Amber Archive Jun 2024 by date

72 messages: Starting Sat Jun 01 2024 - 07:30:02 PDT, Ending Thu Jun 27 2024 - 08:30:02 PDT
This period: Most recent messages
sort by: [ thread ] [ author ] [ date ] [ subject ] [ attachment ]

Saturday, 1 June 2024
- [AMBER] parmed missing in ambertools installation Martin Juhás via AMBER
- Re: [AMBER] parmed missing in ambertools installation David A Case via AMBER
Sunday, 2 June 2024
- Re: [AMBER] Quantum mechanical calculation for charge Kriti Shukla via AMBER
Monday, 3 June 2024
- [AMBER] Compiling AMBER24 for AMDGPU - undeclared identifier 'cusparseErrorCheck' Robert Welch - STFC UKRI via AMBER
- Re: [AMBER] NetCDF variable compression requires compiling with HDF5 support Martin Juhás via AMBER
- [AMBER] Amber24 Installation error Asma Abro via AMBER
Tuesday, 4 June 2024
- [AMBER] tLeap addAtomType usage Hantz, Eric via AMBER
- Re: [AMBER] tLeap addAtomType usage David A Case via AMBER
Wednesday, 5 June 2024
- Re: [AMBER] tLeap addAtomType usage David A Case via AMBER
Friday, 7 June 2024
- [AMBER] Building heavy water using tlep Dulal Mondal via AMBER
- Re: [AMBER] Building heavy water using tlep Carlos Simmerling via AMBER
Saturday, 8 June 2024
- [AMBER] Restarting pH REMD Abdelrahman, Noureen via AMBER
- [AMBER] Transform TIP3P to OPC Abdelrahman, Noureen via AMBER
- Re: [AMBER] Restarting pH REMD He, Amy via AMBER
- Re: [AMBER] Transform TIP3P to OPC He, Amy via AMBER
- Re: [AMBER] Transform TIP3P to OPC Carlos Simmerling via AMBER
- [AMBER] ntmin=5 not valid in Amber 24 Kshatresh Dutta Dubey via AMBER
- [AMBER] Parameterization Issue Kavinda Kashi Juliyan Gunasinghe via AMBER
Sunday, 9 June 2024
- Re: [AMBER] Parameterization Issue He, Amy via AMBER
- Re: [AMBER] Parameterization Issue Kavinda Kashi Juliyan Gunasinghe via AMBER
- Re: [AMBER] Parameterization Issue He, Amy via AMBER
- Re: [AMBER] Parameterization Issue Kavinda Kashi Juliyan Gunasinghe via AMBER
- Re: [AMBER] Parameterization Issue Kavinda Kashi Juliyan Gunasinghe via AMBER
- Re: [AMBER] Parameterization Issue Kavinda Kashi Juliyan Gunasinghe via AMBER
- Re: [AMBER] Parameterization Issue Carlos Simmerling via AMBER
- Re: [AMBER] Parameterization Issue He, Amy via AMBER
- Re: [AMBER] Parameterization Issue Kavinda Kashi Juliyan Gunasinghe via AMBER
- [AMBER] Amber23 Failed cases Vlad via AMBER
Monday, 10 June 2024
- Re: [AMBER] Parameterization Issue Carlos Simmerling via AMBER
- [AMBER] error in reading namelist cntrl when trying to minimize RNA Collin Nisler via AMBER
- Re: [AMBER] error in reading namelist cntrl when trying to minimize RNA Carlos Simmerling via AMBER
- [AMBER] finddgref.py using pH-REMD Dulal Mondal via AMBER
- Re: [AMBER] finddgref.py using pH-REMD Vinicius Cruzeiro via AMBER
- Re: [AMBER] ntmin=5 not valid in Amber 24 Kshatresh Dutta Dubey via AMBER
- Re: [AMBER] finddgref.py using pH-REMD Dulal Mondal via AMBER
- Re: [AMBER] finddgref.py using pH-REMD Vinicius Cruzeiro via AMBER
- Re: [AMBER] finddgref.py using pH-REMD Dulal Mondal via AMBER
Tuesday, 11 June 2024
- [AMBER] PLEASE UNSUBSCRIBE ME! Santiago Movilla via AMBER
- [AMBER] Using fluorine and iodine in Antechamber Pietro Aronica via AMBER
- Re: [AMBER] finddgref.py using pH-REMD Carlos Simmerling via AMBER
- Re: [AMBER] error in reading namelist cntrl when trying to minimize RNA David A Case via AMBER
Wednesday, 12 June 2024
- Re: [AMBER] finddgref.py using pH-REMD Dulal Mondal via AMBER
- Re: [AMBER] QM/MM calculations with different Basis sets Timothy Giese via AMBER
- Re: [AMBER] finddgref.py using pH-REMD He, Amy via AMBER
- [AMBER] Docking proteins to DNA James Kress via AMBER
Thursday, 13 June 2024
- Re: [AMBER] Docking proteins to DNA David A Case via AMBER
- Re: [AMBER] Docking proteins to DNA Cianna Calia via AMBER
- Re: [AMBER] Docking proteins to DNA James Kress via AMBER
Friday, 14 June 2024
- Re: [AMBER] Docking proteins to DNA Andrea H. Kasun via AMBER
- [AMBER] Inquiry about RTX 1650 GPU Support for Amber Simulations Muhammad Tariq via AMBER
- Re: [AMBER] Preparing .pdb file for EGFR Carlos Simmerling via AMBER
Monday, 17 June 2024
- [AMBER] Using ntp=1 for membrane embedded Protein-Ligand System with ifsc=1 Option 변진영 / 학생 / 약학과 via AMBER
- Re: [AMBER] Using ntp=1 for membrane embedded Protein-Ligand System with ifsc=1 Option Dickson, Callum via AMBER
Tuesday, 18 June 2024
- [AMBER] Extended Deadline: AMBER Free Energy Workshop in San Diego, CA, August 12-16, 2024 Darrin York via AMBER
Wednesday, 19 June 2024
- [AMBER] Query regarding interacting residues Sayan Poddar via AMBER
- [AMBER] Lipid Bilayer Water molecule issue Kavinda Kashi Juliyan Gunasinghe via AMBER
Thursday, 20 June 2024
- Re: [AMBER] [Sender Not Verified] Query regarding interacting residues Sayan Poddar via AMBER
- [AMBER] RMSD by residue for enzyme variant with domain insertion Colin Pierce via AMBER
Friday, 21 June 2024
- Re: [AMBER] Modified amino acids in MCPB.py Ingso Limbu via AMBER
Saturday, 22 June 2024
- Re: [AMBER] Ionic and hydrophobic interaction calculation Carlos Simmerling via AMBER
- [AMBER] Amber 24: gamd-restart.dat + frozen jobs Morad Mustafa via AMBER
Sunday, 23 June 2024
- [AMBER] Empty first column and commas in the input Javier Carmona Garcia via AMBER
- Re: [AMBER] Empty first column and commas in the input David A Case via AMBER
- [AMBER] Antechamber error with "$." : Mac issue Ingso Limbu via AMBER
Monday, 24 June 2024
- [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1 MIRA JHAWAR via AMBER
- Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1 MIRA JHAWAR via AMBER
- Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1 MIRA JHAWAR via AMBER
- Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1 Carlos Simmerling via AMBER
- Re: [AMBER] continuous constant pH using iphmd=3 Dulal Mondal via AMBER
Wednesday, 26 June 2024
- [AMBER] glycam or gaff for sugar parametrization Enrico Martinez via AMBER
- [AMBER] Amber Installation Help Anna Stein via AMBER
Thursday, 27 June 2024
- Re: [AMBER] Amber Installation Help Daniel Roe via AMBER

Last message date: Thu Jun 27 2024 - 08:30:02 PDT
Archived on: Mon Sep 16 2024 - 05:56:16 PDT