[gmx-users] about command do_dssp

[Justin Lemkul]

On 4/28/13 4:07 AM, aixintiankong wrote:
> Dear prof.
>       i use the the gromacs 4.6.1 on my centos6.4 system. After MD ending, i use the do_dssp -f md.xtc -s md.tpr  -o secondary-structure.xpm -sc secondary-structure.xvg to analyze the secondary structrue of the protein.
>      when i perform the do_dssp and select MainChain , the fatal erros come out as follow;
> Fatal error:
> DSSP executable (usr/local/bin/dssp) does not exist (use setenv DSSP)
> it is means thant  i don't install do_dssp? however, when i perform the " which do_dssp" at the terminal,  the termianl output "/usr/local/gromacs-4.6.1/bin/do_dssp. i don't know where is wrong. should i reset the environment of the do_dssp?

do_dssp and dssp are different executables.  Please read the following:

http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp

-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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