Setting up QM-MM with homotrimer

From: Francesco Pietra (
Date: Thu Nov 05 2020 - 10:52:27 CST

I would like to carry out QM-MM simulations with a homotrimer bearing the
same peptide ligand at each subunit (chain). Using the unabridged system,
however with QM-MM limited to one subunit (chain)

I am in doubt how to set

# Only part of the receptor composes QM region)
set seltext "(protein and resid ......)"
[atomselect 0 "$seltext"] set beta 1

because neither the resname, nor the resid, nor the segname are able to
specify the QM part. It seems to me that only the atomID can do the job.

With VMD, in order to restrain residues for MD with the above system I used

set allsel [atomselect top "all"]
$allsel set beta 0
set restrainsel [atomselect top "index ID1 to ID2 ID4 to ID6 ID* to ID10
etc "]
$restrainsel set beta 1
$allsel writepdb tag.pdb

could the same be done for QM-MM?

Likewise, the peptide ligand could only be specified from its initial and
final ID. Could that be used?

Or could you think better?

Thanks for advice

francesco pietra

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