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Questions tagged [amber]

Questions about or related to the AMBER software.

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1 vote
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AMBER fails to generate parameters

I'm new to computational chemistry, and I'm trying to model the enzyme EGFR and a molecule named lapatinib with AMBER. I got a .pdb file of Lapatinib attached to EGFR, and a .sdf file of lapatinib ...
Leo's user avatar
  • 57
1 vote
0 answers
26 views

How the center of mass of a large number of atoms influences the performance of Amber in a system?

I'm interested in conducting umbrella sampling between a ligand and the center of mass of a lipid. Initially, I chose the atom numbers for the ligand and all the atom numbers for the lipids. However, ...
Abd-Elazeem Mohamed's user avatar
2 votes
1 answer
67 views

Establishing AAs protonation - which software to choose?

I need to establish protonation of aminoacids composing the studied protein. To my knowledge there are H++ and Pdb2pqr servers that are able to do that. However, they yield quite much different ...
farmaceut's user avatar
  • 566
3 votes
1 answer
77 views

Estimate the time between different residues?

Imagine now, I have 5 structures, and I want to estimate the time when the 5 structures are closer to each other at the same time. I thought I could extract the distance between the different ...
Abd-Elazeem Mohamed's user avatar
1 vote
0 answers
41 views

Apparent change in bond order of a molecule after an amber simulation? [closed]

I have been following along with this tutorial for simulating a small ligand binding a protein receptor. In both the tutorial and my follow-along (which uses the same commands as the tutorial but with ...
weddegege's user avatar
4 votes
2 answers
123 views

Non-Covalent Interaction between drug and DNA?

I am using classical molecular dynamics (MD) to observe a non-covalent interaction between my complex and the DNA, but there is a problem in that the complex interacts with the terminal of the DNA for ...
Abd-Elazeem Mohamed's user avatar
3 votes
0 answers
122 views

I have a problem with Amber18 configuration at the make install step [closed]

I have a problem installing Amber. First, I enter the command: ./configure --with-python /usr/bin/python3 --with-netcdf $AMBERHOME/netCDF gnu Than make: ...
Andrey Buglak's user avatar
2 votes
1 answer
1k 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 ...
lewiso1's user avatar
  • 936
3 votes
0 answers
48 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
3 votes
1 answer
381 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 ...
Abd-Elazeem Mohamed's user avatar
8 votes
0 answers
133 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/...
Pro's user avatar
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