[gmx-users] (no subject)

[MOHD HOMAIDUR RAHMAN]

Dear All Gromacs users

I am try to calculate total no of hydrogen bond present in a system. For
that I am using gromacs 5.0.2 (gmx hbond ). The problem is that I am unable
to specify donor and acceptor during input. I am using Amber coordinate and
topology file that is converted to gromacs topology and coordinate through
acpype.py. Now how to specify no of donor and acceptor for water molecules.

Total 350 water molecules is there in my system . So there should be two H
bond donor and two H bond acceptor, but during calculation it is showing
350 donor and 350 acceptor.

Thanks

[rajan kumar choudhary]

​hello every one,

Actually i want to calculate ​Displacements of the components of the
proteinn residue wise for the first eigenvector in gromacs. is thre is any
option already present in gromacs for such calculation.



thanks in advance--
*Rajan kumar choudhary*
*Senior Research Fellow*
*Department of Atomic Energy(Govt.Of India)*
*ACTREC TATA Memorial Center *
*Kharghar Navi-Mumbai*
*Mumbai-410210*
*India*

[masoud aliyar]

Hello dear friends

I want to simulate a Ligand-Protein complex in GROMACS by using amber
forcefield
<https://www.google.com/search?q=forcefield&newwindow=1&sa=X&biw=1366&bih=657&tbm=isch&tbo=u&source=univ&ei=WEaQVYH_AoWdsgH06q6ICg&ved=0CE4QsAQ>
and need essential MDP files. Can anyone provide me that files?

[Vidyalakshmi CM]

Hi,

You may use the mdp files from the tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
(It has topologies for energy minimzation, nvt and npt simulations and md
simulations run).

Regards,
C.M.Vidyalakshmi

Post by masoud aliyar
Hello dear friends
I want to simulate a Ligand-Protein complex in GROMACS by using amber
forcefield
<
https://www.google.com/search?q=forcefield&newwindow=1&sa=X&biw=1366&bih=657&tbm=isch&tbo=u&source=univ&ei=WEaQVYH_AoWdsgH06q6ICg&ved=0CE4QsAQ
and need essential MDP files. Can anyone provide me that files?
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[Vidyalakshmi CM]

*not topologies - mdp files

Post by Vidyalakshmi CM
Hi,
You may use the mdp files from the tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
(It has topologies for energy minimzation, nvt and npt simulations and md
simulations run).
Regards,
C.M.Vidyalakshmi

Post by masoud aliyar
Hello dear friends
I want to simulate a Ligand-Protein complex in GROMACS by using amber
forcefield
<
https://www.google.com/search?q=forcefield&newwindow=1&sa=X&biw=1366&bih=657&tbm=isch&tbo=u&source=univ&ei=WEaQVYH_AoWdsgH06q6ICg&ved=0CE4QsAQ
and need essential MDP files. Can anyone provide me that files?
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[Justin Lemkul]

Post by Vidyalakshmi CM
Hi,
You may use the mdp files from the tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
(It has topologies for energy minimzation, nvt and npt simulations and md
simulations run).

The tutorial .mdp settings are for OPLS-AA and may not be generally applicable
to any other force field. This is a non-trivial consideration in running
simulations properly.

"AMBER force field" is a bit generic; different parameter sets use subtly
different parameters. The primary literature for the parameter set of interest
will contain the proper run settings. Use whatever those settings are.

-Justin
--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

***@outerbanks.umaryland.edu | [phone]
http://mackerell.umaryland.edu/~jalemkul

==================================================

[Hassan Aaryapour]

Dear Justin,
Where can I find the primary literature for setting up proper parameters in
mdp files? I downloaded all literatures in "General Information" section in
link below (http://ffamber.cnsm.csulb.edu/ffamber.php), but I did not find
anything related to the Cutoffs.

Regards
Hassan

Post by Justin Lemkul

Post by Vidyalakshmi CM
Hi,
You may use the mdp files from the tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
(It has topologies for energy minimzation, nvt and npt simulations and md
simulations run).

The tutorial .mdp settings are for OPLS-AA and may not be generally
applicable to any other force field. This is a non-trivial consideration
in running simulations properly.
"AMBER force field" is a bit generic; different parameter sets use subtly
different parameters. The primary literature for the parameter set of
interest will contain the proper run settings. Use whatever those settings
are.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
http://mackerell.umaryland.edu/~jalemkul
==================================================
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[RINU KHATTRI]

Hello gromacs users
i am working on membrane protein with complex i want to calculate the
distance of a particular amino acid to ligand in all simulation time
period if g_dist is the answer i didn't get the desired output .
kindly help

[Justin Lemkul]

Post by RINU KHATTRI
Hello gromacs users
i am working on membrane protein with complex i want to calculate the
distance of a particular amino acid to ligand in all simulation time
period if g_dist is the answer i didn't get the desired output .
kindly help

There's nothing anyone can do to help a complaint of "didn't get the desired
output." What was your command? What was your output? Why don't you think
that's right? g_dist measures distances; it is what you need to use, provided
you use it correctly.

-Justin
--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

***@outerbanks.umaryland.edu | [phone]
http://mackerell.umaryland.edu/~jalemkul

==================================================

[Sana Saeed]

hican we use multiple files as input in pdb2gmx. i want to merge two different proteins into one coordinate file ad also its topology in one file, for that i am using -merge, but it gives error in reading second pdb file.

[Mayank Dixit]

How to select isovalue in spatial density distribution for solvation shell
and bulk around the solute?
--
*Mayank Kumar Dixit *
Senior Research Fellow
Molecular Dynamics lab
Department of Chemistry
IIT Bombay
Powai, Mumbai.
Mob No 9820697156

[hari ram]

Hi Users,

I have a .pdb file, in this file when I want to use pdb2gmx command there is this error massage:Fatal error:
Incomplete ring in HIS771

this aminoacid is not complete in general, I don't know how can I
complete this such that I don't add HIS for complete? Please give me a
hint.


Thank you

Hari

[hari ram]

Hi Users,

I have a .pdb file, in this file when I want to use pdb2gmx command there is this error massage:Fatal error:
Incomplete ring in HIS771

this aminoacid is not complete in general, I don't know how can I
complete this such that I don't add HIS for complete? Please give me a
hint.


Thank you

Hari

[Justin Lemkul]

Post by hari ram
Hi Users,
Incomplete ring in HIS771
this aminoacid is not complete in general, I don't know how can I
complete this such that I don't add HIS for complete? Please give me a
hint.

http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources

-Justin
--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

***@outerbanks.umaryland.edu | [phone]
http://mackerell.umaryland.edu/~jalemkul

==================================================

[Sotirios Dionysios I. Papadatos]

This is most probably due to some missing atoms. If you are not trying to include "exotic" atoms, meaning that you have to add them to aminoacids.rtp etc then you need a program like "Schrodinger/maestro" to manually add the atoms missing, export it to .pdb and try again.
Hope that helps

________________________________________
From: gromacs.org_gmx-users-***@maillist.sys.kth.se <gromacs.org_gmx-users-***@maillist.sys.kth.se> on behalf of hari ram <***@outlook.com>
Sent: Monday, July 27, 2015 2:04 PM
To: gromacs.org_gmx-***@maillist.sys.kth.se
Subject: [gmx-users] (no subject)

Hi Users,

I have a .pdb file, in this file when I want to use pdb2gmx command there is this error massage:Fatal error:
Incomplete ring in HIS771

this aminoacid is not complete in general, I don't know how can I
complete this such that I don't add HIS for complete? Please give me a
hint.


Thank you

Hari

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