Re: NAMD and new FF CHARMM36

From: Evgeny Bulat (jack.bulat_at_gmail.com)
Date: Wed Dec 12 2012 - 15:24:58 CST

Yea, I ran into that issue early on... I wrote a Python script to address
it, I think. Autoionize becomes an issue, since it misreads the charges.
Earlier, I solved that and posted it on VMD-L. Feel free to check it out!

Jack

On Wed, Dec 12, 2012 at 12:53 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:

> You can use it in a relatively straightforward manner. Just a couple
> lines have to be commented out of the toppar file for NAMD to not choke.
> You'll see when you try it!
>
> On Dec 12, 2012, at 2:26 PM, Gianluca Interlandi wrote:
>
> > Hi,
> >
> > Can the current version of NAMD be used together with the new CHARMM36
> force field? The parameter files are "top_all36_prot.rtf" and
> "par_all36_prot.prm". However, topology and parameters for water and ions
> are now in a CHARMM stream file "toppar_water_ions.str". How can I use this
> in NAMD?
> >
> > Thanks!
> >
> > Gianluca
> >
> > -----------------------------------------------------
> > Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> > +1 (206) 685 4435
> > http://artemide.bioeng.washington.edu/
> >
> > Research Scientist at the Department of Bioengineering
> > at the University of Washington, Seattle WA U.S.A.
> > -----------------------------------------------------
>
>
>

-- 
Jack Bulat
Dept. of Molecular and Cell Biology,
Chemical Biology Graduate Program,
UC Berkeley

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