I tried
python $AMBERHOME/bin/parmed.py -p mol.top -inpcrd mol.crd script.in
with this script.in
printdetails :MET.O
printdetails :MET.OXT
parmout details.out
However, I got this error
Loaded Amber topology file mol.top
Traceback (most recent call last):
File "amber12/bin/parmed.py", line 126, in <module>
amber_prmtop.add_parm(parm)
File "/amber12/lib/python2.7/site-packages/ParmedTools/parmlist.py", line
34, in add_parm
parm = load_file(parm)
File "amber12/lib/python2.7/site-packages/chemistry/formats/registry.py",
line 119, in load_file
name, arg)
TypeError: not enough arguments for format string
Any suggestion ?!
On Fri, Oct 23, 2015 at 12:21 AM, David A Case <
dacase.scarletmail.rutgers.edu> wrote:
> On Thu, Oct 22, 2015, Hadeer ELHabashy wrote:
> >
> > Actually, I wanted to know how can Amber differentiate between terminal
> > Oxygens of certain Amino acid. Suppose that I have two terminal Oxygens
> > one called O from C-O the other called OXT from C=O and they are in
> > resonance of the double bond.
> >
> > Does amber differentiate between these tow atoms ?
>
> Amber uses the same parameters for both oxygens. You can find out the
> answers
> to questions like these (and others) by running the parmed program and
> asking
> it to print out charges, bonding parameters, or whatever.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Oct 26 2015 - 05:00:03 PDT
