[AMBER] problem with CpHMD

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Tue, 21 Feb 2017 12:03:39 +0000

Dear Amber experts,

I have on my Linux server Amber16 and AmberTools16.
I want to use constant pH molecular Dynamics (CpHMD)
for identification of pKa of His residues of my protein.
I have followed the AMBER tutorial:
TUTORIAL A18: Constant pH Molecular Dynamics Example - Calculating pKas for titratable side chains in HEWL<http://ambermd.org/tutorials/advanced/tutorial18/index.htm>
My protein chelates the Na cation.
This circumstance causes the problem in TLEAP.
Please find details below.

What changes and corrections should be added to my tleap.in file
in order TLEAP can accept Na cation ?

Thank you,
Michael

I have ran the command: tleap f tleap.in
Where the input file tleap.in is


source leaprc.constph
# Load the PDBs
mc = loadPDB eq_md15_nh.pdb

# Save topology files
saveAmberParm mc mc.parm7 mc.rst7

# Quit
quit

Computer reported the error:

Building topology.
Building atom parameters.
For atom: .R<NA 376>.A<NA 1> Could not find vdW (or other) parameters for type: Na+
Parameter file was not saved.




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Received on Tue Feb 21 2017 - 04:30:02 PST
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