<br><br><div class="gmail_quote">On Mon, Apr 5, 2010 at 11:06 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Send gmx-users mailing list submissions to<br>
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</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. dssp FATAL ERROR. (vivek modi)<br>
2. Re: dssp FATAL ERROR. (Justin A. Lemkul)<br>
3. Restraints of COM (Eudes Fileti)<br>
4. Restraints of COM 2 (Eudes Fileti)<br>
5. Topology and force fields (Lum Nforbi)<br>
6. Re: Topology and force fields (Gareth Tribello)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 5 Apr 2010 15:42:37 +0530<br>
From: vivek modi <<a href="mailto:modi.vivek2009@gmail.com">modi.vivek2009@gmail.com</a>><br>
Subject: [gmx-users] dssp FATAL ERROR.<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:v2r1d7a8f7a1004050312w1255d51dyb360601b86346dc@mail.gmail.com">v2r1d7a8f7a1004050312w1255d51dyb360601b86346dc@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
hi,<br>
<br>
Although this is already discussed in the mailing list but none of the<br>
solutions mentioned helped me.<br>
<br>
I am using Gromacs-4.0.5. I downloaded dssp from<br>
<a href="http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi" target="_blank">http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi</a><br>
Then I copy this to /usr/local/bin & chmod to executable.<br>
But when I run the program do_dssp it gives the following error:<br>
<br>
<br>
Program do_dssp_4, VERSION 4.0.5<br>
Source code file: do_dssp.c, line: 471<br>
<br>
Fatal error:<br>
Failed to execute command: /usr/local/bin/dssp -na ddXnSQTc ddgMjECf ><br>
/dev/null 2> /dev/null<br>
<br>
Any help is appreciated.<br>
<br>
<br>
Thanks.<br>
<br>
Vivek Modi,<br>
Graduate Student, IITK.<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20100405/8b09e200/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20100405/8b09e200/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Mon, 05 Apr 2010 06:52:04 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] dssp FATAL ERROR.<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:4BB9C0D4.1030207@vt.edu">4BB9C0D4.1030207@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
vivek modi wrote:<br>
> hi,<br>
><br>
> Although this is already discussed in the mailing list but none of the<br>
> solutions mentioned helped me.<br>
><br>
> I am using Gromacs-4.0.5. I downloaded dssp<br>
> from <a href="http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi" target="_blank">http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi</a><br>
> Then I copy this to /usr/local/bin & chmod to executable.<br>
> But when I run the program do_dssp it gives the following error:<br>
><br>
><br>
> Program do_dssp_4, VERSION 4.0.5<br>
> Source code file: do_dssp.c, line: 471<br>
><br>
> Fatal error:<br>
> Failed to execute command: /usr/local/bin/dssp -na ddXnSQTc ddgMjECf ><br>
> /dev/null 2> /dev/null<br>
><br>
> Any help is appreciated.<br>
><br>
<br>
Did you re-name the executable? Have you set the DSSP environment variable<br>
properly?<br>
<br>
-Justin<br></blockquote><div><br></div><div><br></div><div>Yes. I have done both the things.</div><div><br></div><div><br></div><div>Vivek.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
><br>
> Thanks.<br>
><br>
> Vivek Modi,<br>
> Graduate Student, IITK.<br>
><br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Mon, 5 Apr 2010 09:59:23 -0300<br>
From: Eudes Fileti <<a href="mailto:fileti@ufabc.edu.br">fileti@ufabc.edu.br</a>><br>
Subject: [gmx-users] Restraints of COM<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:q2x65e289a21004050559r190f50a9j8eb35736c3839682@mail.gmail.com">q2x65e289a21004050559r190f50a9j8eb35736c3839682@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
Hello everybody, I have two benzene molecules and I<br>
want to restrain them only by their center of mass. The<br>
conversation below (between Shirts and Spoel) gave me<br>
some ideas but still I couldnt solve the problem. In particular<br>
I'm not seeing any way to create this user group, nor how to<br>
calculate its center of mass. Could someone give me a<br>
hand with that?<br>
Bests<br>
eef<br>
_______________________________________<br>
Eudes Eterno Fileti<br>
Centro de Ciências Naturais e Humanas<br>
Universidade Federal do ABC — CCNH<br>
Av. dos Estados, 5001<br>
Santo André - SP - Brasil<br>
CEP 09210-971<br>
+55.11.4996-0196<br>
<a href="http://fileti.ufabc.edu.br" target="_blank">http://fileti.ufabc.edu.br</a><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20100405/6bcd1704/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20100405/6bcd1704/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Mon, 5 Apr 2010 10:04:20 -0300<br>
From: Eudes Fileti <<a href="mailto:fileti@ufabc.edu.br">fileti@ufabc.edu.br</a>><br>
Subject: [gmx-users] Restraints of COM 2<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:z2t65e289a21004050604t270a616cgfb28c4546e511fb9@mail.gmail.com">z2t65e289a21004050604t270a616cgfb28c4546e511fb9@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
Hello everybody, I have two benzene molecules and I want to restrain them<br>
only by their center of mass. The conversation below (between Shirts and<br>
Spoel) gave me some ideas but still I couldnt solve the problem. In<br>
particular I'm not seeing any way to create this user group, nor how to<br>
calculate its center of mass. Could someone give me a hand with that?<br>
<br>
On Sun, 2004-01-25 at 04:00, Michael Shirts wrote:<br>
> Hello, all-<br>
><br>
> So, supposing I had a protein, and wanted to restrain a ligand by<br>
attaching<br>
> it with a spring to some point that wasn't actually an atom -- say it was<br>
> the center of geometry of a number of atoms around the binding pocket, so<br>
that<br>
> it's a point that redefines itself at each step of the simulation.<br>
><br>
> 1) Is this possible to do using either the position restraint or distance<br>
> restraint tools in GROMACS?<br>
><br>
> 2) If not, how might one modify the code to put this in?<br>
If this is dynamic, like the centre of mass of a group, you might add<br>
something using a user group. Compute the center of mass of your user<br>
group and call the position restraint routine. The good thing (TM) is<br>
that you don't have to program any I/O.<br>
<br>
><br>
> Thanks,<br>
> Michael Shirts<br>
> Stanford University.<br>
--<br>
David.<br>
________________________________________________________________________<br>
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: 46 18 471 4205 fax: 46 18 511 755<br>
spoel at <a href="http://xray.bmc.uu.se" target="_blank">xray.bmc.uu.se</a> spoel at <a href="http://gromacs.org" target="_blank">gromacs.org</a> <a href="http://xray.bmc.uu.se/~spoel" target="_blank">http://xray.bmc.uu.se/~spoel</a><br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>
_______________________________________<br>
Eudes Eterno Fileti<br>
Centro de Ciências Naturais e Humanas<br>
Universidade Federal do ABC — CCNH<br>
Av. dos Estados, 5001<br>
Santo André - SP - Brasil<br>
CEP 09210-971<br>
+55.11.4996-0196<br>
<a href="http://fileti.ufabc.edu.br" target="_blank">http://fileti.ufabc.edu.br</a><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20100405/e4a25a37/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20100405/e4a25a37/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Mon, 5 Apr 2010 10:26:53 -0700<br>
From: Lum Nforbi <<a href="mailto:lumngwegia@gmail.com">lumngwegia@gmail.com</a>><br>
Subject: [gmx-users] Topology and force fields<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:s2rf7e1d8851004051026r675119ffs9ebec4f2e13fc59a@mail.gmail.com">s2rf7e1d8851004051026r675119ffs9ebec4f2e13fc59a@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hello all,<br>
<br>
Below are the contents of a water1.top file that I used to simulate<br>
2000 molecules of TIP3P water (NPT). I made this topology file according to<br>
the pattern on page 114 of the manual (topology for Urea in water). My<br>
diffusion coefficient, viscosity and radial distribution functions matched<br>
those for tip3p water in literature.<br>
Recently I was told that I did not need to use another force field<br>
in the topology like ffcharmm27.itp since tip3p.itp is already a forcefield<br>
on its own. Could this be true? I just wanted to verify the authenticity of<br>
my simulation. If the structure of the topology below is not correct, please<br>
let me know.<br>
<br>
; The force field files to be included<br>
#include "ffcharmm27.itp"<br>
<br>
; Include TIP3P water topology<br>
#include "tip3p.itp"<br>
<br>
[ system ]<br>
Pure Water<br>
<br>
[ molecules ]<br>
;molecule name number<br>
SOL 1936<br>
SOL 64<br>
<br>
I appreciate your answers.<br>
<br>
Lum<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20100405/5b0488a9/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20100405/5b0488a9/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Mon, 5 Apr 2010 19:35:36 +0200<br>
From: Gareth Tribello <<a href="mailto:gareth.tribello@gmail.com">gareth.tribello@gmail.com</a>><br>
Subject: Re: [gmx-users] Topology and force fields<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:z2xb83620ff1004051035u896a34d4q9cde7833dd0659bc@mail.gmail.com">z2xb83620ff1004051035u896a34d4q9cde7833dd0659bc@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hello<br>
<br>
I think what you have been told is wrong. You need to include both<br>
"ffcharmm27.itp" and "tip3p.itp" as the atomtypes in your tip3p.itp will<br>
otherwise not be defined. There is an easy way to check though - take out<br>
the include ffcharmm27.itp and try to run grompp on your new topology. My<br>
bet would be that it won't work and, if you are using rigid molecules, it<br>
will tell you that it finds a settles section in the wrong place.<br>
<br>
ciao<br>
Gareth<br>
<br>
On Mon, Apr 5, 2010 at 7:26 PM, Lum Nforbi <<a href="mailto:lumngwegia@gmail.com">lumngwegia@gmail.com</a>> wrote:<br>
<br>
> Hello all,<br>
><br>
> Below are the contents of a water1.top file that I used to simulate<br>
> 2000 molecules of TIP3P water (NPT). I made this topology file according to<br>
> the pattern on page 114 of the manual (topology for Urea in water). My<br>
> diffusion coefficient, viscosity and radial distribution functions matched<br>
> those for tip3p water in literature.<br>
> Recently I was told that I did not need to use another force field<br>
> in the topology like ffcharmm27.itp since tip3p.itp is already a forcefield<br>
> on its own. Could this be true? I just wanted to verify the authenticity of<br>
> my simulation. If the structure of the topology below is not correct, please<br>
> let me know.<br>
><br>
> ; The force field files to be included<br>
> #include "ffcharmm27.itp"<br>
><br>
> ; Include TIP3P water topology<br>
> #include "tip3p.itp"<br>
><br>
> [ system ]<br>
> Pure Water<br>
><br>
> [ molecules ]<br>
> ;molecule name number<br>
> SOL 1936<br>
> SOL 64<br>
><br>
> I appreciate your answers.<br>
><br>
> Lum<br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<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" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20100405/30625f77/attachment.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20100405/30625f77/attachment.html</a><br>
<br>
------------------------------<br>
<font color="#888888"><br>
--<br>
gmx-users mailing list<br>
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
<br>
End of gmx-users Digest, Vol 72, Issue 21<br>
*****************************************<br>
</font></blockquote></div><br>