[gmx-users] Problem executing do_dssp in gromacs

[Aarti rana]

After issuing command as you asked:

>echo $DSSP
>/usr/local/bin/dssp

And yes I downloaded the "dssp-2.0.4-linux-amd64
<ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64>" file from
dssp site.


On Mon, Feb 16, 2015 at 11:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> After looking at this a bit more closely for someone else who asked the
> same question, your clue is here:
>
> dssp cmd='/usr/local/bin/dssp -na dd31ZWbc ddI6at3a > /dev/null 2>
> /dev/null'
>
> For some reason your do_dssp command is triggering version 1 syntax.  A
> version 2 command should be something like:
>
> dssp cmd='/usr/local/bin/dssp -i ddYB5REk -o ddxi1TAx > /dev/null 2>
> /dev/null'
>
> Note the difference in -i/-o vs. -na.  This is the nature of the problem
> when dealing with different versions.  Somehow there's a disconnect between
> your DSSP version or the command you're telling us you're issuing.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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