[gmx-users] DSSP

shahid nayeem msnayeem at gmail.com
Tue May 18 13:46:37 CEST 2010

After posting this mail I did some google search and after changing the
executible name to dssp I moved it in /usr/local/bin/ After this when I did
do_dssp it starts running asks to select a group I choose main chain 5, then
it generates some intermediate file and gives error as segmentation fault. I
though this problem was because of the executible in /usr/local/bin/ and
rest of file in another directory say /home/shahid/software/dssp/. For this
first I set the path in ~/.bascrc as
DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the
same intermediate file generated backing up the previous one. Then I moved
all the files of dssp directory to /usr/local/bin/ and then tried to run
do_dssp I am in the same situation.
waiting for your help
shahid nayeem

On 5/18/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> shahid nayeem wrote:
>> Dear All
>> I downloaded dsspcmbi.tar.gz, and compiled  using command
>> ./DsspCompileGCC as given in Readme.txt file. when I try to run
>> do_dssp command in gromacs I get error
> Well, what happened?
>> Fatal error:
>> DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)
>> I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I
> It won't be there unless you put it there and you have re-named it.  I
> believe the default name of the dssp program is "dsspcmbi," which you need
> to change when you move the executable.
> http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
> -Justin
> even tried dsspcmbi.zip file but again I got the same error. I
>> compiled dssp as root. Now what shoul I do in order to run do_dssp
>> comand of gromacs.
>> Shahid nayeem
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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