From: Mike Makowski (mmakowsk_at_uci.edu)
Date: Tue Aug 19 2014 - 23:34:13 CDT
Hi Basheer,
You're certainly right in assuming that the AMBER to CHARMM format files
are compatible with CHARMM type coordinate files. In fact, NAMD allows
input of AMBER parmtop files with the use of pdb as well. You problem
results from incompatibility between your topology and parameter files. The
parameter file has to define all necessary
bonding/nonbonding/electrostatic/etc. parameters for all atom types
specified in your topology file. If CN7 isn't defined in the AMBER
parameter file, it's likely that it uses a different atom type to represent
that particular atom. More specifically, browse through your topology file
for CN7. Here you define that atom but in the AMBER parameter file, if you
perform a search, you'll notice it's not to be found. One of the troubles
of using these AMBER or OPLS files is constructing topologies that are
compatible with the parameter file. Hope this helps. Good luck!
Mike
Michael Makowski
University of California, Irvine
Department of Chemistry,
Chemical and Material Physics,
Irvine, CA 92617
Cell: 267 588 9865
Office: 949 824 5776
On Tue, Aug 19, 2014 at 5:16 PM, Basheer Subei <basheersubei_at_gmail.com>
wrote:
> Hello all,
>
> *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
> <http://bionano.physics.illinois.edu/Tutorials/nanopore-protocols.pdf> up
> 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
> <http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2007-2008/1856.html>
> 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
> NAMD?
>
> Sorry if some of this makes no sense. Thank you for your time!
> - Basheer Subei
>
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