Dear all,
I am following the p450 tutorial to set up a QM/MM optimization of a metalloprotein in Py-ChemShell, however, I am having problems for copper to be recognized. I am following the structure below in my script:
First, convert user-defined CHARMM files for camphor to DL_FIELD format
udff = DL_FIELD.charmm2udff(rtf=‘…/1_solvation/mytop.rtf’,
prm=‘…/1_solvation/mytop.prm’, version=‘CHARMM36_prot’)
Now use DL_FIELD to define the forcefield using built-in CHARMM36_prot
NB: cutoff distance defined in a.u.
my_ff = DL_FIELD(ff=[‘CHARMM36_prot’, udff],
override_builtin=False, original_tip3p=False)
In mytop.rtf and mytop.prm I have included all my system’s atom types, including the copper ion.
Here is what I get in the output:
Residues (i.e. DL_FIELD molecule types) not found:
CU2P
Any idea how to solve this?
Thank you!