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

From: Vlad Cojocaru <>
Date: Thu, 05 Apr 2012 15:58:42 +0200

Thanks David,

This what I supposed. Just wanted to make sure I am right.
Definitely, we will take a look at ff12SB as soon as we get hold of

Is fff12SB published already or in press ?


On 04/05/2012 03:53 PM, David A Case wrote:
> 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.]
> ....dac
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> AMBER mailing list

Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
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Received on Thu Apr 05 2012 - 07:00:03 PDT
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