As I understand ff03 - is the former file used by me not only for proteins
bur for nucleic acids
simulations with pol + LP for nucleic acids as well.
Piotr
"David A. Case" <case.scripps.edu>
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11/11/2003 09:19 AM
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Re: amber-developers: Added frcmod.ff03
On Mon, Nov 10, 2003, Yong Duan wrote:
>
> Just added frcmod.ff03 to the tree. Parm03.dat, which has a few minor
> changes relative to parm99.dat, should be depreciated soon. Now
> leaprc.ff03 will load
> parm99.dat +
> frcmod.ff03 +
> all_nucleic94.lib +
> all_aminoct94.lib +
> all_aminont94.lib
>
> I will replace the latter two with updated C- and N- libs. It now can
> work on proteins (not just small ACE- and -NMR terminated peptides).
> Still kept leaprc.ff03.old around, just in case ...
>
Thanks, Yong! Since we are moving towards the new naming scheme, maybe
this is a good place to start. My understanding from our discussion in
July was the following:
1. all_nucleic94.lib should not be loaded. We are splitting the protein
and nucleic acid stuff into separate files. Since ff03 is just for
proteins (as I understand it), you should just load protein files here.
2. Correspondingly, I think this new file should be called
"leaprc.prot.ff03",
to identify it as a protein-only file. [There was talk at the meeting
about removing the "leaprc" prefix, but I now think it should remain:
it identifies the type of file, and has a fair amount of history behind
it. It probably would have been better to have a suffix rather than a
prefix, but I am not inclined to change at this point.
Comments/suggestions are solicited. ]
3. Just a note: although not mentioned above, Yong's file also loads
all_amino03.lib, which has all of the new charge model.
..dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
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La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Wed Apr 05 2006 - 23:50:07 PDT
