Amber Archive May 2021: by date

Friday, 30 April 2021
- Re: [AMBER] installation of AmberTools 21 Qinghua Liao
Saturday, 1 May 2021
- Re: [AMBER] Release of AmberTools21 Kshatresh Dutta Dubey
- Re: [AMBER] installation of AmberTools 21 David A Case
- Re: [AMBER] [EXTERNAL] Release of AmberTools21 David A Case
- Re: [AMBER] installation of AmberTools 21 Rudy Richardson
- Re: [AMBER] installation of AmberTools 21 David A Case
- Re: [AMBER] Installation Ambertools21 Mac M1 (arm64) Florian Nachon
- Re: [AMBER] installation of AmberTools 21 Rudy Richardson
- Re: [AMBER] Installation Ambertools21 Mac M1 (arm64) David A Case
- Re: [AMBER] Troubleshooting long idle times in pmemd.MPI David A Case
- Re: [AMBER] Troubleshooting long idle times in pmemd.MPI Kevin Keane
- Re: [AMBER] polarizable FF in amber18 or 20 Ray Luo
- Re: [AMBER] polarizable FF in amber18 or 20 Vaibhav Dixit
Sunday, 2 May 2021
- Re: [AMBER] Installation Ambertools21 Mac M1 (arm64) Yoshitaka Moriwaki
- Re: [AMBER] Installation Ambertools21 Mac M1 (arm64) Florian Nachon
- Re: [AMBER] Troubleshooting long idle times in pmemd.MPI David A Case
- Re: [AMBER] installation of AmberTools 21 Qinghua Liao
- [AMBER] converting gromacs topology to amber Ayesha Fatima
Monday, 3 May 2021
- [AMBER] pmemd.cuda fails with "cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" Laura SCALVINI
- [AMBER] atom-order problem with prmtop and cpptraj Vaibhav Dixit
- [AMBER] Error due to faulty Connection atoms Guillem Vila I Julià
- [AMBER] Distance between nucleotides and amino acids Airy Sanjeev
- Re: [AMBER] pmemd.cuda fails with "cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" David A Case
- Re: [AMBER] atom-order problem with prmtop and cpptraj Vaibhav Dixit
- Re: [AMBER] atom-order problem with prmtop and cpptraj David A Case
- Re: [AMBER] atom-order problem with prmtop and cpptraj Vaibhav Dixit
- Re: [AMBER] atom-order problem with prmtop and cpptraj Daniel Roe
- Re: [AMBER] converting gromacs topology to amber Daniel Roe
- Re: [AMBER] Distance between nucleotides and amino acids Daniel Roe
- Re: [AMBER] converting gromacs topology to amber Ayesha Fatima
- Re: [AMBER] converting gromacs topology to amber Daniel Roe
- Re: [AMBER] converting gromacs topology to amber Ayesha Fatima
- [AMBER] CPPTRAJ nativecontacts Richard Kullmann
- Re: [AMBER] CPPTRAJ nativecontacts Daniel Roe
- Re: [AMBER] polarizable FF in amber18 or 20 Ray Luo
- Re: [AMBER] polarizable FF in amber18 or 20 Vaibhav Dixit
Tuesday, 4 May 2021
- [AMBER] MMPBSA calculation error Yogeshwaran Krishnan
- Re: [AMBER] trpcage benchmark: reduce 32x or dimerize ? Scott Brozell
- [AMBER] converting gromacs topology to amber Ayesha Fatima
- [AMBER] N6-myristoyl lysine parameters Mark Fisher
Wednesday, 5 May 2021
- [AMBER] Query about AmberTools21 conda distribution Jan Brezovsky
- Re: [AMBER] converting gromacs topology to amber David A Case
- [AMBER] guidance for microsecond long MD simulations Vaibhav Dixit
- [AMBER] Inconsistent results on TI with cpu vs gpu code Giorgos Lambrinidis
- Re: [AMBER] guidance for microsecond long MD simulations David A Case
- [AMBER] Questions about QM/MM simulations 马芳芳
- Re: [AMBER] Questions about QM/MM simulations Goetz, Andreas
Thursday, 6 May 2021
- [AMBER] AMBER20/AMBERTools21 Installation Errors when compiling mpich 石谷沁
- Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson
- Re: [AMBER] AMBER20/AMBERTools21 Installation Errors when compiling mpich David A Case
- Re: [AMBER] [EXTERNAL] Release of AmberTools21 David A Case
- Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson
- Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson
- Re: [AMBER] [ambermd.org代发]Re: AMBER20/AMBERTools21 Installation Errors when compiling mpich 石谷沁
- [AMBER] Difficulty in doing umbrella sampling using LCOD method Soumyajit Karmakar
- [AMBER] 答复: [ambermd.org代发]Re: AMBER20/AMBERTools21 Installation Errors when compiling mpich 石谷沁
- [AMBER] differences in counterion position with water models and questions Vaibhav Dixit
- [AMBER] understanding DSSP outout Sadaf Rani
Friday, 7 May 2021
- Re: [AMBER] Questions about QM/MM simulations (Goetz, Andreas) 马芳芳
- Re: [AMBER] [ambermd.org代发]Re: AMBER20/AMBERTools21 Installation Errors when compiling mpich 石谷沁
- [AMBER] Amber20 CUDA.serial tests comparison failed with gb calculation: differences at e-01 level 石谷沁
- Re: [AMBER] 答复: [ambermd.org代发]Re: AMBER20/AMBERTools21 Installation Errors when compiling mpich David A Case
- Re: [AMBER] Amber20 CUDA.serial tests comparison failed with gb calculation: differences at e-01 level David A Case
- [AMBER] Avoiding steric snafus with protein mutations in tleap? Tucker Burgin
- Re: [AMBER] Questions about QM/MM simulations (Goetz, Andreas) Goetz, Andreas
- [AMBER] 答复: [ambermd.org代发]Re: Amber20 CUDA.serial tests comparison failed with gb calculation: differences at e-01 level 石谷沁
Saturday, 8 May 2021
- [AMBER] Digest of issues installing AMBER21 in Centos 7 Azurmendi, Hugo
- Re: [AMBER] Avoiding steric snafus with protein mutations in tleap? Matias Machado
Sunday, 9 May 2021
- Re: [AMBER] Digest of issues installing AMBER21 in Centos 7 David A Case
- [AMBER] Query regarding density analysis ARITRA MITRA
- [AMBER] Inconsistent results on TI with cpu vs gpu code Giorgos Lambrinidis
- Re: [AMBER] Inconsistent results on TI with cpu vs gpu code David A Case
- Re: [AMBER] Query about AmberTools21 conda distribution David A Case
- [AMBER] MBAR energies when using soft-core potential in pmemd TI Hosein Geraili Daronkola
- [AMBER] Test Goetz, Andreas
Monday, 10 May 2021
- Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson
- Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson
- Re: [AMBER] differences in counterion position with water models and questions Dr. Anselm Horn
- Re: [AMBER] MBAR energies when using soft-core potential in pmemd TI David A Case
- Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson
- Re: [AMBER] [EXTERNAL] Release of AmberTools21 David A Case
- Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson
- Re: [AMBER] MBAR energies when using soft-core potential in pmemd TI Brian Radak
- Re: [AMBER] CPPTRAJ nativecontacts Richard Kullmann
- [AMBER] stacking interactions represented by force field equation? Martin Rosellen
- Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson
- Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson
- Re: [AMBER] stacking interactions represented by force field equation? Carlos Simmerling
- Re: [AMBER] stacking interactions represented by force field equation? Jiri Sponer
- [AMBER] Keeping input protein hydrogens? Markus Metz
- Re: [AMBER] Keeping input protein hydrogens? David A Case
Tuesday, 11 May 2021
- [AMBER] FEW MMGBSA calculation Yogeshwaran Krishnan
- Re: [AMBER] stacking interactions represented by force field equation? Matias Machado
- [AMBER] solvent accessibility Cato, Lee
- Re: [AMBER] stacking interactions represented by force field equation? Jiri Sponer
- [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again. ARITRA MITRA
- Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again. Daniel Roe
- Re: [AMBER] CPPTRAJ nativecontacts Daniel Roe
- Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gerald Monard
- [AMBER] Error Installing Amber20 on group's cluster Min Chiang Gary Ong
- [AMBER] AMBER 18 citation endnote file Athena N
Wednesday, 12 May 2021
- [AMBER] MMPBSA.py and rms fit: Results depend on reference frame Lennart Gundelach
- [AMBER] Amber stuck on Control data for the run Victoria E Hill
- Re: [AMBER] Error Installing Amber20 on group's cluster David A Case
- Re: [AMBER] MMPBSA.py and rms fit: Results depend on reference frame David A Case
- Re: [AMBER] Amber stuck on Control data for the run David A Case
- Re: [AMBER] Error due to faulty Connection atoms David A Case
- Re: [AMBER] Amber stuck on Control data for the run Daniel Roe
- [AMBER] Effect of noisy force calculations Thomas Fox
- Re: [AMBER] Amber stuck on Control data for the run Matias Machado
- Re: [AMBER] Error Installing Amber20 on group's cluster Min Chiang Gary Ong
- Re: [AMBER] differences in counterion position with water models and questions Vaibhav Dixit
- [AMBER] Mutate double stranded DNA? Gustavo Seabra
- [AMBER] AmberTools21 cmake build H. Kawasaki
Thursday, 13 May 2021
- Re: [AMBER] Mutate double stranded DNA? Mariano Curti
- Re: [AMBER] Mutate double stranded DNA? Carlos Simmerling
- Re: [AMBER] Mutate double stranded DNA? Vlad Cojocaru
- Re: [AMBER] AmberTools21 cmake build David A Case
- [AMBER] How to calculate the contribution to protein-protein aggregation from hydrophobic interactions ? 刘为
- Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again. ARITRA MITRA
- Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again. Daniel Roe
- Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again. ARITRA MITRA
- Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again. Daniel Roe
- [AMBER] Selenomethionine force field parameters Rafał Madaj
- Re: [AMBER] Mutate double stranded DNA? Gustavo Seabra
- [AMBER] New In CPPTRAJ (May 2021) Daniel Roe
- [AMBER] Error running make install Rodrigo da Silva Bitzer
- [AMBER] CPPTRAJ nastruct not recognising G-U wobble base pairs Francis Acquah
- Re: [AMBER] Selenomethionine force field parameters Kellon Belfon
- Re: [AMBER] Selenomethionine force field parameters David A Case
- Re: [AMBER] Selenomethionine force field parameters Kellon Belfon
Friday, 14 May 2021
- Re: [AMBER] New In CPPTRAJ (May 2021) xichen li
- Re: [AMBER] Error running make install David A Case
- Re: [AMBER] Selenomethionine force field parameters Jeffrey Wagner
- [AMBER] Cpptraj segfaults on single REMD trajectories? Brian Radak
- Re: [AMBER] Cpptraj segfaults on single REMD trajectories? Daniel Roe
- Re: [AMBER] understanding DSSP outout Daniel Roe
- Re: [AMBER] Selenomethionine force field parameters David A Case
- Re: [AMBER] Mutate double stranded DNA? Vlad Cojocaru
- [AMBER] Problem re. non-integer charge in glycoprotein RAJAS MALLENAHALLI RAO
- Re: [AMBER] Cpptraj segfaults on single REMD trajectories? Brian Radak
- Re: [AMBER] Selenomethionine force field parameters Jeffrey Wagner
- Re: [AMBER] Cpptraj segfaults on single REMD trajectories? Daniel Roe
- Re: [AMBER] New In CPPTRAJ (May 2021) Daniel Roe
- Re: [AMBER] CPPTRAJ nastruct not recognising G-U wobble base pairs Daniel Roe
- Re: [AMBER] solvent accessibility Daniel Roe
- Re: [AMBER] Selenomethionine force field parameters Kellon Belfon
- Re: [AMBER] Selenomethionine force field parameters Jeffrey Wagner
- Re: [AMBER] Error running make install Rodrigo da Silva Bitzer
- Re: [AMBER] solvent accessibility David A Case
- Re: [AMBER] Selenomethionine force field parameters Rafał Madaj
Saturday, 15 May 2021
- Re: [AMBER] Selenomethionine force field parameters Kellon Belfon
- Re: [AMBER] solvent accessibility German P. Barletta
- Re: [AMBER] solvent accessibility David A Case
- Re: [AMBER] Selenomethionine force field parameters Kellon Belfon
- Re: [AMBER] Selenomethionine force field parameters Rafał Madaj
- Re: [AMBER] Selenomethionine force field parameters Kellon Belfon
Sunday, 16 May 2021
- [AMBER] Multiple Dihedral Parameters Abdul Basit
- Re: [AMBER] Multiple Dihedral Parameters David A Case
- [AMBER] MMGBSA using charmm36 force field-- positive value 周丽萍
- [AMBER] Surprisingly Poor Performance of Quadro RTX5000 -- Any Ideas on Reasons... 石谷沁
Monday, 17 May 2021
- [AMBER] Miniconda pkg install error H. Kawasaki
- Re: [AMBER] Problem re. non-integer charge in glycoprotein Dr. Anselm Horn
- Re: [AMBER] Problem re. non-integer charge in glycoprotein RAJAS MALLENAHALLI RAO
- Re: [AMBER] Miniconda pkg install error David A Case
- [AMBER] Algorithm Details of Addions/Addions2 Robert Molt
Tuesday, 18 May 2021
- [AMBER] CMake Error at cmake/jedbrown/FindFFTW.cmake:307 (add_library): Akinyemi Omoniyi
- Re: [AMBER] CMake Error at cmake/jedbrown/FindFFTW.cmake:307 (add_library): David A Case
- [AMBER] Combining GLYCAM and AMBER/GAFF Gustaf Olsson
- [AMBER] Applying change to van der Waals for specific pairs of atom Smith, Richard
- [AMBER] Conformation search speed increase with Cartesian restraints Liao
Wednesday, 19 May 2021
- [AMBER] Lite Hash Rate and pmemd.cuda Alessandro Contini
- [AMBER] How do I generate prmtop file for system containing more than 1 ligand? Min Chiang Gary Ong
- Re: [AMBER] Error due to faulty Connection atoms Guillem Vila I Julià
- Re: [AMBER] How do I generate prmtop file for system containing more than 1 ligand? Carlos Simmerling
- [AMBER] Compiling Fortran on M1 chipset Joe Leonard
- Re: [AMBER] How do I generate prmtop file for system containing more than 1 ligand? David A Case
- Re: [AMBER] Conformation search speed increase with Cartesian restraints Charo del Genio
- Re: [AMBER] Conformation search speed increase with Cartesian restraints Liao
- Re: [AMBER] Applying change to van der Waals for specific pairs of atom Song, Lin
- Re: [AMBER] CMake Error at cmake/jedbrown/FindFFTW.cmake:307 (add_library): Akinyemi Omoniyi
Thursday, 20 May 2021
- [AMBER] Restraints and TI in absolute binding free energies Hans De Winter
- Re: [AMBER] Conformation search speed increase with Cartesian restraints Charo del Genio
- Re: [AMBER] Applying change to van der Waals for specific pairs of atom David A Case
- Re: [AMBER] Combining GLYCAM and AMBER/GAFF David A Case
- Re: [AMBER] Algorithm Details of Addions/Addions2 David A Case
- Re: [AMBER] AMBER/EVB David A Case
- [AMBER] Covalent bonds across periodic boundaries supported yet/ever? Tucker Burgin
- Re: [AMBER] Combining GLYCAM and AMBER/GAFF Lachele Foley
- Re: [AMBER] Combining GLYCAM and AMBER/GAFF Gustaf Olsson
Friday, 21 May 2021
- [AMBER] AMberTools21 installation Neha Gandhi
Saturday, 22 May 2021
- [AMBER] Query about AmberTools21 conda distribution David A Case
- [AMBER] Clustering getting killed Sruthi Sudhakar
- Re: [AMBER] Query about AmberTools21 conda distribution Jan Brezovsky
- Re: [AMBER] Clustering getting killed Carlos Simmerling
- Re: [AMBER] Clustering getting killed Daniel Roe
- Re: [AMBER] Clustering getting killed Daniel Roe
Sunday, 23 May 2021
- Re: [AMBER] AMberTools21 installation Gustaf Olsson
Monday, 24 May 2021
- Re: [AMBER] AMberTools21 installation Neha Gandhi
- Re: [AMBER] AMberTools21 installation Gustaf Olsson
- [AMBER] distance matrix all atoms Fabian Glaser
- Re: [AMBER] distance matrix all atoms Daniel Roe
- [AMBER] Residue-Ligand binding free energy calculations Rana Rehan Khalid
- Re: [AMBER] Residue-Ligand binding free energy calculations Carlos Simmerling
- Re: [AMBER] Residue-Ligand binding free energy calculations Rana Rehan Khalid
- [AMBER] - Including ion type of interactions in free energy calculation Patil Pranita Uttamrao
Tuesday, 25 May 2021
- [AMBER] - DFT method for heme QM calculation Patil Pranita Uttamrao
- [AMBER] Joining two molecules Gustaf Olsson
- [AMBER] kindly help with this mmpbsa.py.MPI error Gargi Bhattacharya
- [AMBER] test message David A Case
- Re: [AMBER] - DFT method for heme QM calculation Dawid das
- Re: [AMBER] Joining two molecules Daniel Roe
- Re: [AMBER] kindly help with this mmpbsa.py.MPI error Daniel Roe
- Re: [AMBER] Joining two molecules Dr. Anselm Horn
- Re: [AMBER] DFT method for heme QM calculationPranita, Matthew Guberman-Pfeffer
- Re: [AMBER] DFT method for heme QM calculationPranita, Robert Molt
- [AMBER] Umbrella sampling Rana Rehan Khalid
Wednesday, 26 May 2021
- Re: [AMBER] Joining two molecules Gustaf Olsson
- Re: [AMBER] Joining two molecules Gustaf Olsson
- Re: [AMBER] Joining two molecules Gustaf Olsson
- Re: [AMBER] Joining two molecules Gustaf Olsson
- Re: [AMBER] Joining two molecules Gustaf Olsson
- Re: [AMBER] Covalent bonds across periodic boundaries supported yet/ever? David A Case
- Re: [AMBER] AMberTools21 installation David A Case
- Re: [AMBER] Umbrella sampling David A Case
- Re: [AMBER] Joining two molecules Daniel Roe
- Re: [AMBER] - Including ion type of interactions in free energy calculation David A Case
- [AMBER] ligand receptor dissociation study Rana Rehan Khalid
- Re: [AMBER] ligand receptor dissociation study Song, Lin
- Re: [AMBER] Umbrella sampling Thomas Cheatham
- Re: [AMBER] Covalent bonds across periodic boundaries supported yet/ever? Matias Machado
- Re: [AMBER] Covalent bonds across periodic boundaries supported yet/ever? Thomas Cheatham
- [AMBER] Umbrella Sampling error Rana Rehan Khalid
- [AMBER] Seek a solution for can't generate the mol2 files for the metal site residues Huimin Tian
Thursday, 27 May 2021
- [AMBER] MMGB/PBSA ligand with lone pair Katia Galentino
- Re: [AMBER] MMPBSA.py and rms fit: Results depend on reference frame Lennart Gundelach
- Re: [AMBER] xleap David A Case
- Re: [AMBER] Seek a solution for can't generate the mol2 files for the metal site residues Daniel Roe
- Re: [AMBER] MMGB/PBSA ligand with lone pair David A Case
- [AMBER] A bug in PMEMD which may cause aray (ti_dvdl_values) index out-of-boundary error Ye Mei
Friday, 28 May 2021
- [AMBER] Fortran runtime error: Ephraim Marondedze
- [AMBER] Simulating dehydrated bilayers with a vacuum above and below Blake Armstrong
- Re: [AMBER] Joining two molecules Gustaf Olsson
- Re: [AMBER] Joining two molecules Daniel Roe
- Re: [AMBER] Joining two molecules Gustaf Olsson
- Re: [AMBER] Joining two molecules Daniel Roe
- Re: [AMBER] Fortran runtime error: David A Case
- [AMBER] Regarding the forcefield parameters for cytochrome P450 heme group Patil Pranita Uttamrao
- Re: [AMBER] MULTI_RMSD NFE-Error : Cannot read &colvar namelist! Feng Pan
- Re: [AMBER] Regarding the forcefield parameters for cytochrome P450 heme group Vaibhav Dixit
- Re: [AMBER] Fortran runtime error: Ephraim Marondedze
Saturday, 29 May 2021
- Re: [AMBER] MULTI_RMSD NFE-Error : Cannot read &colvar namelist! Luis Simon
- Re: [AMBER] MULTI_RMSD NFE-Error : Cannot read &colvar namelist! Feng Pan
- [AMBER] Umbrella sampling (Protein Receptor--ligand) Rana Rehan Khalid
- [AMBER] Error: Could not open file frcmod.ions1lm_126_hfe_opc: not found Akinyemi Omoniyi
Sunday, 30 May 2021
- Re: [AMBER] Error: Could not open file frcmod.ions1lm_126_hfe_opc: not found David A Case
- Re: [AMBER] Error: Could not open file frcmod.ions1lm_126_hfe_opc: not found Akinyemi Omoniyi
- [AMBER] APR- Umbrella sampling of Receptor- ligand complex Rana Rehan Khalid
- Re: [AMBER] Umbrella sampling (Protein Receptor--ligand) David A Case
Monday, 31 May 2021
- Re: [AMBER] Joining two molecules Gustaf Olsson
- Re: [AMBER] Joining two molecules Gustaf Olsson
- [AMBER] Error in pca analysis Sruthi Sudhakar
- Re: [AMBER] APR- Umbrella sampling of Receptor- ligand complex Niel Henriksen

Last message date: Mon May 31 2021 - 21:00:02 PDT
Archived on: Fri Nov 15 2024 - 05:56:10 PST

Amber Archive May 2021 by date