From: Ernesto Aleksei Delgado Hurtado (ERDELGADO_at_UDEC.CL)
Date: Thu Jan 19 2023 - 18:09:44 CST

Hi Vardan

In the CHARMM force fields there are groups of atoms which together have 0 charge (check the topology file for CGenFF for example). Each of your fragments is like those groups and should have 0 charge too in the whole molecule.

For the atoms that have hydrogens attached that are absent in the initial structure you delete the hydrogen and add the hydrogen charge to the heavy atom, then once you have all the charges for your different fragments you copy them into the your new str file just like you'd do with bonds, angles and dihedrals.

El 19/1/23 a las 16:39, Vardan Vardanyan escribió:

Dear VMD Comunity,

I have large molecules ( around 131 atoms ) to simulate with the membrane.
My molecules
 have two or three protonated Nitrogens. The protonated Nitorgens are in
the pyrroline group.
I upload the mol2 file of my molecule into CGenFF (ParamChem) to obtain
the parameters of my molecule. As usual, the stream file has parameters
with high penalties ( the pyrroline groups are the ones ruining the score )
that should be further parametrized with ffTK.
Because the molecule is too big and only the pyrroline group has high
penalties, I am trying to use ffTK parametrization only for fragments with
high penalties.
So in the case of bonds, angles, and dihedrals, I can copy the final
results into an initial str file and generate psf, PDB, and par file using
the same ffTK (although coping in the case of the big molecule is very
However, things are more complex in the case of partial charges.
So my question is, are there any code-based procedures to automate this

This question is already discussed in Parameterization strategy with
fragmentation in fftk
however, I am still puzzled about rewriting the partial charges by hand.
In my case, the pyrroline group is neighboring benzene rings, and during
parameterizations, carbons with high penalties have hydrogens that are
absent in initial structures. (P.S. my background is in physics, so I am
sorry if the terms I used for molecular groups sound funny)

Thanks in advance,