On Thu, Jun 20, 2019, Fabian Glaser wrote:
>
>We have found that the DIHE refers to the propyl ring atoms, for which
>I understand there are not parameters with regards to their specific
>environment in this molecule, is that correct?
I don't think the above is correct. In principle, antechamber should
have no trouble with cyclpropyl rings: the sustiva example in
AMBERHOME/AmberTools/test/antechamber/sustiva has such a ring.
Your input structure has hydrogens in very unusal positions for a
cyclopropane ring. But atoms C32/33/34 are properly characterized as atom
type "cx", which is correct.
>
>If so, how should we set those DIHE angle parameters?
It doesn't look like anything is missing. What happens if you load the
mol2 and frcmod file into tleap, create a prmtop file, then minimize it
in sander? My expectation would be that you would get more nearly
tetrahedral carbon atoms in the cylopropyl ring, but most other parameters
would look OK.
>What is the best alternative to do it without gamess / gaussian?
>We obtained this geometry by building the molecule with ChemAxon
>MarvinSketch software.
I don't see anything wrong here, but I might have missed something. If
so, it should show up if you continue as you ordinarily would.
>
>Finally, we don’t understand the following dihedral definition:
>c -c -cd-cc 1.1 180.0 2.0 Using the default value
>
>This should be the C7, C8, C9 (cc, cd, c respectively) atoms, but I
>cannot find the other c-, how is this dihedral defined?
The other c is C35 (the only other atom of type c in the molecule.)
Offhand, I don't see anything wrong with these assignments, and geometry
looks like it should indeed be planar about atom C8. See if that is
what you get upon MM minimization.
You could also geometry optimize in a quantum program (sqm or your
favorite choice), and compare to the MM minimization. But, aside from
the hydrogens in the three-membered ring, I don't see anything that
jumps out at me as wrong here.
....dac
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Received on Thu Jun 20 2019 - 07:30:02 PDT
