amber-developers: some new parm.dat files to try

From: David A. Case <case.scripps.edu>
Date: Tue, 28 Jun 2005 20:35:04 -0700

I have attached two updated files to this e-mail:

   parm94.dat.new
   parm99.dat.new

You can do a diff of these with the originals to see what changes were
made.

Here is what I think from my (limited) testing:

1. parm94.dat.new should change the order of some improper dihedrals
      to correctly follow the rule that the peripheral atoms should be
      in alphabetical order by atom type. This should really have only
      a very minor effect on simulations.

2. parm99.dat.new will add some new torsions that (arguably) should have
      been there all along. It should also fix the following problem
      that was reported on the list:

           tleap -f leaprc.ff99
> saveamberparm DGN prmtop.1 prmtop.2
> DGN2 = copy DGN
> saveamberparm DGN2 prmtop.2 prmcrd.2

      With the new files (but not the originals) the two prmtop files will
      be functionally identical (although the order of torsions will be
      different).

      This version of parm99.dat.new also fixes up the same problems with
      a few of the improper torsions as was the case for parm94.dat.new.


Obviously, I have not given these lots of tests, so don't use them for
anything "real". I'm just trying to see if these will work on your
systems.
Try them out for various proteins and nucleic acid systems, and let the
list
know if you see anything amiss.

[Note: if it turns out that I am wrong, and there should only be a
one-fold
term, and no three-fold term for something like H1-CT-CT-OS, we can easily
modify parm99.dat.new to zero out the three-fold part. The parm99 paper
is
really not clear here: for example, on the top of the second column of p.
1056, it is stated "the second approach is to include other Fourier
components
*in addition to* the E3 term" (emphasis added). At the bottom of the
first
column of p. 1057, one sees this: "Instead of using *only* the default
threefold Fourier component, we applied the onefold Fourier component for
these two torsions" (again, my emphasis).

But only Junmei and Piotr know for sure what was done, and so far they
aren't
talking.

...more later...dac




Received on Wed Apr 05 2006 - 23:49:55 PDT
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