[gmx-users] DSSP installation
spss4 at iacs.res.in
spss4 at iacs.res.in
Sat Dec 9 11:47:27 CET 2017
----- Message from João Henriques <joao.m.a.henriques at gmail.com>
Date: Sat, 9 Dec 2017 11:29:41 +0100
From: João Henriques <joao.m.a.henriques at gmail.com>
Reply-To: gmx-users at gromacs.org
Subject: Re: [gmx-users] DSSP installation
To: gmx-users at gromacs.org
> The output is telling you what is wrong. Gromacs doesn't support version
> Install either version 1 or 2. In fact, I didn't even know there was a
> version 3 of DSSP, where did you get it? It certainly isn't on the
> website (http://swift.cmbi.ru.nl/gv/dssp/).
> I tried with version 2 but same problem was there. I thought gromacs
> 2016.3 is the latest one thats why version 2 is not supported. So I
> downloaded version
> 3 from this link ftp://ftp.cmbi.ru.nl/pub/software/dssp/ . I am very
> new in this field. Please correct me if I am doing something wrong.
> sunipa sarkar
> On Fri, Dec 8, 2017 at 4:04 PM, <spss4 at iacs.res.in> wrote:
>> Hii all
>> I want to calculate the number of helical contain of protein. For that I
>> tried using DSSP-3.0.0(gromacs version is 2016.3). I have downloaded the
>> tar file and extracted it. Then place the dssp fiolder in /usr/local/bin
>> and exported the path to ./bashrc file
>> export DSSP=/usr/local/bin/dssp
>> Then when I was trying to use gmx do_dssp and select protein then the
>> following error comes
>> WARNING: You use DSSP version 3, which is not explicitly
>> supported by do_dssp. Assuming version 2 syntax.
>> dssp cmd='/usr/local/bin/dssp/ -i ddTLo4Hs -o ddP6o9VL > /dev/null 2>
>> trr version: GMX_trn_file (single precision)
>> Reading frame 0 time 0.000
>> Back Off! I just backed up ddTLo4Hs to ./#ddTLo4Hs.1#
>> Program: gmx do_dssp, version 2016.3
>> Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
>> Fatal error:
>> Failed to execute command: Try specifying your dssp version with the
>> Then I tried using the version -ver 3
>> But still the error comes.
>> Please help me to fix this problem.
>> Sunipa Sarkar
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----- End message from João Henriques <joao.m.a.henriques at gmail.com> -----
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