VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 14 2012 - 12:31:18 CDT

Hi,
  Which version of VMD are you using? I wonder if there's something
amiss with the mol2 plugin in your VMD installation, in terms of the
data it originally read in. I don't expect the PDB plugin to do anything
unusual on writing a new file. If you query those atoms with an atom
selection right after loading your mol2 file, do those fields look correct,
or do they exhibit the same problem that you see in the PDB?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 14, 2012 at 06:15:22PM +0100, Francois Martz wrote:
> 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. 

-- 
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