Also some issues with pdbs obtained with charmmlipid2amber.py have been
occured during its processing by tleap (using lipids14 ff)
ERROR: Comparing atoms
.R<OL 363>.A<C13 11>,
.R<OL 363>.A<H2R 9>,
.R<OL 363>.A<H2S 10>, and
.R<PC 362>.A<C21 41>
to atoms
.R<OL 363>.A<C13 11>,
.R<PA 1>.A<C12 44>,
.R<OL 363>.A<H2S 10>, and
.R<PC 362>.A<C21 41>
This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 142
!FATAL: Message: Atom named C12 from PA did not match !
!
!ABORTING.
I had no such error with the same pdbs obtained by .x script (in that case
I've parametrized lipids by lipid11 ff)
James
2014-06-10 9:47 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> 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
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>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>>
>>
>>
>
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Received on Tue Jun 10 2014 - 09:30:03 PDT
