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Problem with executing do_dssp in gromacs

I am new to gromacs and using gromacs 4.6.5 and dssp-2.0.4. When I am running these commands:

export DSSP=/usr/local/bin/dssp
do_dssp -s md_0_1.tpr -f md_0_1_noPBC.xtc -o dssp.xvg -ver 2

I am getting this error:

dssp cmd='/usr/local/bin/dssp -na dd31ZWbc ddI6at3a > /dev/null 2> /dev/null'
Reading frame       0 time    0.000   
Back Off! I just backed up dd31ZWbc to ./#dd31ZWbc.1#

-------------------------------------------------------
Program do_dssp, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/tools/gmx_do_dssp.c, line: 669

Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver option.

I don't know how to fix it. Please help me?

Thanks

do_dssp
• 8,201 views • link
updated by zx8754 zx8754 • written by BI BI

2 answers

Thank you everyone . Finally my do_dssp is working. Problem was with the binary file 'dssp-2.0.4-linux-amd64' .
Now I have installed 'dssp-2.0.4-linux-i386' and it is working fine.
Cheers!!

• 1 views • link
written by BI BI

I'm not sure, the commands look ok.

However, have you tried using the commands below, since my guess would be that you are not working in bash?

setenv DSSP /usr/local/bin/dssp
do_dssp -s md_0_1.tpr -f md_0_1_noPBC.xtc -sc dssp.xvg

Edit: Oh, and an after-thought, you're using -o for output, which will write xpm file. If you want a xvg file, then use -sc flag for output.

• 0 views • link
written by ballisticws • ballisticws

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