sangeeta kundu wrote:
Dear All,
I do not know whether I am interrupting you again and again by
asking the same question, but I am helpless , I can not detect my fault,
When I run the program DSSP it works fine, but while executing do_dssp
or my_dssp (as suggested by Yang) the program seems to be never ending,
intermediate files are prepared for some time, but I never got any .xpm
files, I can not understand whether my system is not working, or I am
making any mistake, but all the other programs of Gromacs like pdb2gmx,
editconf , genbox, grompp, mdrun etc are going on successfully, problem
lies only in case of dssp, I was suggested by Mark to try dssp
independently on a single snapshot extracted from the trajectory, I
took the snapshot of the protein after 500ps with the command *trjconv
-f md.xtc -s md.tpr -o time_500ps.pdb -dump 500*
(I think the command is correct, if not I earnestly request you to
rectify my mistake), When I ran do_dssp on this single structure I
waited for 3 days, but it did not finish and seems to be neverending,
then I killed the program, In order to get that particular coloured plot
of secondary structure vs time which method should I adopt? Seeking your
help and thanks in advance.
It sounds like do_dssp is having problems calling dssp. We can't help
you much further. Try a new computer system, or work out a way to call
dssp "by hand" for the structures you care about.
Mark
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