VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Apr 15 2020 - 05:10:09 CDT

I know now the story. As I plan to carry out QMMM, I commented out the
offending lines and compensated the charges so as neutralization works.
Hopefully QMMM wil not raise other problems
fp

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Tue, Apr 14, 2020 at 9:52 PM
Subject: Fwd: ATOM LPH
To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>

and i can imagine that there what I used is not an updated FF
---------- Forwarded message ---------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Tue, Apr 14, 2020 at 9:48 PM
Subject: Fwd: ATOM LPH
To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>

I forgot to mention that I had loaded to VMD
CGenFF: Topology for the Charmm General Force Field v. 3.1 *
* for Small Molecule Drug Design

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Tue, Apr 14, 2020 at 7:57 PM
Subject: ATOM LPH
To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>

Hello
Parameterizing a small organic molecule bearing a iodine atom with
CHARMM General Force Field (CGenFF) program version 2.2.0, the line

ATOM LP1 LPH 0.050 ! on I

was written in the topology, at the end of the list of atoms.
Autopsf with VMD 1.9.4a38 for that molecule as a ligand of nucleosides,
crashed with error "unknown atom type LPH"

Commenting out that line, psf/pdb were generated.

Is that what is now expected?

thanks for advice

francesco pietra