VMD-L Mailing List

From: Frank Zack (frankzack123_at_REMOVE_yahoo.de)
Date: Mon Sep 21 2015 - 07:06:02 CDT

Hi All,
I've encountered a problem trying to merge 2 different moleculues (All-atom representation, class2 force-field) into a single one...I've provided both *.psf and *.pdb files for each molecule (reading the molecule with topo readlammpsdata, creating psf by "animate write psf mol1.psf" and creating pdb with "set m1 [atomselect top all]; $m1 writepdb mol1.pdb"...)
Then I proceeded according to the tutorial:
package require topotools 1.1
# load to be merged molecules into VMD
set midlist {} set mol [mol new part1.psf waitfor all]
mol addfile part1.pdb
lappend midlist $mol set mol [mol new part2.psf waitfor all]
mol addfile part2.pdb lappend midlist $mol
# do the magic
set mol [::TopoTools::mergemols $midlist]
animate write psf merged.psf $mol
animate write pdb merged.pdb $mol 
It seems to work. But if I now try to write a lammps data-file (topo writelammpsdata) there's only 1 bond-type, 1 angle-type, 1 dihedral-type and 1 improper-type...As a consequence my bonds section looks like
1 1 1 10
2 1 1 4
3 1 1 2
..
268717 1 268816 268818
268718 1 268816 268819
,where the 2nd column represents the bond-type. As you can see the bond-type is 1 for all bonds, irrespective of the actual bond-types as defined in the original lammps data-files (and psf-files, i guess). Is mergemol intended to work like that or did i make a mistake?
The only way I can think of "reconstructing" the proper types is to write my own script and change the bond-,angle-,dihedral- and improper-types according to the corresponding atom-types. However I'm not sure yet if mergemols re-sorts the atom-types or if it just keeps the original ones...

Is there an easy way to avoid scripting? Or can i read multiple data-files into lammps? Do you know if moltemplate can do this?Any help will be highly appreciated, thanks in advance.
regards,frank.