Re: [gmx-users] PROTEIN FOLDING

[Justin Lemkul]

On 12/30/17 11:44 PM, Neha Gupta wrote:

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?


No command is going to work if the contents of the .tpr and .xtc do not 
match. Either you've mixed up your files or you didn't save all 
coordinates during the run, in which case you need to make a matching 
.tpr file. gmx check may provide some clues, but at present it's hard to 
know what has gone wrong.


-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]

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
>
> ==
>
> --
> 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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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] PROTEIN FOLDING

[Justin Lemkul]

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

[Alexandr Nasedkin]

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

Please read this first:
http://manual.gromacs.org/documentation/2016.1/onlinehelp/gmx-trjconv.html

trjconv is quite powerful, so it worth to know available options.

-Alexandr


On 30/12/2017 16:37, Neha Gupta wrote:

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  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

==

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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  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
>
> * 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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Re: [gmx-users] PROTEIN FOLDING

[Justin Lemkul]

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

* 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.

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 
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 
> 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 
> > wrote:
> >
> > > Hi,
> > >
> > > migh be visualization error
> > >
> > > Apply pbc
> > >
> > > On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta 
> > > 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 you talking about gmx cluster
> > > > command?
> > > > > > > > >
> > > > > > > > > "over particular PC sub space"
> > > > > > > > >
> > > 

Re: [gmx-users] PROTEIN FOLDING

[Lakshman Ji Verma]

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  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 
> wrote:
>
> > Hi,
> >
> > migh be visualization error
> >
> > Apply pbc
> >
> > On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta 
> > 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  >
> > > > 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
> > > > > > 

Re: [gmx-users] PROTEIN FOLDING

[Justin Lemkul]

On 12/28/17 6:25 AM, Neha Gupta 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?


http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

-Justin


Thanks,
Neha

On Thu, Dec 28, 2017 at 11:30 AM, RAHUL SURESH 
wrote:


Hi,

migh be visualization error

Apply pbc

On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta 
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 
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?

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/
Support/Mailing_Lists/GMX-Users_List before posting!

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gmx-users

or

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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

before

posting!

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

Support/Mailing_Lists

* For 

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 
wrote:

> Hi,
>
> migh be visualization error
>
> Apply pbc
>
> On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta 
> 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 
> > > 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?
> > > > > > > > >
> > > > > > > > > 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 

Re: [gmx-users] PROTEIN FOLDING

[RAHUL SURESH]

Hi,

migh be visualization error

Apply pbc

On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta 
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 
> > 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?
> > > > > > > >
> > > > > > > > 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
> > > 

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 
> 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  >
> > > 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 
> > > > 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*

Re: [gmx-users] PROTEIN FOLDING

[João Henriques]

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  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 
> > 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 
> > > 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*
> > > > > *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 

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 
> 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 
> > 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  >
> > > wrote:
> > >
> > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta  >
> > > > 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/
> > > > 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.
> > >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > 

Re: [gmx-users] PROTEIN FOLDING

[João Henriques]

"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 
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 
> 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 
> > wrote:
> >
> > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta 
> > > 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/
> > > 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.
> >
> --
> *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.
>
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Re: [gmx-users] PROTEIN FOLDING

[Aman Deep]

You can try rmsd and gyrate plot to see the changes in your complex. It
On Dec 19, 2017 2:22 PM, "RAHUL SURESH"  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 
> 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 
> > wrote:
> >
> > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta 
> > > 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/
> > > 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.
> >
> --
> *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.
>
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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/
> 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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Re: [gmx-users] PROTEIN FOLDING

[RAHUL SURESH]

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  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 
> wrote:
>
> > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta 
> > 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/
> > 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.
>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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Re: [gmx-users] PROTEIN FOLDING

[RAHUL SURESH]

On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta  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?


Yea clustering analysis can interpret a lot datas about your complex
simulation.

Note:  I am not sure whether you Can perform gmx cluster over particular
sub space.

>
>
> Thanks a lot once again.
>
> Thanks,
> Neha
>
> On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH 
> wrote:
>
> > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta 
> > 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!
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> > >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
> > Gromacs Users mailing list
> >
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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 
wrote:

> On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta 
> 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!
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
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Re: [gmx-users] PROTEIN FOLDING

[RAHUL SURESH]

On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta  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!
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> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] PROTEIN FOLDING

[RAHUL SURESH]

On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta  wrote:

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


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

>
>
> 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] PROTEIN FOLDING

[Nikhil Maroli]

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.
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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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Re: [gmx-users] PROTEIN FOLDING

[Vytautas Rakeviius]

Yes, you can open all structural output files with VMD. Or Chimera (tools MD so 
on).
 

On Thursday, April 6, 2017 9:56 AM, Neha Gupta  
wrote:
 

 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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[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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[gmx-users] PROTEIN FOLDING IN GROMACS

[Subashini .K]

Hi gromacs users,


What are the steps for simulation to observe protein folding in gromacs?


Thanks,

Subashini.K

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