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2 votes
Accepted

GROMACS RMSF Result Analysis Problem

The residue numbering in a PDB file mainly depend on the person who deposited it. There are usually reasons for how things are numbered, but ultimately you should look at PDB file, and check the ...
fra's user avatar
  • 567
2 votes

How to make a video of a gromacs gmx dump standard output with VMD

No need to use gmx dump, you can simply load a xtc or trr trajectory in VMD using: ...
O.Laprevote's user avatar
1 vote

Generating 3D cartesian coordinates of a peptide and computing van der Waal interactions (1-4 atoms) for a given set of dihedral angles?

The PDB module in Biopython is worth checking out for obtaining angles, distances, torsion angles. It is described from p208 at http://biopython.org/DIST/docs/tutorial/Tutorial.pdf. It doesn't do van ...
M__'s user avatar
  • 12.5k
1 vote

Energy minimization of molecules

As @M__ has mentioned, the terminology in your Q is a bit confusing. A molecule can be the small molecule (ligand, compound etc.) or a polypeptide chain (protein). Conformer generation of a compound ...
Matteo Ferla's user avatar
  • 4,234
1 vote

Gromacs molecular dynamic simulation throwing error during minimization

Answer from @user1271772, converted from comment: Try on this site: https://mattermodeling.stackexchange.com/questions/tagged/gromacs. There's an entire GROMACS tag there. Answer from @vishal-kumar-...

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