Dear amber developers & users,
I'm trying to get a time series of the intramolecular hydrogen bonds
of titratable residues from a CpH-REMD.
For example, the GL4 at the fourth position:
*hbond donormask :4 series uuseries example_file_donor*
*hbond acceptormask :4 series uuseries example_file_acceptor*
GL4 as a donor works fine, but when using the "acceptormask", I get columns
like these in the "example_file_acceptor" outfile:
GL4_4.HB3-GL4_4.OE2-HE22 ... GL4_4.HB2-GL4_5.N-H ... GL4_4.CA-GL4_4.OE2-HE22
...
*HB2 and HB3* are the beta carbon hydrogens, and then the alpha carbon (*CA*)
shows up too!
The amber manual says cpptraj follows this simple criterion:
*"...hydrogen bonds are FON”, i.e., hydrogens bonded to F, O, and N atoms
are considered donors, and F, O, and N atoms are considered acceptors.". *
So, why am I getting these results?
I know I could just add the atom elements to the *acceptormask*, but I was
wondering why this happens.
Best,
Germán P. Barletta
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Received on Thu Oct 15 2020 - 13:00:02 PDT
