From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Nov 16 2020 - 11:54:04 CST
On Thu, Nov 5, 2020 at 5:52 PM Francesco Pietra <chiendarret_at_gmail.com>
> 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 successfully
> 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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