VMD-L Mailing List

From: Aleksei (erdelgado_at_udec.cl)
Date: Tue Apr 14 2020 - 15:19:45 CDT

Hello

LPH corresponds to a lone pair on your iodine atom and it requires
CGenFF version 4.0 or newer, while the version shipped with VMD
corresponds to 3.0.1. You can get the latest version in
https://mackerell.umaryland.edu/charmm_ff.shtml#charmm and make autopsf
use these topology files.

On 14/4/20 13:57, Francesco Pietra wrote:
> 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
>