<br><div class="gmail_quote"><br>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><font color="#888888">
<br>
Saly</font><div><div></div><div class="h5"><br><br><div class="gmail_quote">On Wed, Apr 27, 2011 at 2:30 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>></span> wrote:<br>
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Today's Topics:<br>
<br>
1. Re: MG-ATP (Mark Abraham)<br>
2. Re: Docking (Mark Abraham)<br>
3. Re: POL3 water model (Ivan Gladich)<br>
4. Re: Docking (mohsen ramezanpour)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 27 Apr 2011 19:09:59 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] MG-ATP<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DB7DD67.2050500@anu.edu.au" target="_blank">4DB7DD67.2050500@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 4/27/2011 6:52 PM, Sajad Ahrari wrote:<br>
> dear users<br>
> is "MG-ATP" known to gromacs ? in my pdb structure I have ADP and MG,<br>
> apart from each other and not being crystallized in the right place.<br>
> can i omit them and replace ADP's with MG-ATP? or I should introduce<br>
> this topology to gromacs?<br>
<br>
You'll have to do your own literature searching about previous<br>
treatments of ADP and ATP, I'm afraid :-) Pretty much anything that has<br>
been done can be made to work in GROMACS, however.<br>
<br>
See also <a href="http://www.gromacs.org/Documentation/How-tos/Parameterization" target="_blank">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>
<br>
Mark<br>
<br>
<br>
<br>
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Message: 2<br>
Date: Wed, 27 Apr 2011 19:18:08 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Docking<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DB7DF50.40403@anu.edu.au" target="_blank">4DB7DF50.40403@anu.edu.au</a>><br>
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<br>
On 4/27/2011 7:05 PM, mohsen ramezanpour wrote:<br>
> Dear Users<br>
><br>
> I read so many emails to mailing list, there were important notes<br>
> about 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<br>
> pymol 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>
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<br>
might be able to afford to run, and if you did happen to have one, what<br>
would you have learned?<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<br>
> docked pdb for them.<br>
><br>
> How can I fit a trajectory with a typical pdb file?<br>
<br>
I don't understand what you are asking.<br>
<br>
Mark<br>
<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Wed, 27 Apr 2011 12:14:42 +0200<br>
From: Ivan Gladich <<a href="mailto:ivan.gladich@marge.uochb.cas.cz" target="_blank">ivan.gladich@marge.uochb.cas.cz</a>><br>
Subject: Re: [gmx-users] POL3 water model<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DB7EC92.7080107@marge.uochb.cas.cz" target="_blank">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 href="mailto:ivan.gladich@uochb.cas.cz" target="_blank">ivan.gladich@uochb.cas.cz</a><br>
web page:<a href="http://www.molecular.cz/%7Egladich/" target="_blank">http://www.molecular.cz/~gladich/</a><br>
-----<br>
<br>
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Message: 4<br>
Date: Wed, 27 Apr 2011 14:22:20 +0430<br>
From: mohsen ramezanpour <<a href="mailto:ramezanpour.mohsen@gmail.com" target="_blank">ramezanpour.mohsen@gmail.com</a>><br>
Subject: Re: [gmx-users] Docking<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:BANLkTikK78dY35r97bniGoysWzVd4cuzbQ@mail.gmail.com" target="_blank">BANLkTikK78dY35r97bniGoysWzVd4cuzbQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<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 href="mailto:Mark.Abraham@anu.edu.au" target="_blank">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>
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