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-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@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-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@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.abra...@anu.edu.au> > Subject: Re: [gmx-users] MG-ATP > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4db7dd67.2050...@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.abra...@anu.edu.au> > Subject: Re: [gmx-users] Docking > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4db7df50.40...@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.glad...@marge.uochb.cas.cz> > Subject: Re: [gmx-users] POL3 water model > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4db7ec92.7080...@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.glad...@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.moh...@gmail.com> > Subject: Re: [gmx-users] Docking > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <banlktikk78dy35r97bnigoyswzvd4cu...@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.abra...@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@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-requ...@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@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 > ****************************************** >
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