VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Wed Oct 11 2017 - 08:07:35 CDT

Sorry for double post, but I got distracted and I left the paths as
pasted, of course the /usr/local/vmd1.9.4a8 part should be replaced with
$VMDDIR.
Greetings,
Pawel

W dniu 11.10.2017 o 11:10, Pawel Kedzierski pisze:
> 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
> $VMDDIR/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:
>
> $VMDDIR/plugins/noarch/tcl/readcharmmpar1.4/par_all36_prot.prm
> $VMDDIR/plugins/noarch/tcl/readcharmmpar1.4/par_all36_na.prm
> $VMDDIR/plugins/noarch/tcl/readcharmmpar1.4/par_all36_lipid.prm
> $VMDDIR/plugins/noarch/tcl/readcharmmpar1.4/par_all36_carb.prm
> $VMDDIR/plugins/noarch/tcl/readcharmmpar1.4/par_all36_cgenff.prm
> $VMDDIR/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
>