I used following commands,then i got some ERROR which i am unable to trace
out..
-$AMBERHOME/ParmEd-master/parmed.py
-chamber -top top_all27_prot_na.rtf -top top_all36_cgenff_mod_vj.rtf -param
par_all27_prot_na.prm -param par_all36_cgenff_mod_vj.prm -str
AEE-ligand_hydrogens.str -psf newpsf.psf -crd newpdb.pdb
ERROR:
Traceback (most recent call last):
File "/home/vj/amber14/ParmEd-master/parmed.py", line 161, in <module>
parmed_commands.cmdloop()
File "/usr/lib/python2.7/cmd.py", line 142, in cmdloop
stop = self.onecmd(line)
File "/usr/lib/python2.7/cmd.py", line 221, in onecmd
return func(arg)
File "<string>", line 1, in <lambda>
File "/home/vj/amber14/ParmEd-master/ParmedTools/parmed_cmd.py", line
141, in _normaldo
action.execute()
File "/home/vj/amber14/ParmEd-master/ParmedTools/ParmedActions.py", line
3530, in execute
parm = ConvertFromPSF(psf, parmset).view(ChamberParm)
File "/home/vj/amber14/ParmEd-master/chemistry/amber/_chamberparm.py",
line 658, in ConvertFromPSF
parm = ChamberParm.load_from_structure(struct)
File "/home/vj/amber14/ParmEd-master/chemistry/amber/_chamberparm.py",
line 195, in load_from_structure
inst.remake_parm()
File "/home/vj/amber14/ParmEd-master/chemistry/amber/_chamberparm.py",
line 210, in remake_parm
self.rediscover_molecules()
File "/home/vj/amber14/ParmEd-master/chemistry/amber/_amberparm.py", line
657, in rediscover_molecules
del self.pointers['IPTRES']
KeyError: 'IPTRES'
Thank you
Regards
Vijay
On Fri, Feb 27, 2015 at 6:57 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Fri, Feb 27, 2015 at 8:25 AM, vijay kumar narsapuram <
> nvijay1991.gmail.com> wrote:
>
> > so, Is there any alternative to calculate total free energy of the 10ns
> > trajectory(.dcd file)..?
> >
>
> ​ParmEd never did that. You use ParmEd to create the chamber topology
> file, then use that topology file with your DCD trajectory in MMPBSA.py to
> calculate the binding free energy for your 10 ns trajectory. I thought
> that was your original plan?
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Mar 06 2015 - 07:30:04 PST
