[gmx-users] Re: Re: How to generate GRO and TOP file for

Mon Nov 13 14:54:34 CET 2006

Thanks Mark,
I tried atleast PRODRG, but it has the limitation on total number of atoms.
Anyway, I will probably try to find a source of other packages for molecue
building.

Mohan

On 12/11/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
wrote:
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> Today's Topics:
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>    1. Re: Re: How to generate GRO and TOP file for (Mark Abraham)
>    2. query (chiradip chatterjee)
>    3. Re: g_density for a micelle (Tsjerk Wassenaar)
>    4. Re: query (Tsjerk Wassenaar)
>    5. Re: query (Paul van Maaren)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 12 Nov 2006 08:49:16 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Re: How to generate GRO and TOP file for
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4556455C.4010001 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Mohan Boggara wrote:
>
> > However, to extend the gro file, we need to use the angle information
> > and may be write a script.
>
> Molecule builders in various chemistry packages may be of help here. You
>   may need to use a text editor to change atom and residue names in the
> resulting structure files (presumably PDB) but it might be better than
> writing your own script.
>
> > I don't know if this a good idea??
>
> A good idea is not to quote an entire daily digest when you intend only
> to refer to a small part of it. That digest gets sent to hundreds of
> people through dozens of computers each... Well done for changing the
> subject line to something relevant, though :-)
>
> Mark
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 12 Nov 2006 04:45:29 +0000 (GMT)
> From: chiradip chatterjee <chiradip75 at yahoo.co.uk>
> Subject: [gmx-users] query
> To: gmx-users at gromacs.org
> Message-ID: <169483.43522.qm at web25409.mail.ukl.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Hi gromacs users,
> I am a new user in Gromacs. I need a help. I want to
> make a solvent box with Trifluoroethanol(TFE) and
> water. Could any one please supply me the *.gro and
> *.itp file for trifluoroethanol? I did not find
> this(TFE) in the library file.
> thanks in advance
> Chiradip Chatterjee
>
> Send instant messages to your online friends http://uk.messenger.yahoo.com
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 12 Nov 2006 10:32:37 +0100
> From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] g_density for a micelle
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID: <8ff898150611120132kcd8b0bq5734faf3e880b7e at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Chris,
>
> Aren't you looking for a radial distribution function (g_rdf)? Maybe
> you'll have to change the code a bit to get exactly what you want, but
> I'd guess that g_rdf is closer to what you want. However, you do not
> state what it is you want.., so it's merely a guess.
>
> Best,
>
> Tsjerk
>
> On 11/10/06, chris.neale at utoronto.ca <chris.neale at utoronto.ca> wrote:
> > Does anybody have a modified g_density for calculation from the center
> > of mass of a micelle?
> > Thanks.
> >
> > _______________________________________________
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> post-doc
> NMR, Utrecht University,
> Padualaan 8,
> 3584 CH Utrecht, the Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 12 Nov 2006 10:42:42 +0100
> From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] query
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
>         <8ff898150611120142t4f010771k2cfda581f4934ffc at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Chiradip,
>
> Probably someone will have a topology and a structure file for TFE
> lying around (not me). But TFE isn't the worst of molecules and since
> your new with Gromacs, I think it would be an excellent opportunity to
> get acquinted with the program and force fields by parameterizing it
> yourself. Find the paper of your favorite force field (choose one) and
> check how the parameterization of the building blocks / molecules was
> done. Take the same steps for TFE.
>
> Maybe this isn't the answer you'd hoped for, but think of the saying
> "give a man a fish and he can eat for a day; teach a man how to fish
> and..." :)
>
> Cheers,
>
> Tsjerk
>
> On 11/12/06, chiradip chatterjee <chiradip75 at yahoo.co.uk> wrote:
> > Hi gromacs users,
> > I am a new user in Gromacs. I need a help. I want to
> > make a solvent box with Trifluoroethanol(TFE) and
> > water. Could any one please supply me the *.gro and
> > *.itp file for trifluoroethanol? I did not find
> > this(TFE) in the library file.
> > thanks in advance
> > Chiradip Chatterjee
> >
> > Send instant messages to your online friends
> http://uk.messenger.yahoo.com
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > 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/mailing_lists/users.php
> >
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> post-doc
> NMR, Utrecht University,
> Padualaan 8,
> 3584 CH Utrecht, the Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
>
> ------------------------------
>
> Message: 5
> Date: Sun, 12 Nov 2006 11:34:08 +0100
> From: Paul van Maaren <maaren at home.nl>
> Subject: Re: [gmx-users] query
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <200611121134.09777.maaren at home.nl>
> Content-Type: text/plain;  charset="iso-8859-1"
>
> On Sunday 12 November 2006 10:42, Tsjerk Wassenaar wrote:
>
> > Probably someone will have a topology and a structure file for TFE
> > lying around (not me). But TFE isn't the worst of molecules and since
> > your new with Gromacs, I think it would be an excellent opportunity to
> > get acquinted with the program and force fields by parameterizing it
> > yourself. Find the paper of your favorite force field (choose one) and
> > check how the parameterization of the building blocks / molecules was
> > done. Take the same steps for TFE.
> >
> > Maybe this isn't the answer you'd hoped for, but think of the saying
> > "give a man a fish and he can eat for a day; teach a man how to fish
> > and..." :)
>
> That's always a good approach, but for starters you might want to take a
> look
> at tfe.itp in the share/top directory.
>
> --
> Groeten,
>
> Paul van Maaren
>
>
> ------------------------------
>
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>
> End of gmx-users Digest, Vol 31, Issue 39
> *****************************************
>

-- 
Mohan Boggara
Graduate Research Assistant
Dept of Chemical Engineering
University of Houston
S222 Engg Bldg 1, 4800 Calhoun Rd,
Houston, Texas-77204, USA
Mobile: 1-832-643-5729
Office: 1-713-743-4314
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Strive for excellence and not for perfection --Kamal Hassan, Indian Actor
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