Dear Nwchem users,
I prepared a simple QM/MM optimization input, where only an aspartate side chain was included in the QM part. The prepare module looks like:
prepare
system spl
source prot.pdb
amber
new_top new_seq
new_rst
modify atom 123:_CB quantum
modify atom 123:2HB quantum
modify atom 123:3HB quantum
modify atom 123:_CG quantum
modify atom 123:_OD1 quantum
modify atom 123:_OD2 quantum
center
orient
solvate
update lists
ignore
write spl_ref.rst
write spl_ref.pdb
end
task prepare
I think the definitions of the QM atoms are as in the example inputs, and in fact they are accepted as QM atoms. However, when I check the pdb file created, the two HB atoms are placed far away from their original positions (the remaining QM atoms are OK). If I remove the two H atoms from the QM part, then they location is correct. I appreciate if someone could explain the reason for this.
Thanks
|