[AMBER] Problem with lone pair

From: Giachetti Andrea - CERM <giachetti.cerm.unifi.it>
Date: Mon, 13 Oct 2014 10:23:03 +0200

Dear all,

I'm trying to create a special residue containing a metal with three
dummy atoms (lone pairs) to define the axes of a tensor, for use with
paramagnetic pseudocontact shifts.
I have created a lib file with tleap using the TNS.cmd and defined the
parameter in TNS.par (attached).
When I try to heat the protein (tensOK.pdb) and run an MD trajectory the
new residue TNS remain frozen in the space. I'm using pmemd (version 14)
compiled with cuda.

Can you think of a possible error I am making?

Also you can find a short movie where the center of the tensor are
constrained with an amino acid nearby.

Link to Dropbox directory with the files:


Thank you,

Andrea Giachetti

University of Florence

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Received on Mon Oct 13 2014 - 01:30:02 PDT
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