I appreciate your time in helping me very much. I realize you are a very
busy scientist.
1.) The reason the process of covalent unit creation in a helix is
seemingly different (at least to my naive eye) compared to the tutorial
on proteins is the linkage. I know how amino acids link internally;
there is only one way to do it (NHCO formation). I am confused on a
helix because I am unsure what unit Leap will look for: nucleic acid,
nucleotide, nucleoside? I am guessing I parameterize ONLY the nucleic
acid, but I am unsure what atoms Leap will automatically assume to add
in to connect.
2.) Using just a nucleic acid as the parameterized units...
I understand that most atom types differ only by case (upper/lower)
between GAFF/Amber style text formatting. However, I am seeing atom
types in the amber parameterization that I cannot identify. For example:
MASS
CA 12.010 0.360 same as c2
C 12.010 0.616 same as c
HA 1.008 0.135 same as hc
O 16.000 0.434 same as o
NA 14.010 0.530 same as na
H 1.008 0.161 same as hn
N2 14.010 0.530 same as n3
NO 0.000 0.000 ATTN, need revision
DU 0.000 0.000 ATTN, need revision
includes "DU," which I do not know how to identify. This does not seem
to be a standard Amber designation of an atom, based on what I google
searched or in the manual? I am guessing I did not ask for Amber
parameters properly:
antechamber -i File.pdb -fi pdb -o File_1.mol2 -fo mol2 -c bcc -s 2 -at
amber
parmchk -i File_1.mol2 -f mol2 -o File_1.frcmod -a Y
3.) I imagine correcting my mistakes above would resolve the subsequent
problems you offered commentary on (the "it fails terribly" comment
referred to the fact that I had overlapping atoms when I load the PDB
into Leap. Leap is adding atoms I do not intend)
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
On 09/14/2015 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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Received on Mon Sep 14 2015 - 11:30:02 PDT
