Amber Archive Sep 2023 by subject
- [AMBER] ?==?utf-8?q? ?==?utf-8?q? ?= Alternatives to NAB for building DN
- [AMBER] [Sender Not Verified] Differences between the same dynamic
- [AMBER] [Sender Not Verified] Query regarding unusual atom
- [AMBER] Adding organic ligand in membrane system
- [AMBER] Alternatives to NAB for building DNA
- [AMBER] AMBER error slurmstepd
- [AMBER] amber unit
- [AMBER] Amber22 DDBoost Install Error
- [AMBER] AmberTools23 fails to build with python 3.11 - Reply
- [AMBER] antechamber error: "This molecule may have more than one unit..."
- [AMBER] attempting to run QUICK
- [AMBER] Autocorrelation function :
- [AMBER] Average RMSF calculation
- [AMBER] Calculation of RMSD
- [AMBER] charge extract from cpin file
- [AMBER] Chirality flipped for 2 identical molecules
- [AMBER] Clarification on attempted TMD run
- [AMBER] Coulomb energy in MMPBSA
- [AMBER] CpHMD in amber18 using cuda
- [AMBER] cpptraj nativecontacts
- [AMBER] CPPTRAJ, protein width
- [AMBER] CUDA version of nabnmode?
- [AMBER] Differences between the same dynamic
- [AMBER] error in amber22 installation
- [AMBER] Error in equillibrium step of MD
- [AMBER] Errors with .dcd files using MMPBSA
- [AMBER] extracting a frame from trajectory at a specific time
- [AMBER] Failed test cases in $AMBERHOME/test/nfe/bbmd in Amber22/Amber23
- [AMBER] high positive values for VDW interactions using LIE function
- [AMBER] How can I resolve the issue of the 'NAB' command not being found in AmberTools23?
- [AMBER] How to designate the Bond type(Sodium) in amber 22
- [AMBER] How to get Inherent structure (Minimization energy)
- [AMBER] How to get the Z component of ions from the trajectory file?
- [AMBER] Incomplete installation: "Fixing Miniconda script shebangs"
- [AMBER] Installing on Ubuntu 22.04/CUDA 12.2
- [AMBER] Installing on Ubuntu Question
- [AMBER] Issue with bond and angle parameters
- [AMBER] Issue with MMPBSA calculation
- [AMBER] Maestro PDB to Amber PDB
- [AMBER] MMPBSA calculation of multiple complex simulations:
- [AMBER] MMPBSA issue:
- [AMBER] MMPBSA PBRadii:
- [AMBER] Optimization and balancing steps for a membrane protein, small molecule and POPC bilayer membrane complex system
- [AMBER] PhD position at University Complutense of Madrid in biocondensate modelling
- [AMBER] Pressure controlling keyword:
- [AMBER] Problem preparing structures
- [AMBER] Problem with adding new atoms in prep file
- [AMBER] Problem with water molecules angle in MD simulation
- [AMBER] Query Regarding PDB2GMX Error with Amber Force Field
- [AMBER] Query regarding unusual atom
- [AMBER] Reagarding AMBER ff14SB-ildn
- [AMBER] Regarding atom types while using antechamber for modified DNA bases
- [AMBER] Regarding issue in the minimization output
- [AMBER] Regarding periodic box dimentions
- [AMBER] RNA simulation basics
- [AMBER] SASA calculation:
- [AMBER] Strategies to run MMPBSA.py for multimeric systems
- [AMBER] Support or H100s
- [AMBER] test message
- [AMBER] the parameter mctrdz in mmpbsa.in
- [AMBER] Umbrella Sampling
- [AMBER] Visualizing amber MD trajectory in vmd:
- [AMBER] watershell cpptraj:
- [AMBER] What is the best way to do triplicate runs
- [AMBER] 回复: extracting a frame from trajectory at a specific time
- Last message date: Sat Sep 30 2023 - 09:00:02 PDT
- Archived on: Mon Dec 09 2024 - 05:56:11 PST