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Dear Saly<br>
I attached for you the SW itp file: inside there is the
reference to the original paper.<br>
You can find the SWM4 topology at the <br>
<br>
<a class="moz-txt-link-freetext" href="http://oldwww.gromacs.org/pipermail/gmx-users/2006-August/023476.html">http://oldwww.gromacs.org/pipermail/gmx-users/2006-August/023476.html</a><br>
<br>
For SWM4-NDP I attach for you the topology that I created from the
reference paper. <br>
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.<br>
<br>
Concerning the force field I would like to advice you. You did not
tell me what you want to do with your water...<br>
If you have to solvate something in water you have to be careful.<br>
Common force field (oplsa, gaff etc.) are not parametrize for these
kind of water models that are quite recent. <br>
For example, I know that there is some recent ion parametrization in
SWM4-NDP water ( J.Chem. Theory Comput. Lamoureux et. al., 2010)....<br>
So I suggest you to check in literature how common force field
behave with these water models or to make some preliminary test...<br>
<br>
All the best<br>
Ivan<br>
<br>
<br>
<br>
On 4/27/2011 10:08 PM, saly jackson wrote:
<br>
<blockquote type="cite" style="color: rgb(0, 0, 0);">Hi Ivan
<br>
<br>
</blockquote>
<br>
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.
<br>
<br>
<blockquote type="cite" style="color: rgb(0, 0, 0);">In which force
field can I find the polarizable water models you said in section
"b" of your reply
<br>
</blockquote>
<br>
Have you done your own literature searching first? Then you'd
already know what force fields they might have been used with...
<br>
<br>
Mark
<br>
<br>
<br>
On 04/27/2011 02:08 PM, saly jackson wrote:
<blockquote
cite="mid:BANLkTik=vhUDegGuwyfmoMWe0gRfBz4ugA@mail.gmail.com"
type="cite">Hi Ivan<br>
<br>
In which force field can I find the polarizable water models you
said in section "b" of your reply<br>
<br>
Thanks alot<br>
<br>
Regards<br>
<br>
Saly<br>
<br>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Wed, 27 Apr 2011 12:14:42 +0200<br>
From: Ivan Gladich <<a moz-do-not-send="true"
href="mailto:ivan.gladich@marge.uochb.cas.cz">ivan.gladich@marge.uochb.cas.cz</a>><br>
Subject: Re: [gmx-users] POL3 water model<br>
To: Discussion list for GROMACS users <<a
moz-do-not-send="true" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a moz-do-not-send="true"
href="mailto:4DB7EC92.7080107@marge.uochb.cas.cz">4DB7EC92.7080107@marge.uochb.cas.cz</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear Saly<br>
from my little experience, POL3 water model is a point
polarizable<br>
water model.<br>
Point polarizable water models are not available in gromacs.<br>
Gromacs uses shell model, i.e. charge attached on a spring to
mimic the<br>
stretching of the electronic cloud.<br>
<br>
So you have 3 solutions<br>
a) You can take the POL3 model, look the polarizability of
oxygen and<br>
hydrogen atom and attach shells on oxygen and hydrogens atoms
in order<br>
to reproduce the model for gromacs.<br>
b) In Gromacs there are other polarizable water models using
shell (e.g.<br>
SWM4-DP, SWM4-NDP, SW ), you could try with one of this...in
my<br>
opinion this is the best solution..;)<br>
c) If you really need POL3 model, try with other molecular
package that<br>
have point polarizable POL3 water (e.g. AMBER)<br>
<br>
I hope this help<br>
Ivan<br>
<br>
<br>
<br>
<br>
On 04/27/2011 11:04 AM, saly jackson wrote:<br>
> Hi all<br>
><br>
> I want to simulate using GROMACS.Before I used LAMMPS but
it has not<br>
> polarizable water models. Therefore I want to use
GROMACS.<br>
><br>
> I need .itp and .mdp files of POL3 water model.<br>
><br>
> Do you have the files.<br>
><br>
> Would you please help me.<br>
><br>
> Thanks alot for your time and attention<br>
><br>
> Regards<br>
><br>
> Saly<br>
<br>
<br>
--<br>
------<br>
Ivan Gladich, Ph.D.<br>
Postdoctoral Fellow<br>
Academy of Sciences of the Czech Republic<br>
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.<br>
Flemingovo nám. 2.<br>
166 10 Praha 6<br>
Czech Republic<br>
<br>
Tel: +420775504164<br>
e-mail: <a moz-do-not-send="true"
href="mailto:ivan.gladich@uochb.cas.cz">ivan.gladich@uochb.cas.cz</a><br>
web page:<a moz-do-not-send="true"
href="http://www.molecular.cz/%7Egladich/" target="_blank">http://www.molecular.cz/~gladich/</a><br>
-----<br>
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Message: 4<br>
Date: Wed, 27 Apr 2011 14:22:20 +0430<br>
From: mohsen ramezanpour <<a moz-do-not-send="true"
href="mailto:ramezanpour.mohsen@gmail.com">ramezanpour.mohsen@gmail.com</a>><br>
Subject: Re: [gmx-users] Docking<br>
To: Discussion list for GROMACS users <<a
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<br>
Dear Mark<br>
Thank you for your reply.yes,you are right.<br>
<br>
Regarding question 2:<br>
I have a pdf file from "Docking Server" for sertraline-SERT
example.Suppose<br>
this is a good docked state.<br>
<br>
In the other hand,I did what I explained in section 1 for
sertraline and<br>
SERT.(by pymol and ...)<br>
Now, I want to check if I have docked sertraline to SERT
correctly or not(<br>
by comparing with Docking server's one)<br>
How can I do that?<br>
<br>
<br>
Do you have any suggestion for doing docking by gromacs? for
example pulling<br>
code, MD , or SMD?<br>
Thanks in advance<br>
<br>
<br>
On Wed, Apr 27, 2011 at 1:48 PM, Mark Abraham <<a
moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>wrote:<br>
<br>
> On 4/27/2011 7:05 PM, mohsen ramezanpour wrote:<br>
><br>
>> Dear Users<br>
>><br>
>> I read so many emails to mailing list, there were
important notes about<br>
>> docking but I couldn't extract a general result.<br>
>> Please let me know:<br>
>><br>
>> 1-Can we dock a ligand to it's protein's binding
pocket with Pymol and<br>
>> Gromacs as following?<br>
>><br>
>> first:locating ligand outside and close to binding
site manually in pymol<br>
>> and saving complex.pdb<br>
>> second:doing all steps for generating complex.top and
complex.gro as<br>
>> Enzyme-Drug tutorial<br>
>> third:running md (with out any pull code and
constraint),in the other<br>
>> words,full flexible system.<br>
>><br>
>> I think drug can move freely and according to it's
interaction with<br>
>> binding site can be attracted by binding site.<br>
>> reside for a distance time and then will come out of
pocket.<br>
>><br>
>> Am I right?<br>
>><br>
><br>
> In principle, yes, but it is wildly unlikely that you
have a system that<br>
> can bind and unbind reliably in the 100ns simulation
range that you might be<br>
> able to afford to run, and if you did happen to have one,
what would you<br>
> have learned?<br>
><br>
><br>
> I know what discussed in mainling list about deffinition
of "Docking".<br>
>><br>
>><br>
>> 2-I have some docked files by "Docking Server " for
some of my<br>
>> drug-protein's complexes.<br>
>> now,I want to obtain them by doing MD in the above
proccess.if I was<br>
>> successful then try to do that for other drugs which
I don't have any docked<br>
>> pdb for them.<br>
>><br>
>> How can I fit a trajectory with a typical pdb file?<br>
>><br>
><br>
> I don't understand what you are asking.<br>
><br>
> Mark<br>
><br>
><br>
><br>
> --<br>
> gmx-users mailing list <a moz-do-not-send="true"
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target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
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<br>
<pre class="moz-signature" cols="72">--
------
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: <a class="moz-txt-link-abbreviated" href="mailto:ivan.gladich@uochb.cas.cz">ivan.gladich@uochb.cas.cz</a>
web page:<a class="moz-txt-link-freetext" href="http://www.molecular.cz/~gladich/">http://www.molecular.cz/~gladich/</a>
-----</pre>
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