May be try using PRODRG. Type PRODRG in google, and then draw your molecule, it will generate a topology and gro file for you.
Mohan
On 12/11/06,
[EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
Send gmx-users mailing list submissions to
gmx-users@gromacs.org
To subscribe or unsubscribe via the World Wide Web, visit
http://www.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject or body 'help' to
[EMAIL PROTECTED]
You can reach the person managing the list at
[EMAIL PROTECTED]
When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."
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 < [EMAIL PROTECTED]>
Subject: Re: [gmx-users] Re: How to generate GRO and TOP file for
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: < [EMAIL PROTECTED]>
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 <[EMAIL PROTECTED]>
Subject: [gmx-users] query
To: gmx-users@gromacs.org
Message-ID: < [EMAIL PROTECTED]>
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" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] g_density for a micelle
To: "Discussion list for GROMACS users" < gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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, [EMAIL PROTECTED] <[EMAIL PROTECTED] > wrote:
> Does anybody have a modified g_density for calculation from the center
> of mass of a micelle?
> Thanks.
>
> _______________________________________________
> gmx-users mailing list gmx-users@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 [EMAIL PROTECTED].
> 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: 4
Date: Sun, 12 Nov 2006 10:42:42 +0100
From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] query
To: "Discussion list for GROMACS users" < gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED] >
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 <[EMAIL PROTECTED]> 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@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 [EMAIL PROTECTED].
> 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 <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] query
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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
------------------------------
_______________________________________________
gmx-users mailing list
gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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
http://polymer.chee.uh.edu/
Strive for excellence and not for perfection --Kamal Hassan, Indian Actor
_______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
