[gmx-users] dssp problem

[Anton Feenstra]

smith wrote:

>   
> dear users and feenstra,
> 
> The ddspcmbi exe is produced after compiling ./dsspcmbigcc for linux nad it works fine for one pdb file.
> ./dsspcmbi pdbsourcefile outputfilename 
> 
> But when I use the command do_dssp it does not produce a output still. dont know why.I have a set the environment variable as 
> setenv DSSP /usr/local/bin/dsspcmbi

 From your explanation, it appears your dsspcmbi binary may be found at:
/usr/local/bin/dsspcmbi/dsspcmbi so you may need to set
# setenv DSSP /usr/local/bin/dsspcmbi/dsspcmbi
in order for do_dssp to work. Otherwise, you may need to check the output
messages of do_dssp, it may print the exact command line it uses for dssp,
so you may look if options match those of your dsspcmbi version. If not,
you may modify the do_dssp code to fix it (or ask someone to do that).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
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