[AMBER] LEaP failing after update to AmberTools17

From: Charles-Alexandre Mattelaer <camattelaer01.gmail.com>
Date: Wed, 3 May 2017 19:35:19 +0200

Dear all

Ever since updating to AT17, Leap is experiencing troubles with generating
my parameter files. The error that is being produced states:

> saveAmberParm foo TTT.prmtop TTT.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -2.000000 is not zero.

 -- ignoring the warning.

Building topology.
Building atom parameters.
For atom: .R<DT5 1>.A<HO5' 1> Could not find vdW (or other) parameters for
type: HO

This error is reproduced for each atom type. My input file is a script (I
reduced it to a minimum which reproduces the error):


cat << eof > leap.in
logfile leap.new.out

source leaprc.DNA.OL15

foo = sequence {DT5 DT DT3}

savePdb foo TTT.pdb
saveAmberParm foo TTT.prmtop TTT.inpcrd

tleap -f leap.in

Additionally, I can add that I can't find any failed test with respect to
Leap. I have no idea what is going on, since the parm10.dat and
frcmod.DNA.OL15 are being loaded in Leap (added log-file).

Hope you can help me

Kind regards

Charles-Alexandre Mattelaer

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Received on Wed May 03 2017 - 11:00:03 PDT
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