Ah...I am quite dense. "DU" is no doubt dummy. Sorry I did not see this
sooner.
Nonetheless, I am still confused on how to proceed. If the Amber FF
types do not include all the ones in GAFF, what is the right procedure?
On 9/14/15 12:01 AM, David A Case wrote:
> 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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--
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
Visiting Associate Professor of Chemistry
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
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Received on Mon Sep 14 2015 - 14:00:03 PDT
