Hi,
I'll try out the 2.1.0 with do_dssp and see if there's something
problematic with this new version. Good thing you brought it up.
Erik
On Mar 1, 2013, at 6:24 PM, Miguel Ángel Mompeán García wrote:
Hi Erik,
Since I read in the mailing list that nobody had asked about 2.1.0,
just
decided to try an older version before going into the trouble
itself...
Kind of coward, I know, but the troubles with that version are already
reported so that I thought things would be easier :)
Thank-you a lot for your comments
2013/3/1 Erik Marklund <er...@xray.bmc.uu.se>
Interesting. Perhaps there are new issues with 2.1.0. Did you try to
execute the command yourself?
Erik
On Mar 1, 2013, at 5:16 PM, Miguel Ángel Mompeán García wrote:
The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and it
works
fine. However, when converting the xpm to eps I get I plot very
small,
where one barely can see the colour code and the legend is sooo
big. Does
anyone know how to change that?
2013/3/1 Erik Marklund <er...@xray.bmc.uu.se>
What happens if you execute the command (/usr/local/bin/dssp/ -i
ddQ3PqtX
-o ddR1HavD) in your terminal?
Erik
On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:
I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error
you
got:
dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/
null 2>
/dev/null'
Reading frame 0 time 0.000
Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1#
------------------------------****-------------------------
Program do_dssp, VERSION 4.6
Source code file: /usr/local/bin/gromacs-4.6/****
src/tools/gmx_do_dssp.c,
line:
667
Fatal error:
Failed to execute command: Try specifying your dssp version with
the
-ver
option.
How can I fix that?
Thanks
2013/1/15 James Starlight <jmsstarli...@gmail.com>
Justin, thanks both options works perfect.
James
2013/1/15 Justin Lemkul <jalem...@vt.edu>:
On 1/15/13 7:13 AM, James Starlight wrote:
Justin,
I want to obtain timescale on X as well as number of
residues on Y
on the xmp graph . By default that graph has not legend so
it's hard
to analyse it .
The legends are printed in the .xvg header. I've never had a
problem
plotting its contents (though they are usually somewhat
unclear when
plotted
together) with xmgrace -nxy scount.xvg
By the way have you forced with some problems with dppc ?
Simetimes
I've obtain error like
There are 286 residues in your selected group
dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/
null 2>
/dev/null'
Reading frame 0 time 0.000
Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1
Fatal error:
Failed to execute command: Try specifying your dssp version
with the
-ver option.
and I dont know how to fix it.
I'm using gromacs-4.6-beta 3 with dssp 2.0.3
Since dssp changed its command line options, Gromacs had to
adapt as
well.
The error tells you to use the -ver option; you should do so.
Version 2
should be the default, so check to make sure you're actually
using
that
version and not the old dssp.
-Justin
--
==============================****==========
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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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