From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Wed Dec 12 2012 - 15:22:03 CST
If you run CHARMM-GUI, you will get a "namd" directory with all the
parameter files in NAMD/CHARMM format. The CHARMM/CHARMM format
parameter files have some extra stuff in them that you may need to strip
out (if statements, BOMBLEV commands, etc) if you want to use them in NAMD.
You could always cut and paste the relevant parameters for water from
the toppar file into one of the other parameter files you are using.
Jeff
On 12/12/2012 3:39 PM, Evgeny Bulat wrote:
> 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
> <gianluca_at_u.washington.edu <mailto:gianluca_at_u.washington.edu>> 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
> <mailto:gianluca_at_u.washington.edu>
> +1 (206) 685 4435 <tel:%2B1%20%28206%29%20685%204435>
> 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
>
-- ====================================================================== Jeffrey J. Potoff jpotoff_at_wayne.edu Associate Professor and Director of Early Engineering Programs Department of Chemical Engineering and Materials Science Wayne State University 5050 Anthony Wayne Dr Detroit, MI 48202 http://potoff1.eng.wayne.edu ======================================================================
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