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.
regards
SANGEETA
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