Thanks Mark, <br>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. <br><br>Mohan <br><br><div><span class="gmail_quote">
On 12/11/06, <b class="gmail_sendername"><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a></b> <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:
</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Send gmx-users mailing list submissions to<br> <a href="mailto:gmx-users@gromacs.org">
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</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of gmx-users digest..."<br><br><br>Today's Topics:<br><br> 1. Re: Re: How to generate GRO and TOP file for (Mark Abraham)
<br> 2. query (chiradip chatterjee)<br> 3. Re: g_density for a micelle (Tsjerk Wassenaar)<br> 4. Re: query (Tsjerk Wassenaar)<br> 5. Re: query (Paul van Maaren)<br><br><br>----------------------------------------------------------------------
<br><br>Message: 1<br>Date: Sun, 12 Nov 2006 08:49:16 +1100<br>From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>Subject: Re: [gmx-users] Re: How to generate GRO and TOP file for
<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:4556455C.4010001@anu.edu.au">4556455C.4010001@anu.edu.au</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
<br><br>Mohan Boggara wrote:<br><br>> However, to extend the gro file, we need to use the angle information<br>> and may be write a script.<br><br>Molecule builders in various chemistry packages may be of help here. You
<br> may need to use a text editor to change atom and residue names in the<br>resulting structure files (presumably PDB) but it might be better than<br>writing your own script.<br><br>> I don't know if this a good idea??
<br><br>A good idea is not to quote an entire daily digest when you intend only<br>to refer to a small part of it. That digest gets sent to hundreds of<br>people through dozens of computers each... Well done for changing the
<br>subject line to something relevant, though :-)<br><br>Mark<br><br><br>------------------------------<br><br>Message: 2<br>Date: Sun, 12 Nov 2006 04:45:29 +0000 (GMT)<br>From: chiradip chatterjee <<a href="mailto:chiradip75@yahoo.co.uk">
chiradip75@yahoo.co.uk</a>><br>Subject: [gmx-users] query<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID: <<a href="mailto:169483.43522.qm@web25409.mail.ukl.yahoo.com">169483.43522.qm@web25409.mail.ukl.yahoo.com
</a>><br>Content-Type: text/plain; charset=iso-8859-1<br><br>Hi gromacs users,<br>I am a new user in Gromacs. I need a help. I want to<br>make a solvent box with Trifluoroethanol(TFE) and<br>water. Could any one please supply me the *.gro and
<br>*.itp file for trifluoroethanol? I did not find<br>this(TFE) in the library file.<br>thanks in advance<br>Chiradip Chatterjee<br><br>Send instant messages to your online friends <a href="http://uk.messenger.yahoo.com">
http://uk.messenger.yahoo.com</a><br><br><br>------------------------------<br><br>Message: 3<br>Date: Sun, 12 Nov 2006 10:32:37 +0100<br>From: "Tsjerk Wassenaar" <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com
</a>><br>Subject: Re: [gmx-users] g_density for a micelle<br>To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:8ff898150611120132kcd8b0bq5734faf3e880b7e@mail.gmail.com">
8ff898150611120132kcd8b0bq5734faf3e880b7e@mail.gmail.com</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Hi Chris,<br><br>Aren't you looking for a radial distribution function (g_rdf)? Maybe<br>
you'll have to change the code a bit to get exactly what you want, but<br>I'd guess that g_rdf is closer to what you want. However, you do not<br>state what it is you want.., so it's merely a guess.<br><br>Best,<br><br>Tsjerk
<br><br>On 11/10/06, <a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a> <<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>> wrote:<br>> Does anybody have a modified g_density for calculation from the center
<br>> of mass of a micelle?<br>> Thanks.<br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org
</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>><br><br><br>--<br>Tsjerk A. Wassenaar, Ph.D.<br>post-doc<br>NMR, Utrecht University,
<br>Padualaan 8,<br>3584 CH Utrecht, the Netherlands<br>P: +31-30-2539931<br>F: +31-30-2537623<br><br><br>------------------------------<br><br>Message: 4<br>Date: Sun, 12 Nov 2006 10:42:42 +0100<br>From: "Tsjerk Wassenaar" <
<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>Subject: Re: [gmx-users] query<br>To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br> <<a href="mailto:8ff898150611120142t4f010771k2cfda581f4934ffc@mail.gmail.com">8ff898150611120142t4f010771k2cfda581f4934ffc@mail.gmail.com</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
<br><br>Hi Chiradip,<br><br>Probably someone will have a topology and a structure file for TFE<br>lying around (not me). But TFE isn't the worst of molecules and since<br>your new with Gromacs, I think it would be an excellent opportunity to
<br>get acquinted with the program and force fields by parameterizing it<br>yourself. Find the paper of your favorite force field (choose one) and<br>check how the parameterization of the building blocks / molecules was<br>
done. Take the same steps for TFE.<br><br>Maybe this isn't the answer you'd hoped for, but think of the saying<br>"give a man a fish and he can eat for a day; teach a man how to fish<br>and..." :)<br><br>Cheers,
<br><br>Tsjerk<br><br>On 11/12/06, chiradip chatterjee <<a href="mailto:chiradip75@yahoo.co.uk">chiradip75@yahoo.co.uk</a>> wrote:<br>> Hi gromacs users,<br>> I am a new user in Gromacs. I need a help. I want to
<br>> make a solvent box with Trifluoroethanol(TFE) and<br>> water. Could any one please supply me the *.gro and<br>> *.itp file for trifluoroethanol? I did not find<br>> this(TFE) in the library file.<br>> thanks in advance
<br>> Chiradip Chatterjee<br>><br>> Send instant messages to your online friends <a href="http://uk.messenger.yahoo.com">http://uk.messenger.yahoo.com</a><br>> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">
http://www.gromacs.org/mailing_lists/users.php</a><br>><br><br><br>--<br>Tsjerk A. Wassenaar, Ph.D.<br>post-doc<br>NMR, Utrecht University,<br>Padualaan 8,<br>3584 CH Utrecht, the Netherlands<br>P: +31-30-2539931<br>F: +31-30-2537623
<br><br><br>------------------------------<br><br>Message: 5<br>Date: Sun, 12 Nov 2006 11:34:08 +0100<br>From: Paul van Maaren <<a href="mailto:maaren@home.nl">maaren@home.nl</a>><br>Subject: Re: [gmx-users] query<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:200611121134.09777.maaren@home.nl">200611121134.09777.maaren@home.nl</a>>
<br>Content-Type: text/plain; charset="iso-8859-1"<br><br>On Sunday 12 November 2006 10:42, Tsjerk Wassenaar wrote:<br><br>> Probably someone will have a topology and a structure file for TFE<br>> lying around (not me). But TFE isn't the worst of molecules and since
<br>> your new with Gromacs, I think it would be an excellent opportunity to<br>> get acquinted with the program and force fields by parameterizing it<br>> yourself. Find the paper of your favorite force field (choose one) and
<br>> check how the parameterization of the building blocks / molecules was<br>> done. Take the same steps for TFE.<br>><br>> Maybe this isn't the answer you'd hoped for, but think of the saying<br>> "give a man a fish and he can eat for a day; teach a man how to fish
<br>> and..." :)<br><br>That's always a good approach, but for starters you might want to take a look<br>at tfe.itp in the share/top directory.<br><br>--<br>Groeten,<br><br>Paul van Maaren<br><br><br>------------------------------
<br><br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users
</a><br><br><br>End of gmx-users Digest, Vol 31, Issue 39<br>*****************************************<br></blockquote></div><br><br clear="all"><br>-- <br>Mohan Boggara<br>Graduate Research Assistant<br>Dept of Chemical Engineering
<br>University of Houston<br>S222 Engg Bldg 1, 4800 Calhoun Rd,<br>Houston, Texas-77204, USA<br>Mobile: 1-832-643-5729<br>Office: 1-713-743-4314 <br><a href="http://polymer.chee.uh.edu/">http://polymer.chee.uh.edu/</a><br>
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