Re: [AMBER] using both the ILDN and NMR-based modifications of ff99SB

From: David A Case <>
Date: Thu, 5 Apr 2012 09:53:18 -0400

On Thu, Apr 05, 2012, Vlad Cojocaru wrote:
> The aminoacids libraries for the ILDN modifications are in
> "all_amino94ildn.lib" (+ the nt and ct aa). So, I assumed that the file
> "all_aminont94.nmr.lib" should contain the corresponding libraries for
> the NMR-based modifications

No. Files like "all_amino94.nmr.lib" have nothing to do with the
Bruschweiler group modifications. These are ancient files originally used
for NMR refinements in gas-phase simulations. I've hesitated to delete
them, since refinement scripts still being used in NMR groups use them.

The Bruschweiler files use the standard "94" lib files, parm99.dat, and a
special frcmod file: see the leaprc.ff99SBnmr file.

> If we load "frcmod.ff99SB-ildn-nmr" (my modified version of frcmod as
> explained above) and "all_amino94ildn.lib" (+ nt and ct) are we sure to
> use the correct parameters for the NMR-based modifications of ff99SB ?

You should get in touch directly with Rafael to discuss this. But the only
files relating to the ff99SBnmr modifications are leaprc.ff99SBnmr and
frcmod.ff99SBnmr. Other files, that contain "nmr" but *not* "ff99SBnmr" are
used for different purposes.

[As an aside, the Simmerling group has created ff12SB, which is certainly also
worth considering for protein simulations.]


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Received on Thu Apr 05 2012 - 07:00:02 PDT
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