VMD-L Mailing List

From: Per Larsson (larsson.r.per_at_gmail.com)
Date: Thu Sep 19 2019 - 06:14:37 CDT

Hi all,

I am trying to use the ffTK to parameterize a rather large (41 atoms) molecule, which consists of a salicylamide part and a hydro-carbon chain ending with a carbonyl group (so essentially a fatty acid) bound to the nitrogen of the salicylamide.
Aside from being quite large, so the QM calculations take quite some time, I also have issues with placing the water molecules properly for determination of interactions energies, presumably due to steric clashes with nearby atoms.

I did submit the molecule to Paramchem, and the high penalties (43 at most for a dihedral, 16 for the charges) are all found in the salicylamide part of the molecule. Therefore I think it makes sense to split the ffTK parameterization, working on the salicylamide and essentially leaving the fatty acid tail as it is.
However, what then becomes the strategy for eventually joining these two fragments at the end? If I do get optimized charges for example, those will then sum to zero, right, but when I add in the fatty acid part, the total sum is not going to be zero again, most likely? Do I include this by saying that the hydrogen atom which is lost upon joining the fragments should bear the full charge sum of the fatty acid tail? And how about bonds, angles, dihedrals that cross between these two fragments?

Many thanks in advance
/Per