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, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
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When replying, please edit your Subject line so it is more specificthan 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: 1Date: Sun, 12 Nov 2006 08:49:16 +1100From: 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.orgMessage-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 theresulting structure files (presumably PDB) but it might be better thanwriting 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 onlyto refer to a small part of it. That digest gets sent to hundreds ofpeople through dozens of computers each... Well done for changing the
subject line to something relevant, though :-)Mark--Message: 2Date: Sun, 12 Nov 2006 04:45:29 + (GMT)From: chiradip chatterjee
[EMAIL PROTECTED]Subject: [gmx-users] queryTo: gmx-users@gromacs.orgMessage-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=iso-8859-1Hi gromacs users,I am a new user in Gromacs. I need a help. I want tomake a solvent box with Trifluoroethanol(TFE) andwater. Could any one please supply me the *.gro and
*.itp file for trifluoroethanol? I did not findthis(TFE) in the library file.thanks in advanceChiradip ChatterjeeSend instant messages to your online friends
http://uk.messenger.yahoo.com--Message: 3Date: Sun, 12 Nov 2006 10:32:37 +0100From: Tsjerk Wassenaar [EMAIL PROTECTED]
Subject: Re: [gmx-users] g_density for a micelleTo: Discussion list for GROMACS users gmx-users@gromacs.orgMessage-ID:
[EMAIL PROTECTED]Content-Type: text/plain; charset=ISO-8859-1; format=flowedHi 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, butI'd guess that g_rdf is closer to what you want. However, you do notstate 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 listgmx-users@gromacs.org
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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php--Tsjerk A. Wassenaar, Ph.D.post-docNMR, Utrecht University,
Padualaan 8,3584 CH Utrecht, the NetherlandsP: +31-30-2539931F: +31-30-2537623--Message: 4Date: Sun, 12 Nov 2006 10:42:42 +0100From: Tsjerk Wassenaar
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Hi Chiradip,Probably someone will have a topology and a structure file for TFElying around (not me). But TFE isn't the worst of molecules and sinceyour new with Gromacs, I think it would be an excellent opportunity to
get acquinted with the program and force fields by parameterizing ityourself. Find the paper of your favorite force field (choose one) andcheck 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 sayinggive a man a fish and he can eat for a day; teach a man how to fishand... :)Cheers,
TsjerkOn 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
