 12:59 PM, Sheeja Vasudevan 
wrote:

>
> Hi Neha,
>
> If I understand correctly pdb file is used for extracting information
> about the topology of the molecule..in this case the atom name and type.
> so it does not matter at which time point of time in your simulation your
> pdb file is generated as long as it is whole molecule.
>
> Best
> Sheeja.
>
> > Hi gromacs users,
> >
> > In the perl script to calculate hydrogen bond %, the command is
> >
> > perl plot_hbmap.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx
> >
> >
> > What should the structure.pdb file contain?
> >
> > How to obtain it?
> >
> > At which point of simulations?
> >
> > Thanks,
> > Neha
> > --
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>
>
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[gmx-users] HYDROGEN BOND EXISTENCE MAP

[Neha Gupta]

Hi gromacs users,

In the perl script to calculate hydrogen bond %, the command is

perl plot_hbmap.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx


What should the structure.pdb file contain?

How to obtain it?

At which point of simulations?

Thanks,
Neha
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[gmx-users] equilibration and production run

[Neha Gupta]

Hi gromacs users,

I intend to do the following steps for protein ligand simulations (for
linear interaction energy)

(1) Energy minimization
(2) NVT equilibration (with restraints on protein  and ligand)
(3) NPT equilibration (with restraints on protein  and ligand)
(4) NPT production

During NVT and NPT equilibration run can we use brendsen method in pcoupl
and Parrinello -Rahman in production run?

Will it yield correct results?

Or should we use the same kind of pcoupl through equilibration and
production?


Thanks,
Neha
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Re: [gmx-users] MMPBSA analysis on GROMACS trajectory

[Neha Gupta]

Thank you for the reply.

I am using cygwin64 for my computations.

Had already tried the above mentioned link.

It is not working in CYGWIN64.

Thanks,
Neha



On Mon, Mar 27, 2017 at 1:07 PM, masoud keramati <keramati.ma3...@gmail.com>
wrote:

> Hi
> They have a web site and all of things you need is there:
> http://rashmikumari.github.io/g_mmpbsa/
>
> On Mar 27, 2017 10:15 AM, "Neha Gupta" <nehaphysic...@gmail.com> wrote:
>
> > Hi gromacs users,
> >
> > How to calculate MMPBSA analysis on Gromacs trajectory using MMPBSA tool
> of
> > amber software package?
> >
> >
> > Thanks,
> > Neha
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[gmx-users] QUERY IN GRO FILE

[Neha Gupta]

Hi gromacs users,


I have a doubt in this command,

grompp -f em.mdp -c conf.gro -p topol.top -o em


mdrun -v -deffnm em


These commands generate em.gro, em.tpr, em.trr, em.log file.


There is another command which is


mdrun -s em.tpr

which generates confout.gro

Does em.gro and confout.gro are one and the same?

What are the technical differences?


Thanks,

Neha
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[gmx-users] MMPBSA analysis on GROMACS trajectory

[Neha Gupta]

Hi gromacs users,

How to calculate MMPBSA analysis on Gromacs trajectory using MMPBSA tool of
amber software package?


Thanks,
Neha
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Re: [gmx-users] COMMAND IN HBOND

[Neha Gupta]

Thank you for the response.

Can you please send the url link for the location of the script (to
calculate the percentage of hydrogen bond)?

Thanks,
Neha

On Sat, Mar 25, 2017 at 1:36 PM, Tasneem Kausar 
wrote:

> If you want to calculate hydrogen bond invloving residue there are two
> steps
> From gmx hbond you can obtain an xpm file where hydrogen bond existance mad
> is plotted.  Then calculate the percentage of hydrogen bond involving
> residues from script given by justin.
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Re: [gmx-users] COMMAND IN HBOND

[Neha Gupta]

Hi,


Thank you for the reply.

Actually, we get the number of hydrogen bonds in .xvg file using

gmx hbond -s prd.tpr -f prd.xtc -n index.ndx -num hbnum.xvg
.

Can we generate an output file similar to that, which prints the bonding
residues of protein and ligand?


Thanks,
Neha



On Fri, Mar 24, 2017 at 8:05 PM, Erik Marklund <erik.markl...@kemi.uu.se>
wrote:

> Dear Neha,
>
> Gromacs doesn’t offer that much in terms of viewing. This sounds more like
> a PyMol/VMD/Other question.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>
>
> On 24 Mar 2017, at 14:33, Neha Gupta <nehaphysic...@gmail.com nehaphysic...@gmail.com>> wrote:
>
> Hi gromacs users,
>
> What is the command to view the residues of protein and atoms of ligand
> involved in hydrogen bond?
>
> Thanks,
> Neha
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[gmx-users] COMMAND IN HBOND

[Neha Gupta]

Hi gromacs users,

What is the command to view the residues of protein and atoms of ligand
involved in hydrogen bond?

Thanks,
Neha
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[gmx-users] HOW TO INSTALL G_MMPBSA IN WINDOWS 7, 64 BIT

[Neha Gupta]

Hi gromacs users,

Has anyone installed G_MMPBSA in windows 7, 64 bit computer?

If so, can anyone let me know the steps of installation in Windows?

Thanks,
Neha
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[gmx-users] COEFFICIENT FOR LINEAR INTERACTION ENERGY IN PROTEIN LIGAND COMPLEX

[Neha Gupta]

Hi gromacs users,

How to derive Linear Interaction Energy Coefficients for protein ligand
complex?

Since the parameters vary for different force fields, how to approach this
problem?

Can anyone suggest relevant papers?

Thanks
Neha
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