AMBER Archive (2003)

Subject: Re: mm-pbsa problem & possible solution

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Thu Jan 30 2003 - 11:22:39 CST

Dear Thomas,

> 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.

You are right. This is not correct. Thank you for pointing this out.

>
> We think that changing the line to:
>
> $line =~ /(ATOM +|HETATM +)(\d+ +)(\S+)( +)(\S+)(
> +\d+)( +-?\d+\.\d+[ \-]+\d+\.\d+[ \-]+\d+\.\d+)/;
>
> solves the problem.

Not completely - instead of having a " " or a "-" within the [...], you
might also have a digit there. I will put a patch to the amber web page
which uses the fact that the pdb format has fixed columns instead of
space-separated columns.

Thank you again

Holger 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++