Dear everyone:
An off topic question. I first build up a model using ARP/wARP,delete the
"DUMP" atoms, add the lost parts directly from the existing model(because of
the sequence identity) and then refine it with simulated annealing
program(anneal.inp) in CNS.The error is:
-------------------------- Torsion Topology -----------------------------------
ERROR: There are no suitable base groups.
This problem can be caused by isolated
bonding networks with undefined or weak
dihedral force constants.
The atoms that cannot be placed in a tree
are listed below:
%atoms " "-1 -LYS -CB
%atoms " "-1 -LYS -CG
%atoms " "-1 -LYS -CD
%atoms " "-1 -LYS -CE
%atoms " "-1 -LYS -NZ
%atoms " "-1 -LYS -C
%atoms " "-1 -LYS -O
%atoms " "-1 -LYS -N
%atoms " "-1 -LYS -CA
%TORSION:TOPOLOGY error encountered: Fatal Topology Error
(CNS is in mode: SET ABORT=NORMal END)
I look at PDB file and find that the coordinates of these manually build parts
are definitely seperated from those automatically build by the ARP/wARP program.
Is there any hint? Any suggestion would be appreciated!
Janxon
