I'm recently switching to AMBER from CHARMM, so I apologize in advance if
any of the following is confused by misunderstandings or incorrect
assumptions about how AMBER works:
I am trying to perform QM/MM simulations of several molecules composed of
non-standard residues (so I constructed them myself from scratch using leap,
etc.). These are small molecules (< 50 atoms), so the QM region will
diffuse significantly during the simulation. A problem that I have
encountered in the past (with other QM/MM codes) is that the SCF calculation
becomes unstable near the periodic boundary due to re-imaging, etc. The
only thing I can think of to prevent this is to re-image by molecule rather
than by residue, so I think my concern is addressed by the following
question (maybe it's not):
Where/how does AMBER define molecules? Is this information in the prmtop
file? I observed that molecules composed of residues do not have "TER"
between them, but that when I convert my crd file to a pdb file, there is a
"TER" between the residues that I would like to be connected. If I simply
delete the "TER", re-load the pdb into leap and save a new prmtop file, will
that re-define the molecule as I want it?
Thanks,
Brian
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Fri May 27 2011 - 07:30:02 PDT
