Re: NAMD and new FF CHARMM36

From: Evgeny Bulat (
Date: Wed Dec 12 2012 - 14:39:48 CST

Hi Gianluca,

I've been using CHARMM36 carbohydrate force fields, some of which are
contained in the stream files. From my experience with using them in
NAMD2.7 as well as 2.9, I've been able to use the .prm and .str files just
fine by calling them both under "parameters" in the NAMD config file.

For the CHARMM water_ions.str file, I remember having some issues (though
it might have been due to the fact that the definitions would've overlapped
with some of the other parameters I specified). Try them by themselves and
see if they work. If not, maybe someone else can help.

Good luck!

Jack Bulat

On Wed, Dec 12, 2012 at 12:26 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
> +1 (206) 685 4435
> http://artemide.bioeng.**>
> 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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