Thanks Charles
The protocol.initParams('protein') statement did in fact allow the calculations
to run. This was with the hand edited psf and pdb files with HB2/3 proton
nomenclature. For the moment we're not using the knowledge based potentials.
If we do want to use them I can try moving them over to CNS and ARIA where we
can use the IUPAC HB2/3 nomenclature.
Brendan
email: bmduggan at musc.edu
phone: (843) 792 5029
fax: (843) 792 4322
________________________________________
From: Charles at Schwieters.org [[email protected]]
Sent: Friday, November 14, 2008 8:50 PM
To: Duggan, Brendan M.
Cc: xplor-nih at nmr.cit.nih.gov
Subject: Re: [Xplor-nih] proton nomenclature
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Hello Brendan--
> We've just tried running some calculations using restraints generated
> with CCPN Analysis but have run into problems with the proton
> nomenclature. Analysis uses the HB2/HB3 style nomenclature, while the
> PSF and PDB files I've generated with Xplor-NIH use the HB1/HB2 style.
> I have edited the PSF and initial PDB file to use the HB2/HB3
> nomenclature but now Xplor-NIH complains about missing angle
> parameters like this,
>
> %CODANG-ERR: missing angle parameters %%%%%%%%%%%%%%%%%%%%%%%%
> angle energy constant missing.
> target angle value missing.
> ATOM1: SEGId=" ", RESId="1 ", NAME="N ", CHEMical="NH3 "
> ATOM2: SEGId=" ", RESId="1 ", NAME="CA ", CHEMical="CT "
> ATOM3: SEGId=" ", RESId="1 ", NAME="HA ", CHEMical="HA "
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> Is it possible to use the HB2/HB3 nomenclature in Xplor-NIH?
There are separate issues. Most parameters depend on chemical names,
which you shouldn't need to change (these names are distinct from atom
names). Anyway, this error message should not appear if you are using
the standard protein parameters
[
in Python:
protocol.initParams('protein')
in XPLOR:
param @TOPPAR:protein.par end
]
You should be able to change HB atom names, but in general, it's
best to stick with Xplor-NIH nomenclature so that knowledge-based
potential terms work correctly.
best regards--
Charles
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.9 (GNU/Linux)
Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/>
iD8DBQFJHirkPK2zrJwS/lYRAj8/AJ9Vh09UoLHJsQjWm4lPm3ONBe3ndwCgg8eo
8UgNFdGxMwII0aom+gssC30=
=AgH5
-----END PGP SIGNATURE-----
