[gmx-users] do_dssp

[James Starlight]

Justin, thanks both options works perfect.


James

2013/1/15 Justin Lemkul <jalemkul at 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
>
> --
> ========================================
>
> 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
>
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