[gmx-users] polarizable water models
Ivan Gladich
ivan.gladich at marge.uochb.cas.cz
Wed Apr 27 15:43:27 CEST 2011
Dear Saly
I attached for you the SW itp file: inside there is the
reference to the original paper.
You can find the SWM4 topology at the
http://oldwww.gromacs.org/pipermail/gmx-users/2006-August/023476.html
For SWM4-NDP I attach for you the topology that I created from the
reference paper.
Please check the parameter values with the ones reported in the original
paper...I am only a man and I usually make a lot of mistakes.
Concerning the force field I would like to advice you. You did not tell
me what you want to do with your water...
If you have to solvate something in water you have to be careful.
Common force field (oplsa, gaff etc.) are not parametrize for these kind
of water models that are quite recent.
For example, I know that there is some recent ion parametrization in
SWM4-NDP water ( J.Chem. Theory Comput. Lamoureux et. al., 2010)....
So I suggest you to check in literature how common force field behave
with these water models or to make some preliminary test...
All the best
Ivan
On 4/27/2011 10:08 PM, saly jackson wrote:
> Hi Ivan
>
Please do not reply to whole digests with non-descriptive subject lines.
It confuses the archives, and alienates people from finding out the
topic of your interest, and thus being bothered to give you free help.
Please leave only the relevant discussion, and use a useful subject line.
> In which force field can I find the polarizable water models you said
> in section "b" of your reply
Have you done your own literature searching first? Then you'd already
know what force fields they might have been used with...
Mark
On 04/27/2011 02:08 PM, saly jackson wrote:
> Hi Ivan
>
> In which force field can I find the polarizable water models you said
> in section "b" of your reply
>
> Thanks alot
>
> Regards
>
> Saly
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 27 Apr 2011 12:14:42 +0200
> From: Ivan Gladich <ivan.gladich at marge.uochb.cas.cz
> <mailto:ivan.gladich at marge.uochb.cas.cz>>
> Subject: Re: [gmx-users] POL3 water model
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4DB7EC92.7080107 at marge.uochb.cas.cz
> <mailto:4DB7EC92.7080107 at marge.uochb.cas.cz>>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Saly
> from my little experience, POL3 water model is a point
> polarizable
> water model.
> Point polarizable water models are not available in gromacs.
> Gromacs uses shell model, i.e. charge attached on a spring to
> mimic the
> stretching of the electronic cloud.
>
> So you have 3 solutions
> a) You can take the POL3 model, look the polarizability of oxygen and
> hydrogen atom and attach shells on oxygen and hydrogens atoms in
> order
> to reproduce the model for gromacs.
> b) In Gromacs there are other polarizable water models using shell
> (e.g.
> SWM4-DP, SWM4-NDP, SW ), you could try with one of this...in my
> opinion this is the best solution..;)
> c) If you really need POL3 model, try with other molecular package
> that
> have point polarizable POL3 water (e.g. AMBER)
>
> I hope this help
> Ivan
>
>
>
>
> On 04/27/2011 11:04 AM, saly jackson wrote:
> > Hi all
> >
> > I want to simulate using GROMACS.Before I used LAMMPS but it has not
> > polarizable water models. Therefore I want to use GROMACS.
> >
> > I need .itp and .mdp files of POL3 water model.
> >
> > Do you have the files.
> >
> > Would you please help me.
> >
> > Thanks alot for your time and attention
> >
> > Regards
> >
> > Saly
>
>
> --
> ------
> Ivan Gladich, Ph.D.
> Postdoctoral Fellow
> Academy of Sciences of the Czech Republic
> Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
> Flemingovo nám. 2.
> 166 10 Praha 6
> Czech Republic
>
> Tel: +420775504164
> e-mail: ivan.gladich at uochb.cas.cz <mailto:ivan.gladich at uochb.cas.cz>
> web page:http://www.molecular.cz/~gladich/
> <http://www.molecular.cz/%7Egladich/>
> -----
>
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> ------------------------------
>
> Message: 4
> Date: Wed, 27 Apr 2011 14:22:20 +0430
> From: mohsen ramezanpour <ramezanpour.mohsen at gmail.com
> <mailto:ramezanpour.mohsen at gmail.com>>
> Subject: Re: [gmx-users] Docking
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <BANLkTikK78dY35r97bniGoysWzVd4cuzbQ at mail.gmail.com
> <mailto:BANLkTikK78dY35r97bniGoysWzVd4cuzbQ at mail.gmail.com>>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Mark
> Thank you for your reply.yes,you are right.
>
> Regarding question 2:
> I have a pdf file from "Docking Server" for sertraline-SERT
> example.Suppose
> this is a good docked state.
>
> In the other hand,I did what I explained in section 1 for
> sertraline and
> SERT.(by pymol and ...)
> Now, I want to check if I have docked sertraline to SERT correctly
> or not(
> by comparing with Docking server's one)
> How can I do that?
>
>
> Do you have any suggestion for doing docking by gromacs? for
> example pulling
> code, MD , or SMD?
> Thanks in advance
>
>
> On Wed, Apr 27, 2011 at 1:48 PM, Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>>wrote:
>
> > On 4/27/2011 7:05 PM, mohsen ramezanpour wrote:
> >
> >> Dear Users
> >>
> >> I read so many emails to mailing list, there were important
> notes about
> >> docking but I couldn't extract a general result.
> >> Please let me know:
> >>
> >> 1-Can we dock a ligand to it's protein's binding pocket with
> Pymol and
> >> Gromacs as following?
> >>
> >> first:locating ligand outside and close to binding site
> manually in pymol
> >> and saving complex.pdb
> >> second:doing all steps for generating complex.top and
> complex.gro as
> >> Enzyme-Drug tutorial
> >> third:running md (with out any pull code and constraint),in the
> other
> >> words,full flexible system.
> >>
> >> I think drug can move freely and according to it's interaction with
> >> binding site can be attracted by binding site.
> >> reside for a distance time and then will come out of pocket.
> >>
> >> Am I right?
> >>
> >
> > In principle, yes, but it is wildly unlikely that you have a
> system that
> > can bind and unbind reliably in the 100ns simulation range that
> you might be
> > able to afford to run, and if you did happen to have one, what
> would you
> > have learned?
> >
> >
> > I know what discussed in mainling list about deffinition of
> "Docking".
> >>
> >>
> >> 2-I have some docked files by "Docking Server " for some of my
> >> drug-protein's complexes.
> >> now,I want to obtain them by doing MD in the above proccess.if
> I was
> >> successful then try to do that for other drugs which I don't
> have any docked
> >> pdb for them.
> >>
> >> How can I fit a trajectory with a typical pdb file?
> >>
> >
> > I don't understand what you are asking.
> >
> > Mark
> >
> >
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
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> End of gmx-users Digest, Vol 84, Issue 213
> ******************************************
>
>
--
------
Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic
Tel: +420775504164
e-mail: ivan.gladich at uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
-----
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