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10 votes
Accepted

How to swap orbitals in ORCA?

I figured out the correct formatting. The section defining the QM needs to have the MORead option, the %moinp section, and the <...
kskinnerx16's user avatar
  • 1,546
7 votes

Constraining a set of atoms in the MM region using pDynamo (CHARMM/ORCA interface)

To tether a set of atoms (index or fragment) in pDynamo, the below lines are needed (energy model can vary): ...
kskinnerx16's user avatar
  • 1,546
7 votes

Alternative to CGenFF for generating large ligand topology

I'd use OpenMM's openmmforcefields package, which is available on GitHub. I haven't used it extensively, but I recommended to a student in a colleague's lab and ...
Geoff Hutchison's user avatar
5 votes
Accepted

Silica (α-cristobalite) water system generation

As you note, any structure with dangling silicon atoms cannot be considered correct. I'm surprised CHARMM-GUI would produce a structure with undercoordinated (<4 bonds) silicon. I can't really tell ...
WaterMolecule's user avatar
5 votes
Accepted

Defining coordinates using Vector3

In pdynamo 3.0.9 A vector3 can be defined by importing from Geometry module. For example, ...
Cody Aldaz's user avatar
  • 8,017
3 votes
Accepted

How to localize orbitals in pDynamo (CHARMM/ORCA interface)?

I found the most consistent way to localize orbitals. Use the orca_loc extension. You must create and input file where define the localization method (PM, Boys, ...), and the orbitals you want to ...
kskinnerx16's user avatar
  • 1,546
3 votes
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CHARMM36 Parameters for Neutral Arginine

A quick search of the toppar folder in CHARMM shows that there are three patches that are available to create neutral arginine from the charged arginine. This is the sample input ...
Hemanth Haridas's user avatar
2 votes
Accepted

My CHARMM IC table generation has caused hydrogen to bond to two carbons. How do I fix this?

I was able to build the structure correctly using the following input file ...
Hemanth Haridas's user avatar

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