[gmx-users] DSSP

[Aishwarya Dhar]

Dear Sir,

Now, I have used one single frame by using this command and tried do_dssp
trjconv -f md.xtc -o md_1_frame.xtc -b 0 -e 0
do_dssp -s  md.tpr -f md_1_frame.xtc -o ss.xpm   -sc scount.xvg

Now  I get the following  and this is still going on

here are 91 residues in your selected group
dssp cmd='/usr/local/bin/dssp -i ddlpFBB7 -o ddZv4Q6o > /dev/null 2>
/dev/null'
Reading frame       0 time    0.000
Back Off! I just backed up ddlpFBB7 to ./#ddlpFBB7.1#


Thanks

Sincerely

Aishwarya Dhar

On Tue, Mar 21, 2017 at 5:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/21/17 5:13 AM, Aishwarya Dhar wrote:
>
>> Following procedure I have used
>> 1. Downloaded  http://swift.cmbi.ru.nl/gv/dssp/
>> dssp-2.0.4-linux-i386 and renamed it dssp
>>
>> 2.made dssp  executable  and moved it to usr/local/bin
>>
>> 3.Then ran the command from the current location where the tpr and trr
>> files are present do_dssp -s  md.tpr -f md.trr -o ss.xpm  -ver 2.0
>>
>> 4.There are 91 residues in your selected group dssp
>> cmd='/usr/local/bin/dssp
>> -i ddixopnV -o dd4YitS9 > /dev/null 2> /dev/null'
>> trn version: GMX_trn_file (single precision)
>> Reading frame       0 time    0.000
>> Back Off! I just backed up ddixopnV to ./#ddixopnV.1#
>>
>> It seems that the run is going on for two weeks and dssp analysis couldnt
>> be done
>>
>>
> How many frames did you save?  do_dssp is a very slow program (it's just a
> wrapper to call dssp) and if you have tons of frames, it will take a long
> time. You can always list the files in the directory in which do_dssp is
> operating and you should see temporary files prefixed with "dd" being
> created and over-written.
>
> You can always test whether or not do_dssp is working by passing it a
> single frame to -f, rather than waiting for a very expensive .trr file to
> be processed in full.
>
> -Justin
>
>
>>
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>> Thanks
>>
>>
>>
>>
>> Sincerely
>>
>> Aishwarya Dhar
>>
>>
> --
> ==================================================
>
> 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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