VMD-L Mailing List

From: Ashish .Chauniyal (ashishchauniyal_at_gmail.com)
Date: Fri Apr 25 2014 - 06:14:22 CDT

Hi all,

In continuation from the last mail, i was able to generate and view two
.pdb files consisting of two types of atoms only. As Josh had pointed I
did exactly the same to combine the two files into one.
I tried this on a dummy run and it worked , however now when i am trying to
join to .pdb files consisting of 256000 atoms each, it says "Segmentation
fault (Core Dumped)"

My tcl script looks like this.

set solute [mol new leftside.pdb]
set solvent [mol new rightside.pdb]
set combined [::TopoTools::mergemols "$solute $solvent"]
topo writelammpsdata data.composite atomic

On Wed, Apr 16, 2014 at 9:34 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Mergemols takes a list argument. Should be:
> set combined [::TopoTools::mergemols [list $solute $solvent]]
> -Josh Vermaas
>
>
> On 04/16/2014 10:07 AM, Ashish .Chauniyal wrote:
>
> Dear all,
>
> I have to merge two .pdb files into one and make a lammps data file out
> of it. Please can someone find what am I doing wrong, my TCL console says
> invalid command name "x" this x keeps on changing and I cant pinpoint where
> the error is. Here is the code.
>
>
> #topotools is already included
>
> mol new MG.xyz
> set Cusel [atomselect top "name H"]
> $Cusel set name Cu
> $Cusel set mass 63.54
> set Zrsel [atomselect top "name He"]
> $Zrsel set name Zr
> $Zrsel set mass 91.224
>
> set all [atomselect top "all"]
> $all writepdb leftside.pdb
>
> $all moveby {80.0 0.0 0.0}
> $all writepdb rightside.pdb
>
> #merging the two files
> set solute [mol new leftside.pdb]
> set solvent [mol new rightside.pdb]
> set combined [::TopoTools::mergemols "$solute $solvent"]
>
> $combined writepdb combine.pdb
> topo writelammpsdata data.composite atomic
>
>
>