Hi modllers,
I am trying to use win version of modeller. I have two problems:
1. Although example files run fine, I get this error message with my proteins: check_337E>structure not read in
2. I have failed to get a log/out file.
Any help will be appreciated.
Regards, S. Zarina
__________________________________________________ Do You Yahoo!? Yahoo! - Official partner of 2002 FIFA World Cup http://fifaworldcup.yahoo.com
Hi,
In mod.bat file, add ' > %1.log' to the last line:
%MODINSTALL6v2%\bin\modeller6v2 %1 %2 %3 %4 %5 %6 %7 %8 %9 > %1.log
For reading in your structures/templates from the directory where you start the program, have the following line in your .top file:
SET ATOM_FILES_DIRECTORY = './'
Cheers,
Mensur
>Hi modllers, > >I am trying to use win version of modeller. I have two >problems: > >1. Although example files run fine, I get this error >message with my proteins: >check_337E>structure not read in > >2. I have failed to get a log/out file.
=========================================================================== | Mensur Dlakic, PhD | Tel (734) 764-3554 | | Department of Biological Chemistry | Fax (734) 615-3397 | | University of Michigan Medical School | http://www.umich.edu/~mensur/ | | 5416 Medical Science I | http://myprofile.cos.com/mensur | | Ann Arbor, MI 48109-0606 | E-mail mensur@umich.edu | ===========================================================================
On Mon, Jun 24, 2002 at 01:56:30AM -0700, Shamshad Zarina wrote: > Hi modllers, > > I am trying to use win version of modeller. I have two > problems: > > 1. Although example files run fine, I get this error > message with my proteins: > check_337E>structure not read in >
Check to make sure the numbering of your atoms and residues in your pdb matches your alignment file. E.g. if you have missing residues in your pdb, you must gap them out in the alignment file; also, make sure that if you are missing residues at the N terminus of the pdb, you have specified the starting residue in the pdb to be read (and not 1). Chain misreference can also cause the structure to be not read in, as in omitting a chain identifier in your alignment file that exists in the pdb.
> 2. I have failed to get a log/out file. > > Any help will be appreciated. > > Regards, > S. Zarina > > __________________________________________________ > Do You Yahoo!? > Yahoo! - Official partner of 2002 FIFA World Cup > http://fifaworldcup.yahoo.com
participants (3)
-
Mensur Dlakic -
Peter C. Lai -
Shamshad Zarina