Re: [gmx-users] Re: Simulation with CsCl
Hello All , I am also trying to simulate my protein with Mn ion present in it. So can I create the topology entry for Mn ion similar to MG2+ ion ? and how can I get the values of C6 and C12 leonard jones potential in [atom type] entry and will it be required to add [nonbond_params] also ? how can I get them ? Also I want to use Fe2+ also, but it is also not included in gromos force field. This problem of adding other ions and molecule in the system always remains. And being new to this field, can someone suggest in simple terms how to include these considering the person is not an expert in this field. Please help. -- Sonali Dhindwal --- On Tue, 8/6/10, Vitaly Chaban vvcha...@gmail.com wrote: From: Vitaly Chaban vvcha...@gmail.com Subject: [gmx-users] Re: Simulation with CsCl To: gmx-users@gromacs.org Date: Tuesday, 8 June, 2010, 9:03 PM Hi all: I am trying to simulate a polysaccharide in solution of water and CsCl, but cesium is not parametrized in the gromacs 4. I am using the force field GROMOS 96. I have looked for the parameters of Cs+ in the OPLS Force field and I have created 4 files: Cs.atp, Cs.itp, Csnb.itp and Cs.rtp. Also I have include the parameters for Cs+ in the ions.itp file, but it didn't work, Can someone help me? Thanks in advance. Cecilia. Cecilia - You do not need so many files so cesium. Just copy your parameters to the force field used and create the topology entry for cesium similar to [ moleculetype ] Ar 1 [ atoms ] 1 Ar 1 Ar Ar 0 0.0 Do not forget, cesium+ is an ion... -- Dr. Vitaly Chaban -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Simulation with CsCl
sonali dhindwal wrote: Hello All , I am also trying to simulate my protein with Mn ion present in it. So can I create the topology entry for Mn ion similar to MG2+ ion ? and how can I get the values of C6 and C12 leonard jones potential in [atom type] entry and will it be required to add [nonbond_params] also ? how can I get them ? Also I want to use Fe2+ also, but it is also not included in gromos force field. This problem of adding other ions and molecule in the system always remains. And being new to this field, can someone suggest in simple terms how to include these considering the person is not an expert in this field. Please consult the link I posted yesterday... http://www.gromacs.org/Documentation/How-tos/Parameterization What you're trying to do is far from trivial. Understand that parameterization, especially for transition metals, is very challenging, and standard molecular mechanics treatment of such species suffers from many limitations, which may or may not influence your results. -Justin Please help. -- Sonali Dhindwal --- On *Tue, 8/6/10, Vitaly Chaban /vvcha...@gmail.com/* wrote: From: Vitaly Chaban vvcha...@gmail.com Subject: [gmx-users] Re: Simulation with CsCl To: gmx-users@gromacs.org Date: Tuesday, 8 June, 2010, 9:03 PM Hi all: I am trying to simulate a polysaccharide in solution of water and CsCl, but cesium is not parametrized in the gromacs 4. I am using the force field GROMOS 96. I have looked for the parameters of Cs+ in the OPLS Force field and I have created 4 files: Cs.atp, Cs.itp, Csnb.itp and Cs.rtp. Also I have include the parameters for Cs+ in the ions.itp file, but it didn't work, Can someone help me? Thanks in advance. Cecilia. Cecilia - You do not need so many files so cesium. Just copy your parameters to the force field used and create the topology entry for cesium similar to [ moleculetype ] Ar 1 [ atoms ] 1 Ar1Ar Ar0 0.0 Do not forget, cesium+ is an ion... -- Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org /mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org /mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Simulation with CsCl
Dear Sonali,
Unfortunately development of force-field parameters is difficult, and
even more so for bivalent ions and transition metals. This is certainly
not suitable as a project to begin with.
Having said that, a careful search in the literature will reveal that
many sets of parameters for metal ions do exist. Try to find a set that
works best with the water model that you're using or your particular
model, and carry out some simulations to validate that the results are
correct, reproducible and robust. The following references discuss some
aspects of simulations of ions and proteins:
@article{Project2006,
Author = {Project, E. and Friedman, R. and Nachliel, E. and Gutman, M.},
Title = {A Molecular Dynamics Study of the Effect of Ca{2+} Removal
on Calmodulin Structure},
Journal = {Biophys. J.},
Volume= {90},
Pages = {3842-3850},
Year = {2006}
}
@Article{Fyta2010,
author = Fyta, M and Kalcher, I and Dzubiella, J and Vrbka, L and Netz,
R R,
title = {Ionic force field optimization based on single-ion and ion-pair
solvation properties},
journal = J Chem Phys,
year = 2010,
volume = 132,
pages = 024911-024911
}
Ran.
sonali dhindwal wrote:
Hello All ,
I am also trying to simulate my protein with Mn ion present in it.
So can I create the topology entry for Mn ion similar to MG2+ ion ?
and how can I get the values of C6 and C12 leonard jones potential in
[atom type] entry and will it be required to add [nonbond_params] also
? how can I get them ?
Also I want to use Fe2+ also, but it is also not included in gromos
force field. This problem of adding other ions and molecule in the
system always remains. And being new to this field, can someone
suggest in simple terms how to include these considering the person is
not an expert in this field.
Please help.
--
Sonali Dhindwal
--- On *Tue, 8/6/10, Vitaly Chaban /vvcha...@gmail.com/* wrote:
From: Vitaly Chaban vvcha...@gmail.com
Subject: [gmx-users] Re: Simulation with CsCl
To: gmx-users@gromacs.org
Date: Tuesday, 8 June, 2010, 9:03 PM
Hi all:
I am trying to simulate a polysaccharide in solution of water
and CsCl, but
cesium is not parametrized in the gromacs 4. I am using the force
field GROMOS 96.
I have looked for the parameters of Cs+ in the OPLS Force field
and I have
created 4 files: Cs.atp, Cs.itp, Csnb.itp and Cs.rtp. Also I
have include
the parameters for Cs+ in the ions.itp file, but it didn't
work, Can
someone help me?
Thanks in advance.
Cecilia.
Cecilia -
You do not need so many files so cesium. Just copy your parameters to
the force field used and create the topology entry for cesium similar
to
[ moleculetype ]
Ar 1
[ atoms ]
1 Ar1Ar Ar0 0.0
Do not forget, cesium+ is an ion...
--
Dr. Vitaly Chaban
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--
--
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-639
Email: r.fried...@bioc.uzh.ch
Skype: ran.friedman
--
--
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[gmx-users] Re: Simulation with CsCl
Hi all: I am trying to simulate a polysaccharide in solution of water and CsCl, but cesium is not parametrized in the gromacs 4. I am using the force field GROMOS 96. I have looked for the parameters of Cs+ in the OPLS Force field and I have created 4 files: Cs.atp, Cs.itp, Csnb.itp and Cs.rtp. Also I have include the parameters for Cs+ in the ions.itp file, but it didn't work, Can someone help me? Thanks in advance. Cecilia. Cecilia - You do not need so many files so cesium. Just copy your parameters to the force field used and create the topology entry for cesium similar to [ moleculetype ] Ar 1 [ atoms ] 1 Ar1Ar Ar0 0.0 Do not forget, cesium+ is an ion... -- Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
