Dear Amber Users,
I'm having problems with parmed. I have a system a dimer in which two
active sites consist of three histidines that are coordinating manganese
ion. I'd like to see what would change in the system (and the ions
behavior) if I use the 12-6-4 Lennard-Jones potential. So I used
frcmod.ionslm_1264_tip3p when preparing the system in leap and add TIP3P
water box around the protein. And when I use parmed commands from this
tutorial: http://ambermd.org/tutorials/advanced/tutorial20/12_6_4.htm I'm
getting this error:
Action add12_6_4 failed
LJ12_6_4Error: Could not find parameters for ATOM_TYPE CX
in .prmtop file I've got two Lennard-Jones flags:
%FLAG
LENNARD_JONES_ACOEF
%FLAG LENNARD_JONES_BCOEF
but not LENNARD_JONES_CCOEF like in the tutorial so it didn't work.
And yes, the .prmtop consists CX atom types. Should I change/remove them?
How?
So I checked in parmed.py the printLJTypes:
Reading input from STDIN...
> parm protein_complex.prmtop
Adding prmtop protein_complex.prmtop to parm list. protein_complex.prmtop
is the active parm.
> printLJTypes :MN
ATOM NUMBER NAME TYPE
---------------------------------------------
ATOM 5931 MN Mn2+: Type index: 15
ATOM 5932 MN Mn2+: Type index: 15
I'm using AmberTools 14.
What could be the problem here?
Best regards,
Karolina Markowska
PhD student
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Received on Tue Sep 08 2015 - 15:00:03 PDT
