VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Wed Oct 11 2017 - 04:10:20 CDT

Dear VMD developers,

AFAIK, the VMD plugins related to prepare modeling with NAMD2 were
changed to support the CHARMM 36 forcefield by default since version
1.9.3. It is the case for "Automatic PSF builder" or AutoPSF (menu
Extensions -> Modeling).

However, the NAMDgui plugin (Extensions -> Simulation -> NAMD Graphical
Interface) still loads the file
/usr/local/lib/vmd1.9.4a8/plugins/noarch/tcl/readcharmmpar1.4/par_all27_prot_lipid_na.inp
by default, with CHARMM27 parameters. A system prepared with AutoPSF
with default settings is incompatible with CHARMM27 parameter files and
the modeling crashes.

The files which should be loaded by the NAMDgui plugin are:

/usr/local/lib/vmd1.9.4a8/plugins/noarch/tcl/readcharmmpar1.4/par_all36_prot.prm
/usr/local/vmd1.9.4a8/plugins/noarch/tcl/readcharmmpar1.4/par_all36_na.prm
/usr/local/vmd1.9.4a8/plugins/noarch/tcl/readcharmmpar1.4/par_all36_lipid.prm
/usr/local/vmd1.9.4a8/plugins/noarch/tcl/readcharmmpar1.4/par_all36_carb.prm
/usr/local/vmd1.9.4a8/plugins/noarch/tcl/readcharmmpar1.4/par_all36_cgenff.prm
/usr/local/vmd1.9.4a8/plugins/noarch/tcl/readcharmmpar1.4/toppar_water_ions_namd.str

This is relatively minor issue but rather confusing for beginners who do
not know that with CHARMM36 all files should be read and also that water
and ions are in separate file without version number.

Cheers,

Pawel