From: Basheer Subei (basheersubei_at_gmail.com)
Date: Tue Aug 19 2014 - 19:16:43 CDT
*How do I use the Amber force field parameters in NAMD in the CHARMM
format?* I found some CHARMM-format Amber parameter and topology files in
the "non_charmm" directory in the c32b1 version of CHARMM ff. I also found
some online here
<http://terpconnect.umd.edu/~jbklauda/research/download.html>, listed under
"AMBER99 for use in CHARMM", and I tried using those parameter files in my
NAMD configuration file (.namd), but it would complain about not finding
"VdW parameter for atom type CN7".
*Specifically, what I did is:*
- I followed the NAMD nanopore tutorial
to section 3.1.9 (for minimizing ssDNA in NAMD).
- In min.namd, I replaced the CHARMM "par_all27_na.prm" file with the
"par_amber_cornell.inp" (the Amber-in-CHARMM-format parameter file).
- When I ran NAMD, I got "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM
TYPE CN7". It works fine when I don't replace the parameter file (so I've
ruled out any problems with not following the tutorial correctly).
I tried using a few variants of these parameter files I found online (Amber
force fields but CHARMM format), but they all give the same error. Now that
I'm inspecting the actual files and comparing them to the default CHARMM
parameter files in c32b1, I notice they're significantly different. And
mailing list threads
about this topic are confusing me.
What am I missing? Can someone please point me in the right direction? Am I
right in assuming it is possible to use these Amber-in-CHARMM-format
parameter files with structures generated using CHARMM (psf and pdb) in
Sorry if some of this makes no sense. Thank you for your time!
- Basheer Subei
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