Re: Merging the two files......

From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Jun 17 2014 - 10:44:36 CDT

and why do you say this is wrong, have you been unable to use it for your
next steps?

The PDB format was made with apparently very little (if any) thought
towards flexibility. As a result, it has a fixed number of columns for
each piece of information, rather than a special separating character.
 Since 5 columns are given to the atom number you can't go past 99999. So
the solution to this is to start using alphabetic characters. I think
you'll find that this works fine for your purposes, and only very old
programs might have a problem reading those in.

Another problem with these fixed columns is that residue and atom names can
only be so many characters, leading to very obfuscated names in many cases,
and a lot of unintentional overlap when mixing forcefields.

On Tue, Jun 17, 2014 at 11:00 AM, Gurpreet Kaur Dhindsa <el2275_at_wayne.edu>
wrote:

> Dear all,
> I am trying to merge two different files, one contains 92000 atoms and the
> other one has
> 40000 atoms. I am using these commands in VMD
> ::TopoTools::mergemols [list 1 2]
>
> 1,2 are the number of my pdb files in VMD main window.
> At the end, I have total of 130000 atoms. VMD gives me the correct atom
> number till 99000
> but after that it starts giving me some type of alphabets.
>
> ATOM 99998 H1 TIP3W5762 -120.414 60.831 -4.134 0.00 0.00
> WT1 H
> ATOM 99999 H2 TIP3W5762 -121.121 60.076 -5.310 0.00 0.00
> WT1 H
> ATOM 186a0 OH2 TIP3W5764 -116.219 60.562 -10.104 0.00 0.00
> WT1 O
> ATOM 186a1 H1 TIP3W5764 -116.062 60.855 -11.001 0.00 0.00
> WT1 H
> ATOM 186a2 H2 TIP3W5764 -115.555 61.039 -9.593 0.00 0.00
> WT1 H
> ATOM 186a3 OH2 TIP3W5765 -122.951 57.343 13.115 0.00 0.00
> WT1 O
> ATOM 186a4 H1 TIP3W5765 -122.161 57.022 13.633 0.00 0.00
> WT1 H
>
> Can someone try merging the files with that number of atoms? Please give
> me your suggestions.
>
> Thanks,
> Gurpreet Dhindsa.
>
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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