http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php CHARMM forums: setup, I/O, and basic questions CHARMM Forums - UBB.threads(tm) http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27872#Post27872 Posted by zzlai:
Thanks!! Now the values are reasonable.]]> Thu, 07 Jul 2011 20:20:17 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27867#Post27867 Posted by lennart:
Note that this only works for a SINGLE file from the Protein Data Bank, not for the entire PDB.]]> Thu, 07 Jul 2011 17:11:46 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27865#Post27865 Posted by rmv:
The proper format is given above. ]]> Thu, 07 Jul 2011 12:08:58 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27853#Post27853 Posted by rmv:
See the detailed description of @@ syntax with the SET command, a bit over halfway through miscom.doc ]]> Tue, 05 Jul 2011 12:31:44 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27840#Post27840 Posted by rmv:
What happens when you start with the 2nd PDB file then? The fact that one of the files can be read doesn't necessarily mean that all of the files are okay. There must be some warning or error messages associated with this in the output log file, ]]> Sun, 03 Jul 2011 13:04:44 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27804#Post27804 Posted by apredeus:
that was MMTSB's fault apparently. Sorry about the confusion and thanks for the help. ]]> Wed, 29 Jun 2011 14:49:00 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27795#Post27795 Posted by rmv:
It's a major error, and the core files are memory dumps triggered by the failure. It may be a source code bug, or possibly related to how the program was compiled. There isn't enough context to say a lot more. It might be informative to run the ]]> Wed, 29 Jun 2011 09:26:54 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27780#Post27780 Posted by lennart:
questions I believe, not doubts :)]]> Tue, 28 Jun 2011 11:47:30 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27772#Post27772 Posted by rmv:
The message does seem to imply that some aspect of the triad SEGID RESID ATOM (a.k.a. TYPE) is not correct. Or it could just be a symptom of some earlier, more serious problem that may have corrupted the PSF. It's not always the last error that's t]]> Mon, 27 Jun 2011 20:24:27 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27733#Post27733 Posted by apredeus:
[quote]In my pdb file, resid starts from 10, not 1 and thus CHARMM can not recognize my pdb file and refuse generate pdb/psf file in CHARMM format for me. Then I have to change the first resid to 1 to make CHARMM produce pdb/psf file.[/quote] this]]> Fri, 24 Jun 2011 04:09:36 CDT