do_dssp calls external dssp program to do the calculation which is slow
but shall not take "lot of time"
. For fast execution of DSSP, you may consider using my_dssp.
Go to your gromacs source directory:
./configure
make
cd src/contrib
make my_dssp
Regards,
Yang Ye
On 2/7/2007 5:41 PM, sangeeta wrote:
Dear Mark,
Previously you suggested to try running dssp independently on a single
snapshot extracted from the trajectory,I took the snapshot of the protein
after 1ns with the command
trjconv -f md.xtc -s md.tpr -o time_1000ps.pdb -dump 1000
then ran dssp program by using the command
dsspcmbi time_1000ps.pdb DSSPtime_1000ps.pdb
The program ran successfully,but again when I used
do_dssp -s md.tpr -f time_1000ps.pdb
the program is taking lot of time.I do not understand where I am making the
mistake, please help and give me solution.Thanks in advance.
regards
SANGEEA
On Mon, 5 Feb 2007 18:56:22 +1100 (EST), Mark Abraham wrote
Dear All,
I want to analyze the secondary structure of a protein after a
10ns
simulation run. Previously I faced difficulty in running dssp program,So
in
order to give a test run I ran the do_dssp program for 100ps
trajectory
only for a protein containing 130 residues.The program continued for
more
than 4 days, yet it was not completed, Only it was giving the
intermediate
files namely ddEyzdyf,ddKDeKnT etc, except that no ouput were produced.I
do
not understand how long it will take or whether I am encountering any
problem , in the manual it is mentioned that the program is very slow,
But
I am not getting any idea whether the time it is taking is normal, or I
am
facing some problem.
Try doing it on one structure in a trajectory by using trjconv
appropriately. If it's not done in ten minutes on a machine under
five years old, then you have a problem.
Also try running dssp independently on a single snapshot extracted from
your trajeotry and put into pdb format (by specifying .pdb suffix on
output file for trjconv). If you can't do that, then the problem has
nothing to do with gromacs.
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Open WebMail Project (http://openwebmail.org)
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
