Dear AMBER users,
We have used the MM-PBSA script to process AMBER7
trajectories and found that the script fails when the
coordinates contain lines like:
ATOM 4136 CB GLN 253 -2.782-100.885 86.358
where the x and y coordinate columns are separated by a
minus sign and no whitespaces.
After some error hunting we presume the problem lies in
line 1316 of mm_pbsa.pl:
$line =~ /(ATOM +|HETATM +)(\d+ +)(\S+)( +)(\S+)(
+\d+)( +-?\d+\.\d+ +-?\d+\.\d+ +-?\d+\.\d+)/;
because it expects the coordinate columns to be seperated
by at least one whitespace and zero or more minus signs.
We think that changing the line to:
$line =~ /(ATOM +|HETATM +)(\d+ +)(\S+)( +)(\S+)(
+\d+)( +-?\d+\.\d+[ \-]+\d+\.\d+[ \-]+\d+\.\d+)/;
solves the problem.
Has anybody experienced the same problem with MM_PBSA runs?
I am no perl expert, so please correct me if the changes
made are not reasonable.
Kind Regards,
Thomas Steinbrecher
Received on Thu Jan 30 2003 - 07:51:57 PST
