VMD-L Mailing List

From: Eduardo Estevez (eduardo45pr_at_gmail.com)
Date: Sun Jan 16 2022 - 14:54:00 CST

Hi all

I built a data.file for LAMMPS, and then converted with the Lammps-master
plugin, lammps2pdb.pl 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