kskinnerx16
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3 answers
16 votes
474 views
Is there any software that is optimized specifically for QM/MM?
Accepted answer
12 votes

pDynamo pDynamo is a program developed by Martin Field, and is a CHARMM/ORCA interface. There is a wiki. Here is the first line from the abstract: The pDynamo program has been developed for the ...

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8 answers
14 votes
2k views
What are some free programs to do docking?
10 votes

CDOCKER CDOCKER is docking program developed by the Brooks Lab and it works with CHARMM. CHARMM does have a free version named charmm. The difference is no DOMDEC or GPU high performance modules. Pros:...

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5 answers
13 votes
2k views
Can I use two different codes?
8 votes

This has been done previously. In my experience the geometry is found with one code, and solvent corrections are performed with another. I have personally done this[1], and have had the results ...

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3 answers
16 votes
333 views
How to calculate homolytic bond dissociation energies?
8 votes

BDEs are calculated by the below procedure: Calculate initial energy Perform homolytic bond cleavage and separate fragments Calculate energies of the fragments, add the energies together Calculate ...

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1 answers
9 votes
88 views
How to swap orbitals in ORCA?
Accepted answer
8 votes

I figured out the correct formatting. The section defining the QM needs to have the MORead option, the %moinp section, and the %scf section. Example: !B3LYP 6-31G* Slowconv MOREAD *xyz 0 3 ... * %...

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1 answers
10 votes
72 views
Constraining a set of atoms in the MM region using pDynamo (CHARMM/ORCA interface)
7 votes

To tether a set of atoms (index or fragment) in pDynamo, the below lines are needed (energy model can vary): tethers = pM.SoftConstraintContainer () system.DefineSoftConstraints ( tethers ) reference ...

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2 answers
11 votes
116 views
Which SCF energy to use to plot PES after calculations with SMD?
7 votes

Generally you want to use the same settings when trying to combine results from different jobs. However, below is the general procedure that I have seen performed for a basic, publishable PES. 1) ...

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3 answers
10 votes
262 views
How I can analyze and present docking results?
7 votes

Docking results can be analyzed in a number of ways by looking at various geometric parameters, such as a distances, angles and dihedrals. These are then typically compared against "ideal" values, ...

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2 answers
8 votes
130 views
Docked pose and energy minimization
6 votes

One way these calculations are performed is using MD and implicit solvent calculations. The general procedure for these simulations are: Perform simulations and get frames Perform implicit solvent ...

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1 answers
7 votes
56 views
How to localize orbitals in pDynamo (CHARMM/ORCA interface)?
Accepted answer
3 votes

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 ...

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1 answers
8 votes
58 views
Generating topology for charged molecules
1 votes

There are two options here and the choice depends on what you intend to do with your results. If you are going to perform QM calculations after MD, then you can just alter the charges as you outlined ...

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