Thank you, Jason, for your advice.
I thought the older version could be the problem. I'll try upgrading
AmberTools and see what will happen then.
Best regards,
Karolina
2015-09-09 17:27 GMT+02:00 Jason Swails <jason.swails.gmail.com>:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Sep 09 2015 - 12:30:03 PDT
