Hi
I used both amber16 and amber18 to run the mmpbsa and got the same error in
the follow:
File "/home/kevin/amber16/bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File
"/home/kevin/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
572, in loadcheck_prmtops
FILES.receptor_prmtop, FILES.ligand_prmtop)
File
"/home/kevin/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 102, in __init__
self.ligand_prmtop = LoadParm(ligand_prmtop)
File
"/home/kevin/amber16/lib/python2.7/site-packages/parmed/amber/readparm.py",
line 70, in LoadParm
parm = parm.view_as(AmberParm)
File
"/home/kevin/amber16/lib/python2.7/site-packages/parmed/amber/amberformat.py",
line 420, in view_as
return cls.from_rawdata(self)
File
"/home/kevin/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 259, in from_rawdata
inst.initialize_topology()
File
"/home/kevin/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 202, in initialize_topology
self.load_pointers()
File
"/home/kevin/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 448, in load_pointers
self.pointers["NATOM"] = self.parm_data["POINTERS"][NATOM]
KeyError: 'POINTERS'
can someone specify the problem I had?
On Fri, Jul 26, 2019 at 12:22 PM David A Case <david.case.rutgers.edu>
wrote:
> On Fri, Jul 26, 2019, Lod King wrote:
> >
> >I would like to calculate the delta G of my protein (no ligand) with
> >different short ns .dcd files.
>
> "delta G" implies a difference in free energy between two end points.
> But it's not clear what the endpoints are that you have in mind.
>
> That said, look for "MM-PBSA" in the Tutorials tab at ambermd.org.
> That will give you and idea of what can be done.
>
> ....dac
>
>
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Received on Fri Jul 26 2019 - 17:30:02 PDT
