Re: [gmx-users] do_dssp crashes on certain machines..
[EMAIL PROTECTED] wrote: Dear community, I have the following problem with do_dssp, when I try analysing a long 70 ns trajectory produced by a REMD calculation. All my previous analysis went fine, when the trajectory had a length of ~= 50ns. However, I now obtain the following errror message, perhaps one hour after launching do_dssp, when the standard error message says frames around 54ns are being analysed: Group12 ( Cl) has 8 elements Group13 ( SOL) has 42228 elements Group14 ( Other) has 42236 elements Select a group: There are 103 residues in your selected group Opening library file /home/coutinho/software/gromacs-3.3.0/icc9.0/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up ddKGQneH to ./#ddKGQneH.1# Reading frame 36630 time 54945.000 --- Program do_dssp, VERSION 3.3 Source code file: futil.c, line: 340 File input/output error: ddr3C7fs --- I guess this problem is due to the architecture/memory of the nodes of the cluster I use (where this error occurs whether do_dssp is the only job on the node or not): The same analysis works fine on another machine. The cluster I use is made of Hewlett-Packard ProLiant DL145 G2 AMD Opteron Model 246 nodes. The nodes contain two AMD opteron 2.4GHz cpus and 4*1GB memory. I thank you very much for any suggestions! Do the analysis piecewise... trjconv to break the .trr into chunks, and now you can even do the analysis in parallel. Mark ___ gmx-users mailing listgmx-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
Re: [gmx-users] do_dssp crashes on certain machines..
hi, On Thursday, 19. April 2007 17:23, Mark Abraham wrote: [EMAIL PROTECTED] wrote: Dear community, I have the following problem with do_dssp, when I try analysing a long 70 ns trajectory produced by a REMD calculation. All my previous analysis went fine, when the trajectory had a length of ~= 50ns. However, I now obtain the following errror message, perhaps one hour after launching do_dssp, when the standard error message says frames around 54ns are being analysed: Group12 ( Cl) has 8 elements Group13 ( SOL) has 42228 elements Group14 ( Other) has 42236 elements Select a group: There are 103 residues in your selected group Opening library file /home/coutinho/software/gromacs-3.3.0/icc9.0/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up ddKGQneH to ./#ddKGQneH.1# Reading frame 36630 time 54945.000 --- Program do_dssp, VERSION 3.3 Source code file: futil.c, line: 340 File input/output error: ddr3C7fs --- I guess this problem is due to the architecture/memory of the nodes of the cluster I use (where this error occurs whether do_dssp is the only job on the node or not): The same analysis works fine on another machine. The cluster I use is made of Hewlett-Packard ProLiant DL145 G2 AMD Opteron Model 246 nodes. The nodes contain two AMD opteron 2.4GHz cpus and 4*1GB memory. I thank you very much for any suggestions! Do the analysis piecewise... trjconv to break the .trr into chunks, and now you can even do the analysis in parallel. Could be a nice application for pushing parallel filesystems to its limits! Perhaps it could be implemented in upcoming gromacs versions, something like mpich wrapper for certain analysis tools. Mark ___ gmx-users mailing listgmx-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 Grettings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ gmx-users mailing listgmx-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
[gmx-users] do_dssp
Dear Gromacs users, As I am simulating many peptides in a box and do_dssp is only a wrapper for calling the program which works on pdb files, I was of the view that it will not take PBC into consideration and will probably not assign beta sheets very well. Please correct me if I am wrong. If this is the case, Is there any other way to assign secondary structure to such a system? Regards, Gurpreet Singh On 12/21/06, singh [EMAIL PROTECTED] wrote: Dear Gromacs users, I have simulated 12 peptide fragments in a cubic box and I want to use do_dssp for secondary structure analysis but I am not sure whether Periodic boundary conditions will be taken in account during assignment (particularly for assigning betasheets). Regards, Gurpreet Singh - University of Dortmund Department of Chemistry Physical Chemistry I - Biophysical Chemistry Otto-Hahn Str. 6 D-44227 Dortmund Germany Office: C1-06 room 176 Phone: +49 231 755 3916 Fax: +49 231 755 3901 - But there could be a problem for beta sheets between different chains and for crystal contacts. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se Hi Gurpreet, The common message is don't worry, mdrun doesn't write broken molecules. So you're secondary structure will not be affected by periodic boundary conditions. Cheers, Tsjerk ___ gmx-users mailing listgmx-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
Re: [gmx-users] do_dssp
singh wrote: Dear Gromacs users, As I am simulating many peptides in a box and do_dssp is only a wrapper for calling the program which works on pdb files, I was of the view that it will not take PBC into consideration and will probably not assign beta sheets very well. Please correct me if I am wrong. If this is the case, Is there any other way to assign secondary structure to such a system? many programs do that, e.g. pymol, or VMD, but you have to verify for yourself. dssp does not take PBC into account. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-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
[gmx-users] do_dssp
Dear Gromacs users, I have simulated 12 peptide fragments in a cubic box and I want to use do_dssp for secondary structure analysis but I am not sure whether Periodic boundary conditions will be taken in account during assignment (particularly for assigning betasheets). Regards, Gurpreet Singh - University of Dortmund Department of Chemistry Physical Chemistry I - Biophysical Chemistry Otto-Hahn Str. 6 D-44227 Dortmund Germany Office: C1-06 room 176 Phone: +49 231 755 3916 Fax: +49 231 755 3901 - ___ gmx-users mailing listgmx-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
[gmx-users] do_dssp, -map option
Dear users, I would like to have some delucidations about the -map option of the do_dssp routine. In the help file, it says File that maps matrix data to colors, and I guess it is an input file to be supplied in order to assign colors to the different ss elements. Is it right? And, if so, how that file has to be edited? Thanks in advance, Fabrizio ___ gmx-users mailing listgmx-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
[gmx-users] do_dssp with no output!
I have the same problem. Any suggestion??? DSSP variable is setup correctly, but nothing happens when I run do_dssp. It just freeze as Elena described. Thanks in advance, César.- ___ gmx-users mailing listgmx-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
[gmx-users] do_dssp : ssdump data
Where can I find the exhaustive list of one letter codes used from secondary structures? (H for helix, T for turn...) I looked at do_dssp.c to figure it out . the array map[]... semes to hold the relevant information, but I got very confused. Any help would be appreciated... Senthil ___ gmx-users mailing listgmx-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
Re: [gmx-users] do_dssp error
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Jahan, First, you must make sure you have the dssp program; it doesn't come with gromacs, but you can download it separately from: http://swift.cmbi.ru.nl/gv/dssp/ Secondly, if 'setenv' is not working you are not on a csh/tcsh shell. Try: export DSSP=/path_to_your_dssp_installation/dssp This should work if you are on a sh/bash shell. HTH, Miguel jahanshah ashkani wrote: Hi, I have a problem with do_dssp command. When I ran it, I found this fatal error ? DSSP executable /usr/local/bin/dssp does not exist. Then I used from setenv DSSP command, but I found this error ?setenv is not recognized as an internal or external command,..? I would be glad if you help me in this case. Thank you very much. Sincerely yours, Jahan Yahoo! Messenger with Voice. Make PC-to-Phone Calls http://us.rd.yahoo.com/mail_us/taglines/postman1/*http://us.rd.yahoo.com/evt=39663/*http://voice.yahoo.com to the US (and 30+ countries) for 2¢/min or less. ___ gmx-users mailing listgmx-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 - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: [EMAIL PROTECTED] www: http://www.ysbl.york.ac.uk/~mol/ ~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.1 (GNU/Linux) iD8DBQFEUHCSF6oOrDvhbQIRAszAAJ9qofxtTpvwqYZcKYmUFzoyy6/uJgCePeiu LzKSZcKBbttCO+r6pU5Uy6E= =jweu -END PGP SIGNATURE- ___ gmx-users mailing listgmx-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
Re: [gmx-users] do_dssp error
Thanks for your reply. I used from Gromacs on WindowsXP with command prompt. How can I change DSSP path in this environment? Thank you very much.Sincerely yours, JahanMiguel Ortiz Lombardia [EMAIL PROTECTED] wrote: -BEGIN PGP SIGNED MESSAGE-Hash: SHA1Hi Jahan,First, you must make sure you have the dssp program; it doesn't comewith gromacs, but you can download it separately from:http://swift.cmbi.ru.nl/gv/dssp/Secondly, if 'setenv' is not working you are not on a csh/tcsh shell. Try:export DSSP=/path_to_your_dssp_installation/dsspThis should work if you are on a sh/bash shell.HTH,Migueljahanshah ashkani wrote: Hi, I have a problem with do_dssp command. When I ran it, I found this fatal error ? DSSP executable does not exist. Then I used from setenv DSSP command, but I found this error ?setenv is not recognized as an internal or external command,..? I would be glad if you help me in this case. Thank you very much. Sincerely yours, Jahan Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+ countries) for 2¢/min or less. ___ 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- --Miguel Ortiz LombardíaCentro de Investigaciones OncológicasC/ Melchor Fernández Almagro, 328029 Madrid, SpainTel. +34 912 246 900Fax. +34 912 246 976email: [EMAIL PROTECTED]www: http://www.ysbl.york.ac.uk/~mol/~~~Je suis de la mauvaise herbe,Braves gens, braves gens,Je pousse en libertéDans les jardins mal fréquentés!Georges Brassens-BEGIN PGP SIGNATURE-Version: GnuPG v1.4.1 (GNU/Linux)iD8DBQFEUHCSF6oOrDvhbQIRAszAAJ9qofxtTpvwqYZcKYmUFzoyy6/uJgCePeiuLzKSZcKBbttCO+r6pU5Uy6E==jweu-END PGP SIGNATURE-___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php New Yahoo! Messenger with Voice. Call regular phones from your PC and save big.___ gmx-users mailing listgmx-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
