Many apologies. That last email was completely wrong on my part; I don't know what I was thinking. I was thinking of the headgroup PH- and P2- (phosphatidic acid) which is where I got PA.
To be clear: PA *is* in Lipid14.
I don't know where this problem is coming in LEaP. Did you check the residue name, atom name, and connectivity of those atoms in LEaP? There must be something in the input structure file that's throwing off the script.
Sorry about that mistake.
All the best,
Ben Madej
UCSD Chemistry and Biochemistry
SDSC
________________________________________
From: Benjamin D Madej [bmadej.ucsd.edu]
Sent: Tuesday, June 10, 2014 11:51 AM
To: AMBER Mailing List
Subject: Re: [AMBER] charmmlipid2amber.py
Hi James,
It looks like there is still a problem with your input PDB file. There is an atom listed named .R<PA 1>.A<C12 44> which is not a residue defined in Lipid14. The Lipid14 parameter set did not include PA nor did we validate and test it in that paper. Lipid11 *did* include this head group and can be used there.
However, it is possible that you could do a RESP charge fit and apply the dihedral and van der Waals parameters in the way that we describe in the Lipid14. However, there may be more parameterization necessary to be able to correctly predict experimental PA properties.
All the best,
Ben Madej
UCSD Chemistry and Biochemistry
SDSC
________________________________________
From: James Starlight [jmsstarlight.gmail.com]
Sent: Tuesday, June 10, 2014 9:06 AM
To: AMBER Mailing List
Subject: Re: [AMBER] charmmlipid2amber.py
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
>>> 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 Tue Jun 10 2014 - 12:30:04 PDT
