Preparing PDB file

Dear Axel,

okay. I try to run it now and come back to you.

My protocol:

  1. use VMD to produce a pdb/psf file pair

  2. use Topotools:

  • topo retypebonds
  • topo guessbonds
  • topo writelammpsdata test full
  1. Detect weird bonds

Best regards,
Stephan

Dear Axel,

okay. I try to run it now and come back to you.

My protocol:
1. use VMD to produce a pdb/psf file pair

​i assume using psfgen?​

2. use Topotools:
   - topo retypebonds
   - topo guessbonds

​why "topo guessbonds" here? you already have the bonds (and angles,
dihedrals, impropers, crossterms) stored in the .psf file. the simple
(distance based and thus probably incorrect heuristic) employed here is far
inferior to the residue template based approach in psfgen or CHARMM.

OTOH, don't you need to retype angles, dihedrals, impropers, to get the
corresponding hints?

   - topo writelammpsdata test full

3. Detect weird bonds

​do those still show up without topo guessbonds​?

Dear Axel,
dear LAMMPS list,

    Dear Axel,

    okay. I try to run it now and come back to you.

    My protocol:
    1. use VMD to produce a pdb/psf file pair

​i assume using psfgen?​

yes!

    2. use Topotools:
       - topo retypebonds
       - topo guessbonds

​why "topo guessbonds" here? you already have the bonds (and angles,
dihedrals, impropers, crossterms) stored in the .psf file. the simple
(distance based and thus probably incorrect heuristic) employed here is
far inferior to the residue template based approach in psfgen or CHARMM.

okay, this did the trick! guessbonds was not necessary, indeed, you're
right I need to retypeangles, retypedihedrals, retypeimpropers too,
I omitted this for illustration purposes. Sorry!

OTOH, don't you need to retype angles, dihedrals, impropers, to get the
corresponding hints?

       - topo writelammpsdata test full

    3. Detect weird bonds

​do those still show up without topo guessbonds​?

Nope!

Thanks you very much.

Best regards,
Stephan