Hello sir,
when i am trying to run for normal pdb file in parmed.py for generation of
.prmtop and .inpcrd it was successfull.
but when i am trying to run for my 9frames .dcd file it gives me below
ERROR.
Command1: $AMBERHOME/ParmEd-master/parmed.py
.
.
.
command2:chamber -top top_all27_prot_na.rtf -param par_all27_prot_na.prm
-psf 2rf9_noh_autopsf.psf -crd out_min.dcd
...
..
Creating chamber topology file from PSF 2rf9_noh_autopsf.psf, RTF files
[top_all27_prot_na.rtf], and PAR files [par_all27_prot_na.prm] Coords from
out_min.dcd. Using CMAP. GB Radius set mbondi.
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
3457, in execute
crd = read_PDB(self.crdfile)
File "/home/vj/amber14/ParmEd-master/chemistry/structure.py", line 2587,
in read_PDB
line = line.decode('ascii')
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe3 in position 44:
ordinal not in range(128)
On Mon, Feb 23, 2015 at 9:26 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Mon, 2015-02-23 at 20:15 +0530, vijay kumar narsapuram wrote:
> > After installing the setup.py I tried with following command
> >
> > COMMAND:
> > $AMBERHOME/ParmEd-master/parmed.py -top top_all36_cgenff.rtf -param
> > par_all36_prot.prm -psf 2rf9_noh_autopsf.psf -crd 2rf9_noh_autopsf.pdb -p
> > prot.prmtop -inpcrd prot.inpcr
>
> This isn't how you do it. You need to use the 'chamber' action inside
> the ParmEd interpreter:
>
> $ parmed.py
>
> ./ | | \.
> .:( |i __ j| ):`.
> .' `._ |`::::'| _.' `.
> .' "---.j `::' f.---" `.
> _____/ ___ ____ __ __ ____ ___
> | \ | | | `__'| \ / || | | \
> | .-. | .' `| | .-. |-/| \/ || ___| | . \
> | |_| | | i | | |_| /"":| || | | | \ \
> | / | .^. | | /::::| || |__. | | \ \
> | ----' | | | | | \ :: | || __| | | | )
> | | .' ''' `.| |\ \ | i i j| | . | / /
> | | | _ || | \ \ | |\/| || |__. | |. / .
> [| | | | | || | \ \ | | | || | | / ].
> ] `--' :--' `--::--' \_|`--' ::--"|____|-"-- / :[
> | __ ::-'''`.:' "--. .----::.----:: ,.---._ :|
> [ .-"" "`' \ / " `' `-. :].
> ]:.' \/ `.:[
> |/ \|
>
> ParmEd: a Parameter file Editor
>
>
> Reading input from STDIN...
> > chamber -top top_all36_cgenff.rtf -param par_all36_prot.prm \
> > -psf 2rf9_noh.autopsf.psf -crd 2rf9_noh_autopsf.pdb
> [snip output]
> > outparm chamber.parm7 chamber.rst7
> Outputting Amber topology file chamber.parm7 and restart chamber.rst7
> > go
> Done!
>
> Note that the 'outparm' action is needed to write a prmtop file. The
> "-p" and "-inpcrd" flags aren't used in ParmEd.
>
> 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 Feb 27 2015 - 05:30:03 PST
