Questions tagged [amber]

Questions about or related to the AMBER software.

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2 votes
1 answer
67 views

Is there a scripted tool to add neutral terminal caps (e.g. NME, ACE) to peptide chains for use with AMBER forcefields?

I have a range of systems consisting of multiple peptide chains, some of which are one residue (i.e. single amino acids), which I'd like to analyse using molecular dynamics and AMBER-flavour ...
  • 778
3 votes
0 answers
38 views

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

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 ...
3 votes
1 answer
68 views

Calculate the atomic charge for transition metal using RESP?

I calculate the atomic charge using restricted electrostatic potential (RESP) and compute with the Hartree Fock method. This method is OK for organic compounds, but for complexes that contain ...
8 votes
0 answers
99 views

Calculate FF interaction energy of small molecular dimers [closed]

I have a set of molecular dimers (~25 atoms) for which DFT-D3 interaction energies are calculated by Psi4 and Turbomole program. Now I want to compare these values against Force-Field methods like UFF/...