[gmx-users] do_dssp

[James Starlight]

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 .

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

James

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
>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists