[gmx-users] Re: gmx-users Digest, Vol 84, Issue 213

Wed Apr 27 14:08:24 CEST 2011

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

On Wed, Apr 27, 2011 at 2:30 PM, <gmx-users-request at gromacs.org> wrote:

> Send gmx-users mailing list submissions to
>        gmx-users at gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>        gmx-users-request at gromacs.org
>
> You can reach the person managing the list at
>        gmx-users-owner at gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>   1. Re: MG-ATP (Mark Abraham)
>   2. Re: Docking (Mark Abraham)
>   3. Re: POL3 water model (Ivan Gladich)
>   4. Re: Docking (mohsen ramezanpour)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 27 Apr 2011 19:09:59 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] MG-ATP
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DB7DD67.2050500 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 4/27/2011 6:52 PM, Sajad Ahrari wrote:
> > dear users
> > is "MG-ATP" known to gromacs ? in my pdb structure I have ADP and MG,
> > apart from each other and not being crystallized in the right place.
> > can i omit them and replace ADP's with MG-ATP? or I should introduce
> > this topology to gromacs?
>
> You'll have to do your own literature searching about previous
> treatments of ADP and ATP, I'm afraid :-) Pretty much anything that has
> been done can be made to work in GROMACS, however.
>
> See also http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> Mark
>
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110427/5a9bd821/attachment-0001.html
>
> ------------------------------
>
> Message: 2
> Date: Wed, 27 Apr 2011 19:18:08 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Docking
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DB7DF50.40403 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 27 Apr 2011 12:14:42 +0200
> From: Ivan Gladich <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>
> Message-ID: <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
> web page:http://www.molecular.cz/~gladich/
> -----
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110427/b4eaeb53/attachment-0001.html
>
> ------------------------------
>
> Message: 4
> Date: Wed, 27 Apr 2011 14:22:20 +0430
> From: mohsen ramezanpour <ramezanpour.mohsen at gmail.com>
> Subject: Re: [gmx-users] Docking
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <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
> >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
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the www
> interface
> > or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110427/5dd8508f/attachment-0001.html
>
> ------------------------------
>
> --
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>
> End of gmx-users Digest, Vol 84, Issue 213
> ******************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110427/24bd5c0a/attachment.html>