| 10:11:43 AM PDT - Mon, Oct 29th 2018 |
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Dear all,
I am experiencing a strange behaviour of the prepare module for a QM/MM calculation. Indeed, when the module runs, it adds missing atoms to my structure, which in this case are hydrogens and terminal oxygen and hydrogen to have COO- and NH3+ groups at both ends of my amino acid chain (composed of 2 SER, since I just wanted to try QM/MM in NWChem with a really simple system).
I wanted to treat SER1 quantum, and SER2 with MM.
However, adding atoms works well for the MM segment (SER2) but not for the QM one (SER1). And I tryed the other way around showing that the problem is always on the QM part. Although there are no error in the output file, the added atoms have non-sense coordinates in the generated pdb file, and are not consistently linked to my residue...
Do you have any idea about the origin of the problem (the PDB file is in the right format by the way, since it works in all MM or all QM calculations).
Many thanks,
Bastien
PS: My input file is:
echo
start lpxr_qmmm
memory 1600 mb
prepare
system lpxrqmmm
source lpxr_fragment.pdb
new_top new_seq
amber
modify segment 1 quantum
update lists
ignore
new_rst
write lpxrqmmm.pdb
write lpxrqmmm.rst
crop
end
task prepare
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