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
>> > >>>
>> > >>> _______________________________________________
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>> > >>>
>> > >>
>> > >>
>> > >
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Received on Wed Jun 11 2014 - 00:00:03 PDT
