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
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Received on Mon Feb 23 2015 - 08:00:07 PST
