VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Jan 19 2004 - 06:50:12 CST

Hi,

You should be able to use different segments for the hetatoms, so you'll
need to figure out that problem (or post the error messages).

If you want all of the hetatoms in the same segment you can change resid's
in VMD. You'd need an algorithm like this to fix them:

  select all hetatoms
  write selected atoms to pdb file
  load new molecule from saved pdb file
  loop over all residues:
    select a residue, then use $sel set resid $i to change id
    (be careful to avoid temporary resid conflicts)
  write to a new file

-Jim

On Mon, 19 Jan 2004, himanshu chandola wrote:

> hi everyone,
> i tried making a psffile from a molecule containing multiple
> chains with hetero atoms in different chains. So - i made a segment for
> each chain and placed the hetero atoms in one segment. Now - each hetero
> atom has a number placed according to its chain. So when i run psfgen - i
> get an error - that multiple id's for same atom.
>
> Any thing which i might been missing. I tried placing hetero atoms of each
> chain into different segments - but that gives results like some atoms
> having uninitialized coordinates - so i think it would be better to place
> all hetero atoms in one segment.
>
>
> thanks in advance,
>
> himanshu chandola
>
> iit delhi
>