-fcust flag in GENENMM specifies custom interactions between elastic network nodes by a passed ffile.
If any two residues in the ffile share a bond in the elastic network model, the lastest spring strength value for the two residues will be assigned to the shared bond.
Figure Residues 61B (orange) and 128A (magenta) share a bond. The resulting bond's spring strength is 9.0 because in force.res file residue 61B was assigned last.
Fix
An algorithm must be implemented which resolves this conflict, There are options for the resulting spring strength:
Assign the lowest or the highest value.
Average the spring constant values.
Specify a value manually.
The last one requires checking if two residues are connected.
Thus, a notification must be in place when spring strengths are modified.
Description
-fcustflag inGENENMMspecifies custom interactions between elastic network nodes by a passedffile. If any two residues in theffileshare a bond in the elastic network model, the lastest spring strength value for the two residues will be assigned to the shared bond.Example
PDB ID: 1G6N
$ GENENMM -pdb 1g6n.pdb -ca -het -c 8.0 -fcust force.resforce.res:force.resfile residue 61B was assigned last.Fix
An algorithm must be implemented which resolves this conflict, There are options for the resulting spring strength:
The last one requires checking if two residues are connected. Thus, a notification must be in place when spring strengths are modified.