[gmx-users] do_dssp fatal error

Paymon Pirzadeh ppirzade at ucalgary.ca
Wed Oct 6 17:56:55 CEST 2010

To investigate the secondary structure I issued the do_dssp command as

 do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s
AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump

Then, I had read somewhere in the archive to select the alpha carbons
for accurate results, and I did, but the following error pops up:

Program do_dssp_d_mpi, VERSION 4.0.5
Source code file: do_dssp.c, line: 471

Fatal error:
Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na
ddOD7WLo ddmJPpUs > /dev/null 2> /dev/null

The cluster technician tested the forwarded procedure (appended below),
and it seems that the backbone structure has some problems. I will be
appreciated if one tells me is it really a problem with backbone or sth
with installation of dssp. If problem is with backbone, then why pdb2gmx
did not issue any warnings?

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