Dear Developers,
After some months in collaboration with Silicon Therapeutics, I am pleased
to announce the first merge to master of code for supporting virtual site
customization in Amber simulations. The pmemd and pmemd.cuda programs have
been upgraded to detect two new fields in the Amber prmtop format,
VIRTUAL_SITE_FRAMES and VIRTUAL_SITE_FRAME_DETAILS, that specify up to
seven unique virtual site frames. (The former provides integer atom indices
for the virtual site and its frame, the latter gives dimensions on the
frame.) All of the frames described in the mdgx chapters of the Amber20
manual are now supported by our main simulations engine, as well as two new
additions: a two-site frame that places the virtual site at a fixed
distance from its parent atom, and a four-site frame that can model objects
like ammonia nitrogen lone pairs. All of the original virtual site
support, inferring the types from bonding patterns, remains active in the
program. Silicon Therapeutics is interested in using the virtual sites for
their free energy calculations, so the new additions in both programs
support TI through the "dual-topology" method as well.
While the pmemd program now detects the new frames, making force fields
with them is another matter. The ideal solution may be to have antechamber
take directives to include virtual sites in the models it makes, and add
information to the prepin / OFF lib formats that tLEaP can read. As CanDo
becomes our authoritative topology and system creator, this functionality
can go there as well. In the near term, however, the mdgx program can take
a simple namelist-format file and apply the information to all residues in
a standard Amber prmtop to create a new prmtop with VIRTUAL_SITE_FRAMES and
VIRTUAL_SITE_FRAME_DETAILS fields. Here is an example of rules for turning
all TIP3P waters in a simulation into TIP5P-Ew:
% These rules add extra points to all waters in a prmtop
&rule
epname EP1
eptype Out-3
parent O
frame2 H1
frame3 H2
residue WAT
v12 -0.344908263
v13 -0.344908263
v12x13 0.644379035
q -0.2410
&end
&rule
epname EP2
eptype Out-3
parent O
frame2 H1
frame3 H2
residue WAT
v12 -0.344908263
v13 -0.344908263
v12x13 -0.644379035
q -0.2410
&end
% These rules modify the existing TIP3P atoms to become TIP5P-Ew
&rule
atom O
eptype NONE
residue WAT
q 0.0
sig 3.09700
eps 0.17800
&end
&rule
atom H1
eptype NONE
residue WAT
q 0.2410
&end
&rule
atom H2
eptype NONE
residue WAT
q 0.2410
&end
Using these &rule namelists, one can add virtual sites to ligands, protein
residues, and any other system component. The mdgx program provides
detailed documentation of how to use the &rule namelist, in addition to the
new &parmedit namelist for rebuilding topologies. Type the name of any
namelist (in all caps) as an argument to mdgx on the command line:
mdgx -RULE
mdgx -PARMEDIT
A number of examples can be found in the mdgx test cases. While the
topology writing feature of mdgx will be superceded by CanDo in time, its
facility for fitting parameters for the new virtual site frames will remain
Amber's primary means for developing these models. For years, mdgx has had
the ability to add these customized virtual sites to a topology and fit
partial charges, and I have done a number of calculations examining what
they can do for ESP fitting and hydration free energies. More recently I
have added support to the valence bond parameter module, but this has not
yet seen a s application. In summary, all the tools are now in place to
create Amber force fields with a diverse selection of massless sites. We
can look forward to a leap forward in model development in the coming years.
Dave
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Received on Wed Jun 24 2020 - 08:00:04 PDT
