Hi,
I am working on a peptide structure determination by NMR. The peptide
has a ACE residue at the N-terminal. I have been unable to generate
the .psf file using generate.inp. Without ACE residue, there is no
problem.
What I have been trying to do is to treat ACE as the residue #1 and
comment out in the generate.inp file the line "first nter tail + * end"
for the CHAIN statement. If kept this line, the output file would
complain about:
COOR>ATOM 1 CA ACE 1 -3.811 -0.502 0.471 1.00 0.00
%PATCH-ERR: atom +N not found
%PATCH-ERR: atom +HN not found
MAPIC: Atom numbers being modified
%PATCH-ERR: bond +HT1 +N not found
%PATCH-ERR: bond +HT2 +N not found
%PATCH-ERR: bond +HT3 +N not found
%PATCH-ERR: angle +HT1 +N +HT2 not found
%PATCH-ERR: angle +HT2 +N +HT3 not found
%PATCH-ERR: angle +HT2 +N +CA not found
%PATCH-ERR: angle +HT1 +N +HT3 not found
%PATCH-ERR: angle +HT1 +N +CA not found
%PATCH-ERR: angle +HT3 +N +CA not found
However, the program execution was still terminated for the following
reason(s):
%CODIMP-ERR: missing improper parameters %%%%%%%%%%%%%%%%%%%%%
improper energy constant missing.
target improper value missing.
periodicity missing.
ATOM1: SEGId=" ", RESId="1 ", NAME="HA1 ", CHEMical="HA "
ATOM2: SEGId=" ", RESId="1 ", NAME="HA2 ", CHEMical="HA "
ATOM3: SEGId=" ", RESId="1 ", NAME="C ", CHEMical="C "
ATOM4: SEGId=" ", RESId="1 ", NAME="HA3 ", CHEMical="HA "
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%CODIMP-ERR: program will be aborted.
Can somebody help me to find out what is the problem and how to
get around with it?
Thanks in advance!
Xin Jia, Ph.D.
The Burnham Institute
La Jolla Cancer Research Center
Email: xjia at burnham-inst.org
