Hi Xplorers,
Can anyone help me?
I am trying to run simulated annealing to make a model of a 60AA protein
that has
one high homology region coresponding to a 3-10 helix. I have made an
approximate
model based on mutating residues of the homologue, checked and removed
any side
chain clashes, Run Gen.inp to make .psf and pdb files, modified the
last line of the
pdb file to be OT, etc.
My restraints are mainly dihedrals for the helix, with a couple of
disulphide noe's,
when I run SA.inp (which was taken from the on-line manual) the logfile
gives:
POWELL: number of degrees of freedom= 2074
%CODBON-ERR: missing bond parameters %%%%%%%%%%%
bond energy constant missing.
target bond length missing.
ATOM1: SEGId=" ", RESId="1 ", NAME="CA ", CHEMical="CH1E"
ATOM2: SEGId=" ", RESId="1 ", NAME ="C ",
CHEMical="C "
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
etc.
However previously in the logfile it accepted all the dihedral
restraints?
I have used another groups sa.inp script as well as the on-line version.
Theirs
gives the same error for me, but runs fine for them?
Any suggestions?
I suspect that if it doesn't understand the restraint I have to add an
additional
parameter file. (currently using @TOPPAR:parallhdg.pro )
Many thanks
Heather Peto
Birkbeck College
University of London
Fax 0171-631-6803
email h.peto at cryst.bbk.ac.uk
