Hi,
I want to titrate a ligand in complex with a protein. By following the
section of "Extending constant pH to additional titratable groups" in
Amber15 manual, I tried to prepare the parameters for Amber14. Now I
already got the reference pKa, partial charges and reference energy (using
TI). Then I added the parameters to the file of
$AMBERHOME/AmberTools/src/etc/cpinutils/residues.py.
But I encountered a problem with cpinutil.py (python
~/software/amber14/bin/cpinutil.py
--describe) to prepare the cpin file. The errors are pasted as below:
Traceback (most recent call last):
File "amber14/bin/cpinutil.py", line 11, in <module>
from chemistry.amber import titratable_residues as residues
File
"amber14/lib/python2.7/site-packages/chemistry/amber/titratable_residues.py",
line 853
XXX = TitratableResidue('XXX', ['C13','H1', 'C17','H2', 'H3',
'C02','N01','H4',
^
SyntaxError: invalid syntax
By the way, I noticed that in Amber16 manual (In page 447), it suggests to
add the parameters to a different file:
$AMBERHOME/AmberTools/src/parmed/parmed/amber/titratable_residues.py
Could anyone comment on this and give me a hand to fix the problem?
Thanks a lot.
Yong
--
==========================
Yong Wang
PhD Student, Structural Biology and NMR Laboratory (SBiNLab)
Department of Biology, University of Copenhagen, Denmark
Ole Maaloes Vej 5, DK-2200 Copenhagen N
https://www.researchgate.net/profile/Yong_Wang15
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Received on Fri May 06 2016 - 14:00:03 PDT
