CHARMM-GUI now supports the following Amber all-atom force fields for
Amber simulations in Solution, Bilayer, Nanodisc, Monolayer, Micelle
Builders:
Protein: FF14SB
DNA: BSC1
RNA: OL3
Lipid: LIPID17
Carbohydrate: GLYCAM 06j
Ligand: GAFF, GAFF2
Water: TIP3P, OPC
Hydrogen mass repartitioning (on or off)
“12-6-4” ions (on or off)
One can select the Amber force fields under available force fields in
the input generation step (generally the last step of any building module).
Note that CHARMM-GUI first uses the current CHARMM-GUI workflow with the
CHARMM all-atom force field to generate a simulation system and then
converts the system into the Amber format using the user-specified Amber
force fields. Therefore, one must know which molecules are available in
the Amber force fields; e.g., choosing certain chemical modifications
and lipids that are available in the CHARMM force field, but not in the
Amber force fields will incur conversation errors. Similarly, although
choosing the Amber force fields is available in Micelle Builder, there
is no supported Amber detergents yet; we will add them as they become
available. N-/O-glycans and carbohydrates are supported, but glycolipids
and lipoglycans (e.g., lipopolysaccharides) are not yet supported. In
addition, Amber users need to be careful about the terminal patches and
histidine residue names; please read the corresponding FAQs
<
http://www.charmm-gui.org/?doc=faq> under PDB Reader.
For Amber users who are not familiar with CHARMM-GUI, please watch
CHARMM-GUI Video Demos <
http://www.charmm-gui.org/?doc=demo>. Please use
the email contact <
http://www.charmm-gui.org/?doc=contact> in CHARMM-GUI
for any problems, questions, and comments.
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Received on Fri Oct 04 2019 - 05:00:01 PDT
