Ben,
Thanks for help again. Yes, it will be interesting to look as some example
how to include cholesterol from the lipid11 ff to the lipid14 params.
Best,
James
2014-06-11 0:38 GMT+04:00 Benjamin D Madej <bmadej.ucsd.edu>:
> Hi James,
>
> I see. In part 1, the problem is that Cholesterol is currently only the
> Lipid11 force field files.
>
> In part 2, I do not know why you removed the hydrogens. You will still
> have the same problem as above.
>
> The problem is trying to load Lipid11 and Lipid14 at the same time. It
> gets complicated because the residue and atom names are largely the same
> are the same but the parameters have changed. If you need to run Lipid14
> lipids and Lipid11 cholesterol, contact me off the list and we can talk
> about how to set it up.
>
> All the best,
> Ben Madej
> UCSD Chemistry and Biochemistry
> SDSC
> ________________________________________
> From: James Starlight [jmsstarlight.gmail.com]
> Sent: Tuesday, June 10, 2014 12:39 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] charmmlipid2amber.py
>
> 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
> > >>>
> > >>
> > >>
> > >
> > _______________________________________________
> > AMBER mailing list
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> >
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Received on Tue Jun 10 2014 - 22:30:02 PDT
