VMD-L Mailing List

From: fan li (fanliqmul_at_gmail.com)
Date: Fri Jun 12 2020 - 14:19:23 CDT

Dear VMD users

I have an input file for lammps in which Bond , angle , dihedral and
improper type are properly defined. I have to add water to this structure,
so I write the psf and pdb by "animate write" command. I have successfully
added the water to psf and pdb file. However, the bond , angle , dihedral
and improper type become unknown type. I checked and found it happened
after animate write command. But the psf and pdb is necessary for adding
water in vmd. I know the "topo guessangles" and similar command can be used
to guess the angle type and others. However, the topology is very complex
in my system so these commands do not generate the correct topology in
comparison with the original input.So I wonder how to how to keep the bond
, angle , dihedral and improper type after solvating the lammps data?

Fan