VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Jul 18 2013 - 09:00:37 CDT

vdwForceSwitching is only needed if you're using C36 lipids.

You should be using C36 for proteins as well.

On Jul 18, 2013, at 12:54 AM, Francesco Pietra wrote:

> Hi Christopher:
> Thanks a lot for commenting on molefacture/CGenFF/FFTK. I got confused
> as I submitted a Sybyl mol2 file instead of a pdb file to molefacture.
> Now, with a pdb file, no problem. I used a gamess us abinitio
> minimized pdb file. Hope that that will speed up the FFTK procedure.
>
> A question remains open (therefore I started a new thread with
> appropriate title), i.e., whether, with namd (and psfgen), charmm36 ff
> can be used for the organic ligand simultaneously with charmm27 ff for
> the protein. As far as I can understand from namd manual, setting in
> the flag vdwForceSwitching results in referring to charmm36 only. But
> I may well have misinterpreted the manual.
>
> Thanks
>
> francesco pietra