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

[chiradip chatterjee]

Thanks Mohan and others thanks a lot..this things help
me a lot...
chiradip

--- Mohan Boggara <mohanbabu.boggara at gmail.com> wrote:

> 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:
> >
> >    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 
=== message truncated ===>
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