From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Jan 16 2022 - 15:40:25 CST

This cannot work. The VMD solvate plugin expects CHARMM force field
settings and parameters and uses the CHARMM force field data to add solvent
molecules.
When you start from a LAMMPS data file, most of the required information is
lost during conversion, if it was available at all.

You have to use a different approach, e.g. you could try the topotools
plugin or use LAMMPS directly by defining the solvent molecule in a
"molecule" file, then add molecules with create_atoms and delete
overlapping molecules with delete_atoms.

On Sun, Jan 16, 2022 at 4:31 PM Eduardo Estevez <eduardo45pr_at_gmail.com>
wrote:

> Hi all
>
> I built a data.file for LAMMPS, and then converted with the Lammps-master
> plugin, lammps2pdb.pl
> <https://urldefense.com/v3/__http://lammps2pdb.pl__;!!DZ3fjg!ocVZ2hEs7BtKFZkYNGEauzHRf1uvXXkGggDGHs7Jfr56W56LXXYLQW71qi4cC8HvbQ$>
> to psf.file and pdb.file format, I opened these files with VMD without
> problem, but when solvating I get the following error :
>
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> while executing
> "readpsf $psffile pdb $pdbfile"
> (procedure "solvate_core" line 216)
> invoked from within
> "solvate_core NT_MoS2_2beg_trj.psf NT_MoS2_2beg_trj.pdb -o solvate -s WT
> -x 0 -y 0 -z 0 +x 0 +y 0 +z 0 -b 2.4"
> ("eval" body line 1)
> invoked from within
> "eval solvate_core $args "
> invoked from within
> "if $errflag { error $errMsg $savedInfo $savedCode }"
> (procedure "solvate" line 8)
> invoked from within
> "solvate {NT_MoS2_2beg_trj.psf} {NT_MoS2_2beg_trj.pdb} -o solvate -s WT -x
> 0 -y 0 -z 0 +x 0 +y 0 +z 0 -b 2.4"
> ("eval" body line 1)
> invoked from within
> "eval solvate $command_line"
> (procedure "::Solvate::run_solvate" line 96)
> invoked from within
> "::Solvate::run_solvate"
> invoked from within
> ".solvategui.solvate invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .solvategui.solvate"
> (command bound to event)
>
>
> What can be a possible solution? Please,
>
> Sincerely
>
> Eduardo
>
>
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!qo3EQSRlOR2ihYr-tIqcwEHc-S6Ach3IfW6NhmvTYntC1RoKKJihC_7J-Cy-zZGrQg$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.