Ben,
please note that such error occured during processing of the pdb created
from the
rhodopsin_step5_assembly.pdb from the tutorial
1- initially I've converted rhodopsin_step5_assembly.pdb to the
rho_amber.pdb using your python script but after processing of this new pdb
by tleap it produced error assosiated with hydrogens
FATAL: Atom .R<CHL 522>.A<H222 58> does not have a type.
FATAL: Atom .R<CHL 522>.A<C23 59> does not have a type.
FATAL: Atom .R<CHL 522>.A<H231 60> does not have a type.
FATAL: Atom .R<CHL 522>.A<H232 61> does not have a type.
FATAL: Atom .R<CHL 522>.A<C24 62> does not have a type.
FATAL: Atom .R<CHL 522>.A<H241 63> does not have a type.
FATAL: Atom .R<CHL 522>.A<H242 64> does not have a type.
FATAL: Atom .R<CHL 522>.A<C25 65> does not have a type.
FATAL: Atom .R<CHL 522>.A<H251 66> does not have a type.
FATAL: Atom .R<CHL 522>.A<C26 67> does not have a type.
FATAL: Atom .R<CHL 522>.A<H261 68> does not have a type.
FATAL: Atom .R<CHL 522>.A<H262 69> does not have a type.
FATAL: Atom .R<CHL 522>.A<H263 70> does not have a type.
FATAL: Atom .R<CHL 522>.A<C27 71> does not have a type.
FATAL: Atom .R<CHL 522>.A<H271 72> does not have a type.
FATAL: Atom .R<CHL 522>.A<H272 73> does not have a type.
FATAL: Atom .R<CHL 522>.A<H273 74> does not have a type.
this is my tleap.in
source leaprc.ff12SB
source leaprc.lipid14
loadamberparams frcmod.ionsjc_tip3p
m = loadpdb rhodopsin_amber_h.pdb
#provide disulphides
bond m.110.SG m.187.SG
#bond m.156.SG m.162.SG
#bond m.106.SG m.191.SG
#bond m.184.SG m.190.SG
set m box { 81.35599899291992 80.00199890136719 70.54999923706055 }
savepdb m test.pdb
saveamberparm m test.prmtop test.inpcrd
thay I've just removed all hydrogens from rho_amber.pdb and tried to load
it into tleap (Assuming that all hydrohgens will be added back in
accordance with the amber params). However it's resulted in
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.
James
2014-06-10 23:16 GMT+04:00 Benjamin D Madej <bmadej.ucsd.edu>:
> 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 - 13:00:03 PDT
