Is it a single structure in the .pdb file? Or is it many frames of a trajectory? It is noted in the manual that do_dssp is very slow. In my experience (on my laptop), I can analyze 50000 frames in roughly 3 hours. Are you waiting long enough for do_dssp to finish?
-Justin Quoting ABEL Stephane 175950 <[EMAIL PROTECTED]>: > I am back :( > > The procedure i did > > 1) do_dssp -s test-Struc.pdb -f test-Struc.pdb -dt 1 -o ss.xpm > The menu appears I choose 5 (Main Chain) and I obtained the following message > -------- > GROningen MAchine for Chemical Simulation > > :-) VERSION 3.3.1 (-: > > > Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2006, The GROMACS development team, > check out http://www.gromacs.org for more information. > > This program is free software; you can redistribute it and/or > modify it under the terms of the GNU General Public License > as published by the Free Software Foundation; either version 2 > of the License, or (at your option) any later version. > > :-) /applications/gromacs-3.3.1-fftw/bin/do_dssp (-: > > Option Filename Type Description > ------------------------------------------------------------ > -f test-Struc.pdb Input Generic trajectory: xtc trr trj gro g96 pdb > -s test-Struc.pdb Input Structure+mass(db): tpr tpb tpa gro g96 pdb > xml > -n index.ndx Input, Opt. Index file > -ssdump ssdump.dat Output, Opt. Generic data file > -map ss.map Input, Lib. File that maps matrix data to colors > -o ss.xpm Output X PixMap compatible matrix file > -sc scount.xvg Output xvgr/xmgr file > -a area.xpm Output, Opt. X PixMap compatible matrix file > -ta totarea.xvg Output, Opt. xvgr/xmgr file > -aa averarea.xvg Output, Opt. xvgr/xmgr file > > Option Type Value Description > ------------------------------------------------------ > -[no]h bool no Print help info and quit > -[no]X bool no Use dialog box GUI to edit command line options > -nice int 19 Set the nicelevel > -b time 0 First frame (ps) to read from trajectory > -e time 0 Last frame (ps) to read from trajectory > -dt time 1 Only use frame when t MOD dt = first time (ps) > -tu enum ps Time unit: ps, fs, ns, us, ms or s > -[no]w bool no View output xvg, xpm, eps and pdb files > -[no]xvgr bool yes Add specific codes (legends etc.) in the output > xvg files for the xmgrace program > -sss string HEBT Secondary structures for structure count > > Opening library file > /applications/gromacs-3.3.1-fftw/share/gromacs/top/phbres.dat > Opening library file > /applications/gromacs-3.3.1-fftw/share/gromacs/top/aminoacids.dat > Group 0 ( System) has 1674 elements > Group 1 ( Protein) has 1623 elements > Group 2 ( Protein-H) has 796 elements > Group 3 ( C-alpha) has 101 elements > Group 4 ( Backbone) has 304 elements > Group 5 ( MainChain) has 405 elements > Group 6 (MainChain+Cb) has 494 elements > Group 7 ( MainChain+H) has 405 elements > Group 8 ( SideChain) has 1218 elements > Group 9 ( SideChain-H) has 391 elements > Group 10 ( Prot-Masses) has 1623 elements > Group 11 ( Non-Protein) has 51 elements > Group 12 ( HSD) has 51 elements > Group 13 ( Other) has 51 elements > > I select a group: 5 > Selected 5: 'MainChain' > There are 102 residues in your selected group <--- OK for me > Opening library file > /applications/gromacs-3.3.1-fftw/share/gromacs/top/ss.map > Reading frame 0 time -1.000 > Back Off! I just backed up ddsGGvys to ./#ddsGGvys.1# > > The ddsGGvys is indeed a pdb file with the protein atoms (main chain). But > the program seems to run because the prompt did not appear but the ouput > ss.xpm is never present. > > What is the problem ? > > Thank you > > > > Thanks Justin for your reply > > > > So I used the choice 5(MainChain), 6(MainChain+Cb) and 7(MainChain+H)to > test. > > I obtained always the same error. > > > > Opening library file /applications/gromacs-3.2.1/share/top/ss.map > > Reading frame 0 time -1.000 > > Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1# > > What error? It appears that do_dssp is backing up an old intermediate file > that > gets generated as part of the calculation. > > -Justin > > > > > Note that the pdb seems correct because the secondary structure can be > > obtained with Stride available in VMD. And my trajectory was made CHARMM > > ffield. is this a problem in this case > > > > Thank a lot > > > > My story with do_dssp > > > > As suggested David and others i rename my pdb file with the extension .pdb > > > > i used the following command > > > > ./do_dssp -s RM106-Cytc-CH22-SecStruc.pdb -f RM106-Cytc-CH22-SecStruc.pdb > > > > A menu appears, I choose the group 1 (protein) and i obtained the error > > message > > > > Opening library file /applications/gromacs-3.2.1/share/top/ss.map > > Reading frame 0 time -1.000 > > Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1# > > > > What iis the problem. I give below a part of my pdb file > > > > ATOM 1 CAY ACE 1 6.421 -7.877 -11.574 -0.27 0.00 > > ATOM 2 HA1 ACE 1 6.050 -8.804 -12.062 0.09 0.00 > > ATOM 3 HA2 ACE 1 6.728 -7.203 -12.402 0.09 0.00 > > ATOM 4 HA3 ACE 1 5.529 -7.417 -11.098 0.09 0.00 > > ATOM 5 C ACE 1 7.470 -8.140 -10.510 0.51 0.00 > > ATOM 6 O ACE 1 7.594 -9.280 -10.074 -0.51 0.00 > > ATOM 7 N GLY 2 8.125 -7.096 -10.030 -0.47 0.00 > > ATOM 8 HN GLY 2 7.927 -6.156 -10.295 0.31 0.00 > > ATOM 9 CA GLY 2 8.970 -7.131 -8.819 -0.02 0.00 > > ATOM 10 HA1 GLY 2 8.889 -8.007 -8.193 0.09 0.00 > > ATOM 11 HA2 GLY 2 8.638 -6.265 -8.265 0.09 0.00 > > ATOM 12 C GLY 2 10.408 -6.734 -9.033 0.51 0.00 > > ATOM 13 O GLY 2 11.313 -7.365 -8.492 -0.51 0.00 > > ATOM 14 N ASP 3 10.647 -5.532 -9.599 -0.47 0.00 > > ATOM 15 HN ASP 3 9.863 -5.073 -10.011 0.31 0.00 > > ATOM 16 CA ASP 3 11.864 -4.806 -9.831 0.07 0.00 > > ATOM 17 HA ASP 3 12.713 -5.321 -9.406 0.09 0.00 > > ATOM 18 CB ASP 3 12.026 -4.347 -11.282 -0.28 0.00 > > ATOM 19 HB1 ASP 3 11.065 -4.008 -11.725 0.09 0.00 > > ATOM 20 HB2 ASP 3 12.877 -3.652 -11.448 0.09 0.00 > > ATOM 21 CG ASP 3 12.414 -5.579 -12.163 0.62 0.00 > > ATOM 22 OD1 ASP 3 11.641 -5.923 -13.130 -0.76 0.00 > > ATOM 23 OD2 ASP 3 13.571 -5.997 -12.137 -0.76 0.00 > > > > Thank you again for your kindly help > > > > Stefane > > > > ABEL Stephane 175950 wrote: > > > I used the following command > > > > > > ./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with > a > > part is show below. I obtained a segmentation fault. > > > > > > Maybe it is not a the good command. Remember that my trajectories are not > > made/compatible with GROMACS and i have only a pdb coordinates of my MD. > > > > > don't rename the .pdb file to .tpr. Just use .pdb > > > > -- > > David van der Spoel, Ph.D. > > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > > > > > ------------------------------ > > > > Message: 2 > > Date: Fri, 11 Jan 2008 09:30:47 +1100 > > From: Mark Abraham <[EMAIL PROTECTED]> > > Subject: Re: [gmx-users] Re: Targeted MD > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Message-ID: <[EMAIL PROTECTED]> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Steven Kirk wrote: > > > Mark Abraham <[EMAIL PROTECTED]> wrote > > > > >> "Non-Protein" serves well here. So a usual tc-grps line has "Protein > > >> Non-Protein" for a protein simulation. > > >> > > >> Mark > > > > > > A supplementary question. > > > > > > The tc-grps line can take predefined standard group names such as > > > 'System', 'Protein' and 'Non-Protein'. > > > > > > Does the 'Protein' group need to actually BE a protein, or are 'Protein' > > > and 'Non-Protein' really synonyms for > > > 'PresumablyBigMoleculeOfInterestProteinOrNot' and 'EverythingElse' ? > > > > I haven't read the code or found any mention in the manual, but I expect > > that src/share/top/aminoacids.dat contains the names of any amino acids, > > and thus implicitly defines these groups. > > > > Mark > > > > > > ------------------------------ > > > > Message: 3 > > Date: Fri, 11 Jan 2008 09:24:40 +0800 > > From: "xuji"<[EMAIL PROTECTED]> > > Subject: [gmx-users] Asking help about PME > > To: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > > Message-ID: <[EMAIL PROTECTED]> > > Content-Type: text/plain; charset="gb2312" > > > > Hi all gromacs users: > > > > I am digging into the PME method in gromacs. Can someone tell > > me what files have something to do with PME and the corresponding > > method FFT? > > > > Thanks! > > ¡¡¡¡ > > > > > > Best wishes! > > > > Ji Xu > > Institute of Process Engineering > > Chinese Academy of Sciences > > P.O.Box 353, Beijing, 100080, China > > Tel: +86-10-82627076 > > Fax:+86-10-62558065 > > [EMAIL PROTECTED] > > > > 2008-01-11 > > ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > http://www.gromacs.org/pipermail/gmx-users/attachments/20080111/ca6a4e79/attachment-0001.html > > > > ------------------------------ > > > > Message: 4 > > Date: Fri, 11 Jan 2008 13:10:11 +1100 > > From: Mark Abraham <[EMAIL PROTECTED]> > > Subject: Re: [gmx-users] Asking help about PME > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Message-ID: <[EMAIL PROTECTED]> > > Content-Type: text/plain; charset=GB2312 > > > > xuji wrote: > > > > > > Hi all gromacs users: > > > > > > I am digging into the PME method in gromacs. Can someone tell > > > me what files have something to do with PME and the corresponding > > > method FFT? > > > > >From the gromacs source directory, try > > > > find * -name "*pme*" > > > > and > > > > grep -i pme src/*/*.c include/*.h include/*/*.h | grep -v -i development > > > > Mark > > > > > > ------------------------------ > > > > Message: 5 > > Date: Fri, 11 Jan 2008 10:44:05 +0800 > > From: Yang Ye <[EMAIL PROTECTED]> > > Subject: Re: [gmx-users] Asking help about PME > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Message-ID: <[EMAIL PROTECTED]> > > Content-Type: text/plain; charset="us-ascii" > > > > An HTML attachment was scrubbed... > > URL: > > > http://www.gromacs.org/pipermail/gmx-users/attachments/20080111/295b0c2d/attachment-0001.html > > > > ------------------------------ > > > > Message: 6 > > Date: Fri, 11 Jan 2008 09:55:19 +0530 (IST) > > From: [EMAIL PROTECTED] > > Subject: [gmx-users] (no subject) > > To: gmx-users@gromacs.org > > Message-ID: > > <[EMAIL PROTECTED]> > > Content-Type: text/plain;charset=iso-8859-1 > > > > Hi all, > > I have been trying to generate .rtp, .top files from having input of .gro > > file for particular molecule in gromacs. I tried this with (x2top) command > > implemented in gromacs but i have encountered a problem while executing > > this command , that i am mentioning below. > > > > Fatal error: Library file ffG43a1.n2t not found in current dir nor in > > default directories. > > (You can set the directories to search with the GMXLIB path variable.) > > > > So how do i will be able to resolve this problem. > > If i will be getting any help i will be very thankful for you. > > > > Kinshuk Raj Srivastava > > IIT-Bombay > > India > > > > > > > > > > ------------------------------ > > > > Message: 7 > > Date: Fri, 11 Jan 2008 10:02:06 +0530 (IST) > > From: [EMAIL PROTECTED] > > Subject: [gmx-users] x2top & Library file ffG43a1.n2t > > To: gmx-users@gromacs.org > > Message-ID: > > <[EMAIL PROTECTED]> > > Content-Type: text/plain;charset=iso-8859-1 > > > > > > Hi all, > > I have been trying to generate .rtp, .top files from having input of .gro > > file for particular molecule in gromacs. I tried this with (x2top) command > > implemented in gromacs but i have encountered a problem while executing > > this command , that i am mentioning below. > > > > Fatal error: Library file ffG43a1.n2t not found in current dir nor in > > default directories. > > (You can set the directories to search with the GMXLIB path variable.) > > > > So how do i will be able to resolve this problem. > > If i will be getting any help i will be very thankful for you. > > > > Kinshuk Raj Srivastava > > IIT-Bombay > > India > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > 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 > > > > > > > > > > ------------------------------ > > > > Message: 8 > > Date: Fri, 11 Jan 2008 16:23:52 +1100 > > From: Mark Abraham <[EMAIL PROTECTED]> > > Subject: Re: [gmx-users] (no subject) > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Message-ID: <[EMAIL PROTECTED]> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > [EMAIL PROTECTED] wrote: > > > Hi all, > > > I have been trying to generate .rtp, .top files from having input of .gro > > > file for particular molecule in gromacs. I tried this with (x2top) > command > > > implemented in gromacs but i have encountered a problem while executing > > > this command , that i am mentioning below. > > > > > > Fatal error: Library file ffG43a1.n2t not found in current dir nor in > > > default directories. > > > (You can set the directories to search with the GMXLIB path variable.) > > > > > > So how do i will be able to resolve this problem. > > > If i will be getting any help i will be very thankful for you. > > > > So what value does GMXLIB have? What value should it have? Where did you > > install GROMACS? Can you find this file anywhere? Have you read the > > x2top documentation? > > > > Mark > > > > > > ------------------------------ > > > > _______________________________________________ > > gmx-users mailing list > > gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > > > End of gmx-users Digest, Vol 45, Issue 32 > > ***************************************** > > > > -------------- next part -------------- > > A non-text attachment was scrubbed... > > Name: not available > > Type: application/ms-tnef > > Size: 6833 bytes > > Desc: not available > > Url : > > > http://www.gromacs.org/pipermail/gmx-users/attachments/20080111/94d28610/attachment.bin > > > > ------------------------------ > > > > _______________________________________________ > > gmx-users mailing list > > gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > > > End of gmx-users Digest, Vol 45, Issue 36 > > ***************************************** > > > > > > > > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ======================================== > > > ------------------------------ > > Message: 2 > Date: Fri, 11 Jan 2008 11:01:58 -0500 > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] chromophore parameters for Molecular > Dynamics > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1 > > Quoting Anthony Cruz <[EMAIL PROTECTED]>: > > > Hi users: > > I am working in a new projec and we plan to do some molecular dynamic > > experiment to an engineered GFP molecule. I have been searching for the > > parameters for the GFP chromophore without success. Can some one help me? > Any > > reference or parameters?? > > Unless someone has already developed them, you'll have to do it yourself (not > an > easy task). See here: > > http://wiki.gromacs.org/index.php/Exotic_Species > > and > > http://wiki.gromacs.org/index.php/Parameterization > > -Justin > > > > > Best Regards, > > Anthony > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > 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 > > > > > > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ======================================== > > > ------------------------------ > > Message: 3 > Date: Fri, 11 Jan 2008 12:34:51 -0500 > From: "Myunggi Yi" <[EMAIL PROTECTED]> > Subject: [gmx-users] Re: Invalid order for directive defaults > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > I solved the problem. > I found one more "ffgmx.itp" in my pro.itp. > > > > On Jan 11, 2008 12:29 PM, Myunggi Yi <[EMAIL PROTECTED]> wrote: > > > Dear gromca users, > > > > I'm a new user of gromacs. > > I'm trying to run energy minimization on the system of a short peptide and > > a lipid bilayer. > > The following is my top file. > > > > ++++++++++++++++++++ > > ; > > #include "ffgmx.itp" > > #include "../lipid.popc.itp" > > #include "popc.itp" > > #include "pro.itp" > > #include "ions.itp" > > #include "spc.itp" > > > > > > [ system ] > > ; name > > Fusion peptide on POPC > > > > [ molecules ] > > ; name number > > Protein 1 > > POPC 128 > > Na 2 > > SOL 3655 > > +++++++++++++++++++ > > > > > > > > And I copied em.mdp with a little modification from the tutorial. > > > > > > > > +++++++++++++++++++ > > ; User spoel (236) > > ; Wed Nov 3 17:12:44 1993 > > ; Input file > > ; > > cpp = cpp > > define = -DPOSRES > > constraints = none > > integrator = steep > > nsteps = 100 > > ; > > ; Energy minimizing stuff > > ; > > emtol = 2000 > > emstep = 0.01 > > > > nstcomm = 1 > > ns_type = grid > > rlist = 1 > > rcoulomb = 1.0 > > rvdw = 1.0 > > Tcoupl = no > > Pcoupl = no > > gen_vel = no > > ++++++++++++++++++ > > > > > > After runing grompp I've got the following error message. > > > > > > ++++++++++++++++++++++ > > Program grompp, VERSION 3.3.1 > > Source code file: topio.c, line: 388 > > > > Fatal error: > > Invalid order for directive defaults, file > > > ""/panfs/storage.local/scs/home/myunggi/gromacs-openmpi/share/gromacs/top/ffgmx.itp"", > > line 4 > > ++++++++++++++++++++ > > > > I think I have only one [ defaults ] section. > > Does Anybody have an idea? What is wrong? > > > > Have a great day. > > > > > > -- > > Best wishes, > > > > MYUNGGI YI > > ================================== > > KLB 419 > > Institute of Molecular Biophysics > > Florida State University > > Tallahassee, FL 32306 > > > > Office: (850) 645-1334 > > http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi> > > > > > -- > Best wishes, > > MYUNGGI YI > ================================== > KLB 419 > Institute of Molecular Biophysics > Florida State University > Tallahassee, FL 32306 > > Office: (850) 645-1334 > http://www.scs.fsu.edu/~myunggi > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080111/99bda33a/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Fri, 11 Jan 2008 12:29:59 -0500 > From: "Myunggi Yi" <[EMAIL PROTECTED]> > Subject: [gmx-users] Invalid order for directive defaults > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > Dear gromca users, > > I'm a new user of gromacs. > I'm trying to run energy minimization on the system of a short peptide and a > lipid bilayer. > The following is my top file. > > ++++++++++++++++++++ > ; > #include "ffgmx.itp" > #include "../lipid.popc.itp" > #include "popc.itp" > #include "pro.itp" > #include "ions.itp" > #include "spc.itp" > > > [ system ] > ; name > Fusion peptide on POPC > > [ molecules ] > ; name number > Protein 1 > POPC 128 > Na 2 > SOL 3655 > +++++++++++++++++++ > > > > And I copied em.mdp with a little modification from the tutorial. > > > > +++++++++++++++++++ > ; User spoel (236) > ; Wed Nov 3 17:12:44 1993 > ; Input file > ; > cpp = cpp > define = -DPOSRES > constraints = none > integrator = steep > nsteps = 100 > ; > ; Energy minimizing stuff > ; > emtol = 2000 > emstep = 0.01 > > nstcomm = 1 > ns_type = grid > rlist = 1 > rcoulomb = 1.0 > rvdw = 1.0 > Tcoupl = no > Pcoupl = no > gen_vel = no > ++++++++++++++++++ > > > After runing grompp I've got the following error message. > > > ++++++++++++++++++++++ > Program grompp, VERSION 3.3.1 > Source code file: topio.c, line: 388 > > Fatal error: > Invalid order for directive defaults, file > ""/panfs/storage.local/scs/home/myunggi/gromacs-openmpi/share/gromacs/top/ffgmx.itp"", > line 4 > ++++++++++++++++++++ > > I think I have only one [ defaults ] section. > Does Anybody have an idea? What is wrong? > > Have a great day. > > > -- > Best wishes, > > MYUNGGI YI > ================================== > KLB 419 > Institute of Molecular Biophysics > Florida State University > Tallahassee, FL 32306 > > Office: (850) 645-1334 > http://www.scs.fsu.edu/~myunggi > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080111/0e299745/attachment.html > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 45, Issue 38 > ***************************************** > > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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