jmsstarlight at gmail.com
Tue Jan 15 13:13:07 CET 2013
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 .
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
Failed to execute command: Try specifying your dssp version with the
and I dont know how to fix it.
I'm using gromacs-4.6-beta 3 with dssp 2.0.3
2013/1/15 Justin Lemkul <jalemkul at vt.edu>:
> On 1/15/13 3:19 AM, James Starlight wrote:
>> Dear Gromacs Users!
>> I'd like to know if it's possible to obtain some values from do_dssp
>> except the graph diagrams of the ss dynamics ? For example I wounder
>> to know values of how many residues were in helix, sheet or coil
>> conformation during my simulation ?
> That's what scount.xvg contains.
>> By the way during analysis of the graph obtained from do_dssp produced by
>> do_dssp -s minim -f md_noPBC.xtc -o ./results/dssp
>> I didnt found legend on the x and y (time, number of residue) as well
>> as color scheme of particular ss element. How I can add it to that
>> graph ?
> I don't understand what you're asking here.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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