Amber Archive Jun 2021: by date

Tuesday, 1 June 2021
- Re: [AMBER] Error in pca analysis Daniel Roe
- Re: [AMBER] Error in pca analysis Sruthi Sudhakar
- [AMBER] Identical results from thermodynamics integration runs zz sheng
- Re: [AMBER] Identical results from thermodynamics integration runs Adrian Roitberg
- Re: [AMBER] Identical results from thermodynamics integration runs zz sheng
- Re: [AMBER] APR- Umbrella sampling of Receptor- ligand complex Rana Rehan Khalid
- [AMBER] radiopt=1 in not working in MMPBSA.py Abdul Basit
- Re: [AMBER] radiopt=1 in not working in MMPBSA.py Ray Luo
- Re: [AMBER] xleap Wu Xu
- Re: [AMBER] Error in pca analysis Sruthi Sudhakar
- [AMBER] Nastruct reference file format Robert Molt
Wednesday, 2 June 2021
- [AMBER] A40 vs A5000 Fabian Glaser
- [AMBER] Running cpptraj in hpc Jenny 148
- [AMBER] Regarding MMPBSA calculation Rinsha Chk
- Re: [AMBER] Running cpptraj in hpc Daniel Roe
- Re: [AMBER] Error in pca analysis Daniel Roe
- Re: [AMBER] Error in pca analysis Sruthi Sudhakar
- Re: [AMBER] Regarding MMPBSA calculation ABDUL BASIT
- [AMBER] position coordinate precision Lambach, Lauren
- Re: [AMBER] position coordinate precision Daniel Roe
- Re: [AMBER] position coordinate precision Daniel Roe
- Re: [AMBER] position coordinate precision Carlos Simmerling
- Re: [AMBER] position coordinate precision Lambach, Lauren
Thursday, 3 June 2021
- [AMBER] gti_add_sc Holly Freedman
Friday, 4 June 2021
- Re: [AMBER] CMAP topology flag skipped Daniel Roe
- Re: [AMBER] CMAP topology flag skipped Loki
- [AMBER] Nastruct reference file format Robert Molt
- [AMBER] Query on Rmsd between clusters and population Athena N
- Re: [AMBER] Nastruct reference file format Daniel Roe
- [AMBER] Adding several Helium atoms to a Lipid bilayer structure in AMBER Maghsoud, Yazdan
Saturday, 5 June 2021
- [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Akinyemi Omoniyi
- Re: [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. David A Case
- Re: [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Akinyemi Omoniyi
Sunday, 6 June 2021
- [AMBER] Possible impact of cryptomining limitations on new NVidia GPUs on pmemd performances Pietro Amodeo
- Re: [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. David A Case
- [AMBER] How to fix the numbering of amino acid that got shifted in topology file that created in amber Tleap priya murugan
Monday, 7 June 2021
- Re: [AMBER] How to fix the numbering of amino acid that got shifted in topology file that created in amber Tleap Dr. Anselm Horn
- Re: [AMBER] How to fix the numbering of amino acid that got shifted in topology file that created in amber Tleap David A Case
- [AMBER] [MCPB.py]_KeyError: 'HZ2' sabrine kh
- [AMBER] What does the UVV file output for a LJ only system and why cant I recreate it? Daniel Fowles
- [AMBER] [MCPB.py]_KeyError: 'HZ3' sabrine kh
- Re: [AMBER] [MCPB.py]_KeyError: 'HZ3' Gustaf Olsson
- Re: [AMBER] How to fix the numbering of amino acid that got shifted in topology file that created in amber Tleap Daniel Roe
- [AMBER] about pytraj/cpptraj aishen
- Re: [AMBER] [MCPB.py]_KeyError: 'HZ3' sabrine kh
- [AMBER] knlskintest error when using HMR with 4fs Neville Bethel
- Re: [AMBER] about pytraj/cpptraj David A Case
- Re: [AMBER] knlskintest error when using HMR with 4fs David A Case
- [AMBER] NAB superimpose issue Mandar Kulkarni
- [AMBER] Pressure tensor components in the GPU code. James Moraes de Almeida
- [AMBER] Error in calculating pair distribution function Umesh Roy
Tuesday, 8 June 2021
- [AMBER] Question about ff14SB parameters/atom types for TYR Dr. Anselm Horn
- Re: [AMBER] [MCPB.py]_KeyError: 'HZ3' sabrine kh
- Re: [AMBER] [MCPB.py]_KeyError: 'HZ3' Gustaf Olsson
- Re: [AMBER] NAB superimpose issue David A Case
- Re: [AMBER] Question about ff14SB parameters/atom types for TYR Carlos Simmerling
- [AMBER] Incomplete trajectory due to calculation halted error Razil Tahir
- Re: [AMBER] [MCPB.py]_KeyError: 'HZ2' Pengfei Li
Wednesday, 9 June 2021
- [AMBER] tleap error creating prmtop file Vaibhav Dixit
- Re: [AMBER] tleap error creating prmtop file Carlos Simmerling
- Re: [AMBER] Incomplete trajectory due to calculation halted error David A Case
- Re: [AMBER] What does the UVV file output for a LJ only system and why cant I recreate it? David A Case
- Re: [AMBER] Adding several Helium atoms to a Lipid bilayer structure in AMBER David A Case
- [AMBER] Error in pdb4amber for AmberTools21 Bhattacharjee, Sinjini
- [AMBER] Pressure tensor components in the GPU code. James Almeida
- Re: [AMBER] Error in pdb4amber for AmberTools21 David A Case
- Re: [AMBER] Error: Could not open file frcmod.ions1lm_126_hfe_opc: not found Pengfei Li
- [AMBER] pKa Calculation using PMEMD Monika Pareek
Thursday, 10 June 2021
- [AMBER] Some Problems by using NAB of AmberTools21 to model Circle-DNA 韩正威
- [AMBER] The code for modeling circular DNA is in the attachment 韩正威
- Re: [AMBER] NAB superimpose issue Mandar Kulkarni
- Re: [AMBER] CMAP topology flag skipped Loki
- Re: [AMBER] pKa Calculation using PMEMD David A Case
- Re: [AMBER] Some Problems by using NAB of AmberTools21 to model Circle-DNA David A Case
- Re: [AMBER] NAB superimpose issue David A Case
- [AMBER] TypeError: %c requires int or char Computational Chemistry
- Re: [AMBER] NAB superimpose issue Mandar Kulkarni
- [AMBER] an illegal memory access Reza Esmaeeli
- Re: [AMBER] TypeError: %c requires int or char David A Case
- Re: [AMBER] TypeError: %c requires int or char Bhattacharjee, Sinjini
- [AMBER] To increase timesteps in MD simulations Syeda Amna Arshi
- Re: [AMBER] To increase timesteps in MD simulations Carlos Simmerling
- [AMBER] Norleucine in ff99sb_ildn? Kenneth Huang
- Re: [AMBER] an illegal memory access David A Case
- Re: [AMBER] Norleucine in ff99sb_ildn? David A Case
- Re: [AMBER] NAB superimpose issue Mandar Kulkarni
- Re: [AMBER] knlskintest error when using HMR with 4fs Neville Bethel
Friday, 11 June 2021
- [AMBER] how does amber calculate the water bridge fraction Ming Tang
- Re: [AMBER] NAB superimpose issue David A Case
- Re: [AMBER] how does amber calculate the water bridge fraction Daniel Roe
- Re: [AMBER] CMAP topology flag skipped Daniel Roe
- Re: [AMBER] how does amber calculate the water bridge fraction Ming Tang
- [AMBER] strange tleap error with bond command Vaibhav Dixit
- Re: [AMBER] Error in pca analysis Sruthi Sudhakar
- [AMBER] query on principal component analysis trajectory Sruthi Sudhakar
Saturday, 12 June 2021
- Re: [AMBER] NAB superimpose issue Mandar Kulkarni
- Re: [AMBER] Error in pca analysis Sruthi Sudhakar
Sunday, 13 June 2021
- [AMBER] Problem of running a simulation in A100 GPU server. Jong Young Joung
- [AMBER] use QUICK for QM/MM simulation accelerated by gpu wangjianing_mail
- Re: [AMBER] use QUICK for QM/MM simulation accelerated by gpu wangjianing_mail
- Re: [AMBER] strange tleap error with bond command David A Case
- Re: [AMBER] Problem of running a simulation in A100 GPU server. David A Case
- Re: [AMBER] strange tleap error with bond command Vaibhav Dixit
Monday, 14 June 2021
- [AMBER] Which gpu should I select between tesla k80 and RTX30 series 东不拉
- Re: [AMBER] Which gpu should I select between tesla k80 and RTX30 series Adrian Roitberg
- Re: [AMBER] Which gpu should I select between tesla k80 and RTX30 series Ross Walker
- [AMBER] mmgbsa results raissa.conceicao.bol.com.br
- [AMBER] Amber20 5 times slower than Amber18? Yu Chen
- [AMBER] Restart the crashed MD run in Amber18 Amir Zeb
Tuesday, 15 June 2021
- Re: [AMBER] Amber20 5 times slower than Amber18? David A Case
- Re: [AMBER] Restart the crashed MD run in Amber18 David A Case
- [AMBER] Fluctuation in GPU usage Aravind R
- Re: [AMBER] Fluctuation in GPU usage Ross Walker
- Re: [AMBER] Amber20 5 times slower than Amber18? Yu Chen
- Re: [AMBER] Restart the crashed MD run in Amber18 Amir Zeb
- [AMBER] Execution Trouble ankita mehta
- Re: [AMBER] Error in pca analysis Sruthi Sudhakar
Wednesday, 16 June 2021
- [AMBER] issues in non-bonded and bonded force parameters Dr. Srinivasa B. Ramisetti
- [AMBER] cpptraj align using the same numbering Martin Rosellen
- Re: [AMBER] Execution Trouble David A Case
- Re: [AMBER] cpptraj align using the same numbering David A Case
- Re: [AMBER] Restart the crashed MD run in Amber18 David A Case
- Re: [AMBER] Error in pca analysis Daniel Roe
- Re: [AMBER] cpptraj align using the same numbering Daniel Roe
- Re: [AMBER] cpptraj align using the same numbering Martin Rosellen
- Re: [AMBER] cpptraj align using the same numbering Daniel Roe
- [AMBER] Can not locate tordef.lib file Souvik Dey
- [AMBER] Calculation of ligand restraints in TI Josiah Bones
- Re: [AMBER] Troubleshooting long idle times in pmemd.MPI Kevin Keane
- [AMBER] compilation error jamal kazazi
- [AMBER] issues with non-bonded and bonded force field parameterisation for Arsenic Dr. Srinivasa B. Ramisetti
Thursday, 17 June 2021
- [AMBER] Amber20 installation, Amber.pip file broken Balogh Álex Kálmán
- Re: [AMBER] Error in pca analysis Dr. Anselm Horn
- [AMBER] use QUICK for QM/MM simulation accelerated by gpu wangjianing_mail
- Re: [AMBER] Error in pca analysis Sruthi Sudhakar
- [AMBER] TI for inclusion complexes Eduardo R. Almeida
- [AMBER] issues with non-bonded and bonded force field parameterisation for Arsenic Srinivasa Ramisetti
- Re: [AMBER] Error in pca analysis Daniel Roe
- Re: [AMBER] Error in pca analysis Sruthi Sudhakar
- Re: [AMBER] Amber20 installation, Amber.pip file broken aishen
- Re: [AMBER] Amber20 installation, Amber.pip file broken jamal kazazi
- [AMBER] error with solvate.sh at remove command tleap Vaibhav Dixit
- [AMBER] Fw: [josiah.bones.anu.edu.au: Calculation of ligand restraints in TI] Josiah Bones
- Re: [AMBER] issues with non-bonded and bonded force field parameterisation for Arsenic Pengfei Li
- Re: [AMBER] Restart the crashed MD run in Amber18 Amir Zeb
- Re: [AMBER] Execution Trouble ankita mehta
- [AMBER] Absolute Binding Free Energy of Protein+Ligand Complex in AMBER20 - Boresch restraints, Smoothstep Josiah Bones
Friday, 18 June 2021
- Re: [AMBER] error with solvate.sh at remove command tleap Vaibhav Dixit
- [AMBER] install Amber20 GPU Centos 7 Sebastian Brickel
- Re: [AMBER] error with solvate.sh at remove command tleap David A Case
- Re: [AMBER] Restart the crashed MD run in Amber18 David A Case
- Re: [AMBER] Execution Trouble David A Case
- Re: [AMBER] install Amber20 GPU Centos 7 David A Case
- Re: [AMBER] error with solvate.sh at remove command tleap Vaibhav Dixit
- Re: [AMBER] Absolute Binding Free Energy of Protein+Ligand Complex in AMBER20 - Boresch restraints, Smoothstep Dickson, Callum
- Re: [AMBER] Error in pca analysis Sruthi Sudhakar
Saturday, 19 June 2021
- Re: [AMBER] Preparation of i-Motif structures Sruthi Sudhakar
- Re: [AMBER] Preparation of i-Motif structures Petr Stadlbauer
Sunday, 20 June 2021
- [AMBER] RMSD plot in ns Sadaf Rani
- Re: [AMBER] RMSD plot in ns Reza Esmaeeli
- [AMBER] Installation error AMBERTOOLS21 Mandar Kulkarni
- Re: [AMBER] error with solvate.sh at remove command tleap Daniel Roe
- Re: [AMBER] RMSD plot in ns Daniel Roe
- Re: [AMBER] Restart the crashed MD run in Amber18 Amir Zeb
Monday, 21 June 2021
- Re: [AMBER] RMSD plot in ns Dr. Anselm Horn
- Re: [AMBER] Amber20 installation, Amber.pip file broken David A Case
- Re: [AMBER] Installation error AMBERTOOLS21 David A Case
- Re: [AMBER] Error in pca analysis Daniel Roe
- Re: [AMBER] Amber20 installation, Amber.pip file broken Balogh Álex Kálmán
- Re: [AMBER] Amber20 installation, Amber.pip file broken aishen
- Re: [AMBER] Amber20 installation, Amber.pip file broken aishen
- Re: [AMBER] Fw: [josiah.bones.anu.edu.au: Calculation of ligand restraints in TI] accuratefreeenergy.gmail.com
- Re: [AMBER] Amber20 installation, Amber.pip file broken David A Case
- [AMBER] 3080Ti Nvidia Jaime Rubio Martinez
- Re: [AMBER] 3080Ti Nvidia Ross Walker
Tuesday, 22 June 2021
- [AMBER] HREMD with similar replicas Richard Kullmann
- Re: [AMBER] Preparation of i-Motif structures Sruthi Sudhakar
- [AMBER] .rst7 output coordinate file error GALLO FACUNDO NAHUEL
- Re: [AMBER] Preparation of i-Motif structures David A Case
- Re: [AMBER] .rst7 output coordinate file error Carlos Simmerling
- [AMBER] Breaking of complex molecule richa anand
Wednesday, 23 June 2021
- Re: [AMBER] Installation error AMBERTOOLS21 Mandar Kulkarni
- [AMBER] How to use a relatively smaller cutoff in the GB simulation jinfeng liu
- Re: [AMBER] How to use a relatively smaller cutoff in the GB simulation Carlos Simmerling
- [AMBER] ambertools20 - request for older version Ruben Cruz
- Re: [AMBER] .rst7 output coordinate file error David A Case
- Re: [AMBER] Breaking of complex molecule Dr. Anselm Horn
- Re: [AMBER] Installation error AMBERTOOLS21 David A Case
- Re: [AMBER] How to use a relatively smaller cutoff in the GB simulation David A Case
- Re: [AMBER] ambertools20 - request for older version David A Case
- Re: [AMBER] Preparation of i-Motif structures Daniel Roe
- Re: [AMBER] Breaking of complex molecule Daniel Roe
- Re: [AMBER] .rst7 output coordinate file error Daniel Roe
- [AMBER] Antechamber error when attempting Tutorial B5 David Wright
- Re: [AMBER] Antechamber error when attempting Tutorial B5 David A Case
- Re: [AMBER] Installation error AMBERTOOLS21 Mandar Kulkarni
- Re: [AMBER] Installation error AMBERTOOLS21 David A Case
- [AMBER] regarding parameters for protonated guanosine Sayilpreet Kaur
Thursday, 24 June 2021
- Re: [AMBER] How to use a relatively smaller cutoff in the GB simulation jinfeng liu
- Re: [AMBER] Antechamber error when attempting Tutorial B5 David Wright
- Re: [AMBER] How to use a relatively smaller cutoff in the GB simulation David A Case
- [AMBER] Constant pH for large number of titratable residues Matthew Guberman-Pfeffer
- Re: [AMBER] Constant pH for large number of titratable residues Cruzeiro, Vinicius
- Re: [AMBER] Constant pH for large number of titratable residues Matthew Guberman-Pfeffer
- Re: [AMBER] Installation error AMBERTOOLS21 Mandar Kulkarni
- Re: [AMBER] Constant pH for large number of titratable residues Cruzeiro, Vinicius
- Re: [AMBER] Constant pH for large number of titratable residues Matthew Guberman-Pfeffer
- [AMBER] Multi-Monomer Polymer Swisher, Justin S
Friday, 25 June 2021
- Re: [AMBER] Multi-Monomer Polymer Dr. Anselm Horn
- Re: [AMBER] Installation error AMBERTOOLS21 David A Case
- [AMBER] How to create a model of a G-Quadruplex and imotif structure using the sequence information Ramanathan Rajesh
- Re: [AMBER] Error in pca analysis Sruthi Sudhakar
Saturday, 26 June 2021
- [AMBER] Error in TI analysis Ephraim Marondedze
- Re: [AMBER] Installation error AMBERTOOLS21 Mandar Kulkarni
- [AMBER] sqm seeks the Boron parameter file instead of Bromine Thomas Evangelidis
- Re: [AMBER] sqm seeks the Boron parameter file instead of Bromine Roitberg,Adrian E
Monday, 28 June 2021
- Re: [AMBER] sqm seeks the Boron parameter file instead of Bromine Thomas Evangelidis
- Re: [AMBER] How to create a model of a G-Quadruplex and imotif structure using the sequence information David A Case
- Re: [AMBER] sqm seeks the Boron parameter file instead of Bromine Thomas Evangelidis
- Re: [AMBER] Constant pH for large number of titratable residues Adrian Roitberg
- Re: [AMBER] Constant pH for large number of titratable residues Matthew Guberman-Pfeffer
- [AMBER] How to set a check point in Amber Ramin Mehrani
- [AMBER] Installing compilers/libraries on Ubuntu 18.04 without root access Smith, Ally
- [AMBER] AMBER-Reflector e-mails being sent to SPAM Gustavo Seabra
- Re: [AMBER] AMBER-Reflector e-mails being sent to SPAM Carlos Simmerling
- Re: [AMBER] AMBER-Reflector e-mails being sent to SPAM Gustavo Seabra
- [AMBER] Estimating protein-protein interactions Matthew Guberman-Pfeffer
Tuesday, 29 June 2021
- Re: [AMBER] How to set a check point in Amber Dr. Anselm Horn
- [AMBER] Regarding protein - nucleic acid contacts Sruthi Sudhakar
- [AMBER] Amber for AMD GPUs? Shenglong Wang
- Re: [AMBER] Fw: [josiah.bones.anu.edu.au: Calculation of ligand restraints in TI] Josiah Bones
- Re: [AMBER] Installing compilers/libraries on Ubuntu 18.04 without root access Gerald Monard
- Re: [AMBER] Fw: [josiah.bones.anu.edu.au: Calculation of ligand restraints in TI] Josiah Bones
Wednesday, 30 June 2021
- Re: [AMBER] Installing compilers/libraries on Ubuntu 18.04 without root access Åke Sandgren
- Re: [AMBER] Estimating protein-protein interactions David A Case
- Re: [AMBER] Amber for AMD GPUs? David A Case
- Re: [AMBER] Estimating protein-protein interactions Matthew Guberman-Pfeffer
- [AMBER] Apply negative lateral pressure to membrane Amir Zeb
- Re: [AMBER] Fw: [josiah.bones.anu.edu.au: Calculation of ligand restraints in TI] accuratefreeenergy.gmail.com
- [AMBER] Error charges ligand having Selenium Renato Araujo
- Re: [AMBER] HREMD with similar replicas Jason Swails
- Re: [AMBER] AMBER-Reflector e-mails being sent to SPAM Jason Swails

Last message date: Wed Jun 30 2021 - 20:30:02 PDT
Archived on: Fri Apr 26 2024 - 05:56:10 PDT

Amber Archive Jun 2021 by date