N-terminal Proline residue

Dr. C.M. Read chris.read at port.ac.uk
Fri Feb 6 07:38:00 EST 1998


Dear All,

I am having a problem with generating .psf and template.pdb files for a
protein containing an N-terminal Proline residue, using Xplor v3.851. I
am able to produce them with Xplor v3.1. Input is via the sequence
command with the appropiate parallhdg.pro and toppallhdg.pro parameter
files.

Xplor v3.851 produces a .psf file OK, but not a template.pdb file. The
generate_template output gives the following error just as it goes into
the powell minimisation:

POWELL: number of degrees of freedom= 3591
%CODANG-ERR: missing angle parameters$$$$$$$$$$$$$
angle energy constant missing.
target angle value missing.
ATOM1: SEGID="  ", RESID="1", NAME="HT1", CHEMical="HC"
ATOM2: SEGID="  ", RESID="1", NAME="N", CHEMical="NH3"
ATOM3: SEGID="  ", RESID="1", NAME="CD", CHEMical="CP"

and similarly for HT2.

As judged from the parallhdg.pro and toppallhdg.pro files, Xplor v3.851
appears to treat Prolines differently to that in v3.1. Is there
something in the parallhdg.pro and topallhdg.pro files in v3.1 that is
missing in v3.851, so that it cannot cope with an N-terminal Proline?

Any ideas would be appreciated.

Cheers Chris Read
-- 

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