Ben,
sorry for some of topic
but could you suggest me the same solution for sh scripts
e.g trying
own.starlight ~/Desktop/Amber/tutorials/membrane $ sh vmd_box_dims.sh -i
xz222.pdb -s water
: not founds.sh: 2: vmd_box_dims.sh:
: not founds.sh: 21: vmd_box_dims.sh:
vmd_box_dims.sh: 23: vmd_box_dims.sh: Syntax error: word unexpected
(expecting "in")
own.starlight ~/Desktop/Amber/tutorials/membrane $ sh vmd_box_dims.sh -i
./xz222.pdb -s water
: not founds.sh: 2: vmd_box_dims.sh:
: not founds.sh: 21: vmd_box_dims.sh:
vmd_box_dims.sh: 23: vmd_box_dims.sh: Syntax error: word unexpected
(expecting "in")
own.starlight ~/Desktop/Amber/tutorials/membrane $ bash vmd_box_dims.sh -i
./xz222.pdb -s water
vmd_box_dims.sh: line 2: $'\r': command not found
vmd_box_dims.sh: line 21: $'\r': command not found
vmd_box_dims.sh: line 23: syntax error near unexpected token `$'in\r''
'md_box_dims.sh: line 23: ` case $opt in
although #!/bin/bash path set in sh script is correct
James
2014-06-10 9:36 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> 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
>> >
>> _______________________________________________
>> 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
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 09 2014 - 23:00:02 PDT
