Feature to control max bondlength for specific atom names

[khavernathy]

external request.

e.g. instead of a list of manual changes in hardcoded form here:

mcmd/src/bonding.cpp

Line 308 in e222d20

else if ((a1=="Zn" || a2=="Zn") && r <= 2.1) // Zn4O group

modify the bondlength command to accept atoms names in a modular fashion. Like the custom UFF sigma/epsilon options.

many thanks for providing the MCMD code to the scientific community.
I have a question refering to the generation of the force field topology
by your program
(in order to include MOF dynamics in my simulations, for instance).
I am facing problems with the automatic generation of the connectivity
matrix with the
includes parser. The issue is that increasing the bondlength value to
include metal-ligand bonds, for instance
will create extra bonds within the organic part of the linkers. This
most often occurs in MOFs that contain
5-membered ring systems, such as triazoles, pyrazoles, etc.
Is there a possible input to search for longer pair distances for single
atoms only, i.e.
something like "bondlength Zn * 2.4 to search for possible bonds around
a metal center only ?
Alternatively, can I include a correct bond matrix in the pdb file by
"CONNECT" ?
Looking forward to your comment !