Hi all,
I have a little issue in order to generate the right parameters for atom type Mg2+ with Amber14.
Please see below the input file and commands.
PDB file:
ATOM 30471 MG MG A2001 -1.069 -2.616 46.237 1.00 96.20 MGMG
ATOM 30472 MG MG A2002 -3.875 -3.619 47.929 1.00100.04 MGMG
TER 30473 MG A2002
After executing the following xleap commands:
source leaprc.ff14SB
sys = loadpdb mg.pdb
and when executing the following xLeap command:
saveamberparm sys mg.prmtop mg.inpcrd
xLeap does not appear to find a non-bonded parameter in its internal libraries for atom type MG:
“Checking Unit.
WARNING: The unperturbed charge of the unit: -81.000000 is not zero.
WARNING: The perturbed charge: -81.000000 is not zero.
-- ignoring the warnings.
Building topology.
Building atom parameters.
For atom: .R<MG 3760>.A<MG 1> Could not find vdW (or other) parameters for type: Mg2+
For atom: .R<MG 3761>.A<MG 1> Could not find vdW (or other) parameters for type: Mg2+
Parameter file was not saved. “
Could someone help me with this issue?
Kind regards,
Nicolas Genin
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Received on Wed Nov 12 2014 - 08:00:03 PST
