Hello All,
This is my first message to the AMBER list, sorry if I am doing it wrong.
I am trying to use SHIFTS 5.0.1 to calculate theoretical proton shifts in a
protein structure. I have found success with apo simulations, however
SHIFTS will not recognize ligand molecules in my input PDB files and
removes them to a separate nonprot.pdb file before performing calculations
on the apo structure.
I have the ligand separated from the protein with a TER line as I read in a
tutorial like this:
ATOM 1388 HD11 ILE A 92 -15.141 5.860 11.058 1.00 0.00 H
ATOM 1389 HD12 ILE A 92 -13.718 5.355 11.970 1.00 0.00 H
ATOM 1390 HD13 ILE A 92 -14.445 6.933 12.274 1.00 0.00 H
TER
HETATM 1391 C * 93 -28.606 28.826 -8.262 1.00 0.00 C
HETATM 1392 C * 93 -28.500 28.237 -9.604 1.00 0.00 C
HETATM 1393 O * 93 -27.395 27.783 -10.013 1.00 0.00 O
HETATM 1394 O1 * 93 -29.514 28.192 -10.353 1.00 0.00 O1-
If I run: shifts -csa -HN "::H*" <basename>.pdb
with this file I get no errors until HETATM is encountered. I'm
assuming my problem is the asterisk for the "Residue name" field. But
I can't figure out what to change it to. I tried following the ligand
preparation tutorial found here
(
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm) for
creating mol2 files but attempts to reprotonate the ligand with reduce
also results in a warning about * not being in the HETATM connection
database and I am stuck there.
Any advice would be greatly appreciated. To put this into perspective
I have a database of ligand pose coordinates all bound to the apo
structure of my protein. I'm trying to compare simulated chemical
shift perturbation to experimental shifts so I can computationally
filter the poses.
Thank You,
Daniel Morris
The University of Akron
Department of Chemistry
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Received on Mon Feb 22 2016 - 12:30:03 PST
