Hi Ben,
I didn't noticed any warnings during Tleap processing
How its possible to check charge of the selected part of the system (e.g of
protein only or lipids)?
in tleap I've been able to check only total charge
> charge m
Total unperturbed charge: 1.999040
Total perturbed charge: 1.99904
but not of the specified parts of the model
> charge m.5
charge: Argument #1 is type String must be of type: [unit molecule residue
atom list]
usage: charge <object>
James
2014-06-12 22:27 GMT+04:00 Benjamin D Madej <bmadej.ucsd.edu>:
> James,
>
> Yes, it is a bit strange that the charges do not add up to zero. Any
> combination of Lipid14 charges should sum to zero charge. Meaning, any
> combination of PC, PE, LA, MY, PA, OL should sum to 0.0. What type of
> lipids are you using again and how many?
>
> Also, I would verify that LEaP is correctly recognizing all of the
> residues in your system and correctly assigning atom types and charges. I
> would check the warnings and errors again for any problems.
>
> The issue might be in the protein portion of your system as well. For
> example, are the amino acids correctly assigned? These are the things that
> I would examine before going further with ionization and MD simulation.
>
> All the best,
> Ben Madej
> UCSD Chemistry and Biochemistry
> SDSC
> ________________________________________
> From: James Starlight [jmsstarlight.gmail.com]
> Sent: Wednesday, June 11, 2014 10:45 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] charmmlipid2amber.py
>
> Ben,
>
> Thanks a lot! It's strange that having the same input I've obtained
> difference in total charge with different lipid force fields. It indicates
> that problem might be with the lipid not protein mightn't it? In any case
> is there any possibility to 0.999040 => 1 for further proper ionization of
> my system
>
> James
>
>
> 2014-06-12 0:47 GMT+04:00 Benjamin D Madej <bmadej.ucsd.edu>:
>
> > James,
> >
> > The charge of the unit is 0.999040 which is fairly close to 1.0. This
> > warning is useful for checking your units total charge because it may
> > indicate missing atoms or incorrect unit topology. Check that all the
> atoms
> > are present and that the bonding is correct in that unit.
> >
> > I think it should be fairly easy to search for atoms within a certain
> > range of Z coordinates. Probably VMD or PyMOL can do this. Or it could be
> > scripted in BASH or Python as well. Once you know which molecules need to
> > be deleted, then it's just a matter of writing a script to remove the
> > molecules from your input structure file.
> >
> > All the best,
> > Ben Madej
> > UCSD Chemistry and Biochemistry
> > SDSC
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Jun 12 2014 - 13:00:03 PDT
