Hi
already done the MD production so I want to analyse the helical
>>> structure of my protein by using do_dssp program.The command is like
>>> below :
>>>
>>> do_dssp -s md_18.tpr -f md_18.trr -n mainchain.ndx -sc
>>> dssp_scount.xvg -a dssp_area.xvg -ta dssp_totarea.xvg -aa
>>> dssp_averarea.xvg
>>>
>>> but after i run the command the result show like :
>>>
>>> Reading file md_18.tpr, VERSION 4.5.5 (double precision)
>>> Reading file md_18.tpr, VERSION 4.5.5 (double precision)
>>> Segmentation fault (core dumped)
>>>
>>>
>>> I already install the dssp program
Version 4.5.5 requires an old version of DSSP that is no longer available (or is otherwise very hard to find). Upgrade to a new Gromacs version for analysis, one that will let you select the version of DSSP that you have.
Justin, what do you mean with hard to find? Aren't we talking about the DSSP versions available from this side? http://swift.cmbi.ru.nl/gv/dssp/ Both old and new DSSP are offered for download there.
Indeed, I misspoke slightly. DSSP is of course easy to find but it is difficult for novice users to understand the differences in version and what is necessarily required by Gromacs. Using the newest version of everything is of course generally preferred, but if people need/want to use old versions of things, there are considerations that are non-obvious.
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