Yes, Mark is exactly correct about the glitch. I had just forgotten to
change this default charge in the ffnonbonded.itp when copying from
another atom. As mentioned this has no impact as these charges are never
used by pdb2gmx.
Cheers
Tom
Mark Abraham wrote:
On 6/04/2011 2:51 PM, Peter C. Lai wrote:
Hello
I am constructing a ligand for which I wish to use the new Charmm CGenFF
parameters (a long aliphatic ketone).
I am using Tom/Par's charmm36 lipid conversion as a baseline template for
comparison:
For reference, c36 lipid CTL3 atoms (in the case of POPC) map to CG331
in CGenFF; they are both to represent alkane CH3 carbons. Same with
CTL2 -> CG321. In my case I am particularly interested in CGenFF's
parameterization of a ketone carbonyl and oxygen: CG2O5 and OG2D3
(without any associated carboxylic bias or bias from non-carbons found
in other parameters. For example C=O in amino acid backbone appears in
ffbonded.itp as 5.188e+05 for kB whereas Mark's script yielded a kB of
5.858e+05 for CG2O5=OG2D3, not to mention the bond angles should be
different and especially the nonbonded interactions since we've replaced
N with C and we have an extra H etc. etc.).
My ligand for now is pretty simple:
OG2D3
||
CG331-CG321-...-CG321-CG2O5-CG331
or, in c36 lipid/prot terms:
O
||
CTL3-CTL2-...-CTL2-C-C-CTL3
How would I convert the relevant atoms in CGenFF's prm file to both
dihedral and nonbonded interaction .itp for gromacs?
The standard CHARMM .prm files give an indication of how the parameters
will be used, so it's just a matter of converting units and taking care
of any constants.
I tried using Mark's
perl scripts and it is giving me wrong LJ terms as well as not picking up
any 1,4 interactions (not to mention it has no knowledge of Par's
functype 9 for converting Charmm dihderals - we should no longer be using
R-B functions).
This script predates dihedral functype 9, and implements a
post-processing approach to deal with LJ, 1-4 and some dihedrals. I
assume you haven't done the latter. In any case, the form of my
solutions do not mesh at all with Par's solutions - forget about my scripts.
You seem to be only interested in about two atom types, so I'd expect
you can convert all the relevant things by hand in under an hour.
Finally, a slightly (un)related question:
in ffnonbonded.itp, why does CTL2 get a charge of 0.05 when in reality we
usually give it -0.18 for associated molecules in the rtp? Is there
something I'm missing there? (CTL3 has -0.27 in both the itp and rtp files
which makes sense to me).
Sounds like a glitch when the file was written - I guess some other
carbon also has 0.05 and this was copied and pasted. In any case, the
charges in ffnonbonded.itp are never used by pdb2gmx, because
precedence-taking residue-specific charges are defined in the .rtp. If
one were to use some other tool for generating topologies, I don't know
whether charges missing from a [moleculetype] definition are looked up
in ffnonbonded.itp.
Mark
--
Dr Thomas Piggot
University of Southampton, UK.
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