On Fri, May 27, 2011 at 10:02 AM, Brian Radak <radak004.umn.edu> wrote:
> 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):
>
As far as I know, AMBER images by molecule (see the sections
SOLVENT_POINTERS and ATOMS_PER_MOLECULE, with the details of those sections
described in
http://ambermd.org/formats.html).
> 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?
>
TER cards *do* define molecules, but adding/deleting them changes the
topology completely. The molecule definitions are set when the prmtop is
created by LEaP. Ideally, it should be that any atom within a molecule must
be reachable by every other atom within the molecule by a set of bonds, and
there are NO atoms outside of the molecule that can be reached via bonds
from any atom within that molecule.
That is, it is a closed set. If this wasn't true, MM energies would blow up
as well (not just QM SCF convergence failures).
HTH,
Jason
>
> 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri May 27 2011 - 09:30:04 PDT
