VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 11 2017 - 09:57:26 CDT

Pawel,
  Thanks for the note. I've updated the code to address your suggestion, the
next VMD 1.9.4 alpha build I post will incorporate them. It still needs testing
so I will appreciate further feedback once you're able to try it out.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 11, 2017 at 03:07:35PM +0200, Pawel Kedzierski wrote:
> 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
> >
>

> begin:vcard
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> org;quoted-printable:Wroc=C5=82aw University of Technology, Faculty of Chemistry;Advanced Materials Engineering and Modelling Group
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-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/