VMD-L Mailing List

From: Francois Martz (francois.martz_at_icsn.cnrs-gif.fr)
Date: Wed Mar 14 2012 - 12:15:22 CDT

Dear all,

I have done a simple script to superimpose multiple (45) mol2 files on
the same structure.
To save results as pdb files it uses 'writepdb' command for each input
mol2 files.

But in 28 of the 45 pdb, few (between 2 and 4 on 51) lines are wrong
(like here the ATOM 21 line):
    
ATOM 19 H19 5202X**** -18.490 3.871 -9.493 0.00
0.00
ATOM 20 C20 0 X 0 -20.028 4.492 -8.167 0.00
0.00
ATOM 21 N21 -237X-251643850 -20.577 4.610 -6.911 0.00 0.00
ATOM 22 C22 62 X 62 -21.760 5.291 -7.080 0.00
0.00
ATOM 23 C23 0 X 0 -21.961 5.607 -8.475 0.00
0.00

It can be fixed by replacing '-251643850' by '0'.
But since I have to compute multiple files, I would like to understand
why 'writepdb' generates this, taking into account that all input mol2
files, are generated by one of my script and are equally formatted.

Thanks you,

Martz François.