Questions tagged [charmm]

Questions about the molecular simulation program CHARMM (Chemistry at HARvard Macromolecular Mechanics). CHARMM primarily targets biological systems including peptides and proteins, but also finds broad applications for inorganic materials with applications in materials design.

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

As above, I am attempting to generate an IC table for decanoic acid using CHARMM (version 48b1) so I have a minimized geometry. I have attached my build.inp script and the stream file I have written. ...
Thomas's user avatar
  • 81
3 votes
1 answer
60 views

CHARMM36 Parameters for Neutral Arginine

I am looking for CHARMM36 parameters for Neutral Arginine. Protonated form of Argnine is already available in CHARMM36 library, but not the same for Neutral. Thanks. With best regards
Roshan Shrestha's user avatar
4 votes
0 answers
47 views

MMGBSA: Electrostatic and van der Waals

I ran a molecular dynamics simulation using Gromacs 2023.2, with the CHARMM36 forcefield. And I ran a per-residue energy decomposition calculation using gmx_MMPBSA, with MMGBSA model. MMGBSA model ...
Bruce Zhou's user avatar
8 votes
2 answers
416 views

Silica (α-cristobalite) water system generation

I'm trying to model the silica-water interface using classical molecular dynamics. Hope to use LAMMPS for the simulations and CHARMM potential to model the atomic interactions. I wonder how to ...
WhiteLeo9's user avatar
  • 183
3 votes
0 answers
46 views

Creating Amber/CHARMM style force field potential for energetic materials using DFT [duplicate]

What are the basic steps and methodologies used in creating inter-atomic force field potential for CHARMM/Amber style for energetic materials with the help of DFT? What are the best possible free ...
Md. Rifat Hossain Kawshik's user avatar
2 votes
0 answers
58 views

CHARMM-gui creates empty space between LPS-s and terminates while building e. coli outer membrane with peptides above it [closed]

I'm trying to build outer membrane of e. coli with small peptides above it, with CHARMM-GUI. Peptides should be positioned above the membrane, but CHARMM-GUI creates space for them between LPS (...
multipole's user avatar
  • 121
8 votes
1 answer
589 views

Alternative to CGenFF for generating large ligand topology

I am now preparing a ligand topology following GROMACS protein-ligand tutorial. However, I have a large ligand (446 atoms). $ wc -l my_ligand.pdb 446 my_ligand.pdb ...
littleworth's user avatar
  • 1,674
8 votes
0 answers
344 views

Lone pairs in CHARMM for molecular dynamics [closed]

I have a substrate that has a Br-C bond. In CHARRM the line below is included in the .str file: ...
kskinnerx16's user avatar
  • 1,546
4 votes
1 answer
49 views

Defining coordinates using Vector3

I am trying to implement a tether restraint in the MM region of my QM/MM calculation using pDynamo (CHARMM/ORCA interface). I need to define the origin as a Vector3. Does anyone know how to do this?
kskinnerx16's user avatar
  • 1,546
10 votes
1 answer
114 views

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

I am trying to perform a QM/MM optimization in which my substrate is in the MM region. However when this happens there are significant changes to the geometry (undesired). I want to avoid fixing all ...
kskinnerx16's user avatar
  • 1,546
7 votes
1 answer
120 views

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

Does anyone know how to localize orbitals in pDynamo (CHARMM/ORCA interface). I am trying to identify the correct orbitals to swap for my high-spin iron(IV) system.
kskinnerx16's user avatar
  • 1,546
10 votes
1 answer
199 views

How to swap orbitals in ORCA?

I am trying to swap orbitals for a high-spin iron(IV) complex. The orbitals that correspond to the iron are not in any of the SOMOs. I am using the pDynamo QM/MM program, which is an interface for ...
kskinnerx16's user avatar
  • 1,546