Hi Ben,
yes, it works correct now. Many thanks!
James
2014-06-10 2:48 GMT+04:00 Benjamin D Madej <bmadej.ucsd.edu>:
> Hi James,
>
> Yes, this is normal. When Amber installs the python scripts, it checks
> what Python executable you're system is using and puts an appropriate
> shebang line (#!) where PYTHONEXE currently is. Usually it's something like:
> #!/usr/bin/python
>
> So all you need to do now is change that line to your Python (probably
> something like /usr/bin/python) OR just run the script like this:
> python $AMBERHOME/AmberTools/src/etc/charmmlipid2amber.py -i input_file -o
> output_file
>
> All the best,
> Ben Madej
> UCSD Chemistry and Biochemistry
> SDSC
>
> ________________________________________
> From: James Starlight [jmsstarlight.gmail.com]
> Sent: Monday, June 09, 2014 12:18 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] charmmlipid2amber.py
>
> Hi Ben,
>
>
> I've faced with the problem loading scripts from membrane tutorial.
> Initially all scripts have been placed to
> $AMBERHOME/AmberTools/src/etc
> and corresponded path have been added to /etc/bash.bashrc
>
> now all scripts from /etc/ works fine but not two recently scripts from
> tutorial
>
> own.starlight ~/Desktop/Amber/tutorials/membrane $ charmmlipid2amber.py -i
> b2ar_charm.pdb -c
> $AMBERHOME/AmberTools/src/etc/charmmlipid2amber/charmmlipid2amber.csv -o
> b2ar_amber.pdb
> bash: ./charmmlipid2amber.py: PYTHONEXE: bad interpreter: No such file or
> directory
> own.starlight ~/Desktop/Amber/tutorials/membrane $ cpinutil.py
> CpinInputError: prmtop file (prmtop) is missing
> own.starlight ~/Desktop/Amber/tutorials/membrane $ vmd_box_dims.sh
> bash: /home/own/amber14/AmberTools/src/etc/vmd_box_dims.sh: /bin/bash^M:
> bad interpreter: No such file or directory
>
> Does it some problem with my bash or something else ?
>
>
> James
>
>
>
>
> 2014-06-09 23:02 GMT+04:00 Benjamin D Madej <bmadej.ucsd.edu>:
>
> > Hi James,
> >
> > Sorry about the problem with charmmlipid2amber.py. It was a problem with
> > residue numbering. I am currently working on getting the fix out to all
> > users.
> >
> > Here is an updated version of the script for you to use now:
> > https://dl.dropboxusercontent.com/u/26203202/charmmlipid2amber.tar.bz2
> >
> > As for your protein system, it appears that that LEaP may be trying to
> > connect a lipid molecule and a protein molecule. Make sure that you have
> > appropriate TER cards in your structure. For example, the protein chains
> > must be ended with a TER card and the lipids should follow the Lipid14
> PDB
> > format.
> >
> > All the best,
> > Ben Madej
> > UCSD Chemistry and Biochemistry
> > SDSC
> >
> > ________________________________________
> > From: James Starlight [jmsstarlight.gmail.com]
> > Sent: Friday, June 06, 2014 9:26 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] charmmlipid2amber.py
> >
> > also below error have been appeared during processing of the rhodopsin
> by
> > tleap wih he same membrane (this time I had no problem with the
> conversion
> > of charm to amber pdb in comparison to the above case) using rhodopsin
> from
> > the tutorial.
> >
> > input
> >
> > source leaprc.ff12SB
> > source leaprc.lipid14
> > m = loadpdb rho_amber.pdb
> > #check m
> > saveamberparm m rhodopsin.prmtop rhodopsin.inpcrd
> >
> >
> > output
> >
> >
> > .R<PA 349>.A<C13 41>,
> > .R<ALA 348>.A<C 9>,
> > .R<PA 349>.A<H2R 45>, and
> > .R<PA 349>.A<H2S 46>
> > to atoms
> > .R<PA 349>.A<C13 41>,
> > .R<PC 1>.A<C11 5>,
> > .R<PA 349>.A<H2R 45>, and
> > .R<ALA 348>.A<C 9>
> > This error may be due to faulty Connection atoms.
> > !FATAL ERROR----------------------------------------
> > !FATAL: In file [chirality.c], line 142
> > !FATAL: Message: Atom named C11 from PC did not match !
> > !
> >
> >
> >
> > 2014-06-06 16:40 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
> >
> > > Dear Amber's users!
> > >
> > >
> > > I have a problem in the conversion charm gui PDB to amber PDB
> > >
> > > charmmlipid2amber.py -i b2ar_charm.pdb -c
> > > $AMBERHOME/AmberTools/src/etc/charmmlipid2amber/charmmlipid2amber.csv
> -o
> > > b2ar_amber.pdb
> > > Error: Number of atoms in residue does not match number of atoms in
> > > residue in replacement data file
> > >
> > >
> > > here you can find my pdb
> > > http://www.charmm-gui.org/?doc=input/membrane&time=1402044938
> > >
> > > I suppose this is some bud isn't it?
> > >
> > >
> > > TFH
> > >
> > > James
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Jun 09 2014 - 23:00:02 PDT
