[AMBER] Problems with cpinutil.py in CpHMD as adding a new titratable ligand

From: Yong Wang <wyongciac.gmail.com>
Date: Fri, 6 May 2016 22:43:20 +0200


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

But I encountered a problem with cpinutil.py (python
--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

line 853

    XXX = TitratableResidue('XXX', ['C13','H1', 'C17','H2', 'H3',


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:

Could anyone comment on this and give me a hand to fix the problem?

Thanks a lot.


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
AMBER mailing list
Received on Fri May 06 2016 - 14:00:03 PDT
Custom Search