Forgot to mention that such non-integer charge have been obtaining only
after parametrization in ff14 using python script for initial pdb
processing (in case of processing of the same pdb by .x script and ff11 the
charges have been OK).
James
2014-06-11 10:54 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> Some additional questions about preparation of protein-membrane systems
> with latest workflow
>
> 1- What should I do if as the result of the tleap processing I've obtained
>
> WARNING: The unperturbed charge of the unit: 0.999040 is not zero.
>
>
> 2- For example charm-gui produced bilayer with big Z dimension including
> some unusefull water in both layers. Are there any possibilities to cut
> water both upper and down Z layers decreasing Z to specified value in both
> layers?
>
>
> TFH,
>
> James
>
>
> 2014-06-11 9:15 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
>
> 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
>>> > 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
>>>
>>
>>
>
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Received on Wed Jun 11 2014 - 00:30:02 PDT
