VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Feb 23 2018 - 04:02:27 CST

On Fri, Feb 23, 2018 at 10:34 AM, Manoj Dhiman <manoj1733_at_gmail.com> wrote:

> Dear users,
>
> I am trying to solvate a molecule by following axel's tutorial
> https://sites.google.com/site/akohlmey/software/
> topotools/topotools-tutorial---various-tips-tricks. The strange thing is
> that molinfo command transfers the information as it is to the top
> molecule, without changing the atom type integer to a new value. In detail,
> the solute molecule with atom, different from oxygen and hydrogen, has atom
> type integer equal to 1 in its pdb and psf file and the water molecule has
> 1 and 2 for O and H, after merging though the total number of atoms,
> angles, bonds and dihedral are correct but atom types are only 1 and 2,
> rather than 1 2 and 3. HELP!!!
>

​this is deliberately so, since TopoTools cannot know whether you want to
retain the atom types or modify them. since any kind of guess is likely to
fail from some cases, TopoTools does nothing and requires you to make sure
that you reset atom types properly *before* attempting to merge. this is
easily done with VMD scripting.

axel.

>
> --
> *Regards:*
> *Manoj Dhiman*
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.