On Sun, Sep 13, 2015, Robert Molt wrote:
>
> I am having difficulty inserting a covalently bound unit within a DNA
> helix (it is internal, not terminal).
>
> 2.) I do not believe that this is an option for me; there are "missing
> parameters" using "amber" force fields (the GAFF parameters are complete
> when I check them). Can this advice be modified for using a nucleotide
> with purely GAFF generated parameters?
You can, but then there will be missing parameters at the intersection between
the modified nucleotide (which has gaff atom types), and the regular
nucleotides (which will have Amber atom types).
I recommed that you run antechamber twice, once with Amber atom types and once
with gaff. Use the gaff results to fill in the missing parameters in the
Amber atom type result. (You'll have to do this by hand, by editing the
frcmod file). Then use the Amber atom type unit.
> 3.) I have thus tried to create a new unit based on the advice on
> creating a new unit, but failed. I think this is because I do not
> understand why one cannot simply
>
> UNIT_NAME=loadmol2 NAME.mol2
> loadamberparams NAME.frcmod
You can do this. Just saying the "it failed" (or "it fails terribly")
doesn't give us anything to go on in terms making suggestions.
>
> and make sure the pdb name matches NAME for the unit? This fails
> terribly, but I do not understand why (because I am not really sure I
> understand how leap "recognizes" units and adds in the "right" missing
> atoms (like a terminal P or O in a helix, or a missing hydrogen). I get
> atoms overlapping ontop of one another.
Once you load the units (as above), you can use the "desc" command in LEaP
to find out what LEaP thinks the residue name and atom names are in the unit
you loaded. You have to make sure that the residue and atom names in the pdb
file match those you get from the "desc" command.
If there are atoms in the library but which are missing from the pdb file,
LEaP will try to build them in. The other mismatch (where you have atoms
in the pdb file that are missing in the library) is almost always a fatal
error. From the very brief account you have given, I'm guessing that the
atom names in your pdb file don't match those in the NAME.mol2 file.
>
> 4.) I do apologize if this information is in the Amber tutorials; to my
> knowledge, 2 of them deal with non-connected ligand parameterization,
> and one deals with connected-non-standard residue insertion in a protein
> (whose process seems very different than for a helix).
>
Tutorial B5 is the one that is closest to what you are doing. There is no
fundamental different in procedure between modified amino acids and modified
nucleotides.
...good luck....dac
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Received on Sun Sep 13 2015 - 21:30:03 PDT
