From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Dec 12 2012 - 14:49:46 CST
Thanks Jack!
I hope that the same applies to psfgen when loading topology files. psfgen
is not able to deal with extended atom names as they occur for example
with sugars. So, I always have to "re-compose" my system with the CHARMM
program.
Gianluca
On Wed, 12 Dec 2012, 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> 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 BulatDept. of Molecular and Cell Biology,
> Chemical Biology Graduate Program,
> UC Berkeley
>
>
>
-----------------------------------------------------
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.
-----------------------------------------------------
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