Re: [gmx-users] make_ndx and residue name length
Thanks... I think I'll just get the CVS make_ndx and integrate that into my current CVS copy, rather than try to hunt the different locations down! - Original Message From: Berk Hess <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Wednesday, September 5, 2007 11:22:15 AM Subject: RE: [gmx-users] make_ndx and residue name length >From: Alan Dodd <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: gmx-users@gromacs.org >Subject: [gmx-users] make_ndx and residue name length >Date: Tue, 4 Sep 2007 10:55:07 -0700 (PDT) > >The maximum permissible residue name length is at least 5 characters long >for a tpr or gro, but the length of residue name permitted by make_ndx is >only 4 characters. And of course, pdb should have only 3 characters. >While I can change the names in a gro or a pdb quite quickly and easily, is >there a way to change this in a tpr? I'm currently getting around the >problem by converting tprs to pdbs for use by make_ndx, but it's messy... >Alternatively, is there any fundamental reason why the string in make_ndx >inputs is less than that for files, or can I safely bump up the relevant >digit in the code and recompile? I did not know about this check, but now that I have looked at the code it seems I have programmed it myself a decade ago. The only reason for a limit was/is programming convenience. You can change it and recompile, but be careful that the number 5 occurs at multiple places in make_ndx.c I was too lazy to remove the limit, so I have set it to 30 now in the CVS (and also put defined this number in one place only). Berk. _ Live Search, for accurate results! http://www.live.nl ___ 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 Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 ___ 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] make_ndx and residue name length
From: Alan Dodd <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] make_ndx and residue name length Date: Tue, 4 Sep 2007 10:55:07 -0700 (PDT) The maximum permissible residue name length is at least 5 characters long for a tpr or gro, but the length of residue name permitted by make_ndx is only 4 characters. And of course, pdb should have only 3 characters. While I can change the names in a gro or a pdb quite quickly and easily, is there a way to change this in a tpr? I'm currently getting around the problem by converting tprs to pdbs for use by make_ndx, but it's messy... Alternatively, is there any fundamental reason why the string in make_ndx inputs is less than that for files, or can I safely bump up the relevant digit in the code and recompile? I did not know about this check, but now that I have looked at the code it seems I have programmed it myself a decade ago. The only reason for a limit was/is programming convenience. You can change it and recompile, but be careful that the number 5 occurs at multiple places in make_ndx.c I was too lazy to remove the limit, so I have set it to 30 now in the CVS (and also put defined this number in one place only). Berk. _ Live Search, for accurate results! http://www.live.nl ___ 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] make_ndx and residue name length
The maximum permissible residue name length is at least 5 characters long for a tpr or gro, but the length of residue name permitted by make_ndx is only 4 characters. And of course, pdb should have only 3 characters. While I can change the names in a gro or a pdb quite quickly and easily, is there a way to change this in a tpr? I'm currently getting around the problem by converting tprs to pdbs for use by make_ndx, but it's messy... Alternatively, is there any fundamental reason why the string in make_ndx inputs is less than that for files, or can I safely bump up the relevant digit in the code and recompile? Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. http://mobile.yahoo.com/go?refer=1GNXIC ___ 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