Try upgrading to AmberTools 15 -- I think the list there is more complete
than what is available in AmberTools 14.
HTH,
Jason
On Tue, Sep 8, 2015 at 5:41 PM, Karolina Markowska <markowska.kar.gmail.com>
wrote:
> 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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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 09 2015 - 08:30:06 PDT
