Amber Archive May 2020 by author
349 messages
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Starting
Thu Apr 30 2020 - 14:30:03 PDT,
Ending
Sun May 31 2020 - 17:00:02 PDT
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Adrian Roitberg
Re: [AMBER] Steered MD with COM_ANGLE
(Wed May 13 2020 - 16:36:49 PDT)
Re: [AMBER] Temperature and total energy keeps dropping with NVE ensemble
(Sat May 09 2020 - 08:52:55 PDT)
Adrianne Lee
[AMBER] Minimum recommended hardware specs for AmberTools20 and Amber20
(Wed May 06 2020 - 14:57:49 PDT)
Alan
Re: [AMBER] Installing latest ambertools (2020) with conda
(Thu May 28 2020 - 06:04:48 PDT)
[AMBER] Installing latest ambertools (2020) with conda
(Thu May 28 2020 - 02:41:50 PDT)
Amanda Buyan
Re: [AMBER] Steered MD with COM_ANGLE
(Thu May 14 2020 - 19:20:28 PDT)
Re: [AMBER] Steered MD with COM_ANGLE
(Wed May 13 2020 - 23:18:43 PDT)
Re: [AMBER] Steered MD with COM_ANGLE
(Wed May 13 2020 - 16:43:06 PDT)
[AMBER] Steered MD with COM_ANGLE
(Wed May 13 2020 - 16:32:22 PDT)
Andrew Waight
Re: [AMBER] installation failed libsanderles.dir amd plumed
(Wed May 27 2020 - 07:11:45 PDT)
[AMBER] installation failed libsanderles.dir amd plumed
(Tue May 26 2020 - 21:07:59 PDT)
Arnaud Bondon
Re: [AMBER] wrong geometry amide nitrogen
(Sat May 02 2020 - 05:30:27 PDT)
Re: [AMBER] wrong geometry amide nitrogen
(Fri May 01 2020 - 03:54:42 PDT)
Arthur Glasfeld
[AMBER] installation problem
(Wed May 13 2020 - 16:05:06 PDT)
Athena N
[AMBER] Small molecules paramters
(Thu May 28 2020 - 05:47:24 PDT)
[AMBER] Xmin minimisation
(Fri May 08 2020 - 10:18:41 PDT)
Baker, Joseph
[AMBER] amber20 output header
(Sat May 30 2020 - 19:18:49 PDT)
Brent Krueger
Re: [AMBER] Amber20 pmemd.cuda performance problems (especially on Turing-based GPUs)
(Mon May 25 2020 - 06:04:28 PDT)
Re: [AMBER] FRCMOD FILE DATABASE
(Wed May 06 2020 - 05:17:17 PDT)
Carl Heroneme
[AMBER] Free energy of solvation using polarizable force fields
(Thu May 21 2020 - 14:11:06 PDT)
Carlos Simmerling
Re: [AMBER] Amber99SB force field
(Thu May 28 2020 - 07:12:52 PDT)
Re: [AMBER] Amber99SB force field
(Thu May 28 2020 - 06:16:02 PDT)
Re: [AMBER] how to compute the protein interaction surface with the ligand
(Sat May 23 2020 - 16:45:00 PDT)
Re: [AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model
(Sat May 23 2020 - 07:16:56 PDT)
Re: [AMBER] how to compute the protein interaction surface with the ligand
(Wed May 20 2020 - 12:43:24 PDT)
Re: [AMBER] Could not find control namelist error
(Sat May 16 2020 - 04:39:08 PDT)
Re: [AMBER] Query regarding force fields
(Fri May 15 2020 - 11:25:18 PDT)
Re: [AMBER] Free energy calculation and system crash
(Mon May 04 2020 - 06:11:04 PDT)
Re: [AMBER] Simulation stops during NPT
(Sun May 03 2020 - 05:07:25 PDT)
Re: [AMBER] Free energy calculation and system crash
(Sat May 02 2020 - 16:44:52 PDT)
Re: [AMBER] NPT 2 ns of equilibration
(Sat May 02 2020 - 12:44:56 PDT)
Re: [AMBER] Simulation stops during NPT
(Sat May 02 2020 - 03:30:55 PDT)
Re: [AMBER] SHAKE ALgorithm and frcmod file
(Fri May 01 2020 - 05:25:48 PDT)
Casalini Tommaso
[AMBER] CO atom type missing in PARMCHK.DAT
(Tue May 05 2020 - 11:53:42 PDT)
Charo del Genio
[AMBER] Amber20 sander speed difference between cmake and old configure method (addendum)
(Wed May 06 2020 - 06:35:18 PDT)
[AMBER] Amber20 sander speed difference between cmake and old configure method
(Wed May 06 2020 - 05:07:51 PDT)
Christina Bergonzo
Re: [AMBER] Tool to calculate CSP and NOE for DNA trajectory?
(Thu May 28 2020 - 05:42:20 PDT)
Re: [AMBER] OHE residue and crashing
(Mon May 11 2020 - 05:48:28 PDT)
Re: [AMBER] addions
(Wed May 06 2020 - 09:17:48 PDT)
Re: [AMBER] Abasic Site and Errant OH Group on Sugar
(Mon May 04 2020 - 06:13:53 PDT)
Cong Liu
Re: [AMBER] Amber20 serial make test FAILUREs on IBM Power9
(Thu May 21 2020 - 14:03:33 PDT)
Re: [AMBER] Amber20 serial make test FAILUREs on IBM Power9
(Thu May 21 2020 - 07:08:05 PDT)
[AMBER] Amber20 serial make test FAILUREs on IBM Power9
(Thu May 21 2020 - 07:03:12 PDT)
Daniel Roe
Re: [AMBER] Different LJ parameters in .dat file and 'atominfo' output
(Wed May 27 2020 - 07:59:41 PDT)
Re: [AMBER] Different LJ parameters in .dat file and 'atominfo' output
(Tue May 26 2020 - 08:23:36 PDT)
Re: [AMBER] clustering parameter files
(Tue May 26 2020 - 07:54:07 PDT)
Re: [AMBER] QM/MM MD: Error reading box
(Fri May 22 2020 - 08:55:51 PDT)
Re: [AMBER] QM/MM MD: Error reading box
(Fri May 22 2020 - 08:05:03 PDT)
Re: [AMBER] QM/MM MD: Error reading box
(Fri May 22 2020 - 04:44:34 PDT)
Re: [AMBER] can i analysis number of water molecules in protein by watershell
(Wed May 20 2020 - 09:20:05 PDT)
Re: [AMBER] Questions about PCA
(Wed May 20 2020 - 09:16:42 PDT)
Re: [AMBER] how to compute the protein interaction surface with the ligand
(Wed May 20 2020 - 09:00:42 PDT)
Re: [AMBER] COM position
(Tue May 19 2020 - 04:30:22 PDT)
Re: [AMBER] Query regarding calculating RMSF.
(Mon May 18 2020 - 09:03:46 PDT)
Re: [AMBER] autoimage waters
(Wed May 13 2020 - 15:07:25 PDT)
Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible?
(Thu May 07 2020 - 12:47:11 PDT)
Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible?
(Wed May 06 2020 - 06:52:58 PDT)
Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible?
(Tue May 05 2020 - 06:08:34 PDT)
Re: [AMBER] cpptraj PCA PC-mode pseudo traj
(Mon May 04 2020 - 13:46:52 PDT)
Re: [AMBER] CPPTRAJ: distance between atoms
(Mon May 04 2020 - 04:35:17 PDT)
Re: [AMBER] Leaprc error
(Sat May 02 2020 - 04:33:32 PDT)
David A Case
Re: [AMBER] cellulose chain
(Fri May 29 2020 - 09:32:06 PDT)
Re: [AMBER] Simulating pyridine in water TIP3P
(Thu May 28 2020 - 18:33:01 PDT)
Re: [AMBER] Installing latest ambertools (2020) with conda
(Thu May 28 2020 - 08:34:10 PDT)
Re: [AMBER] Installing latest ambertools (2020) with conda
(Thu May 28 2020 - 05:59:13 PDT)
Re: [AMBER] installation failed libsanderles.dir amd plumed
(Wed May 27 2020 - 05:25:20 PDT)
Re: [AMBER] QM/MM MD: Error reading box
(Sun May 24 2020 - 06:26:43 PDT)
Re: [AMBER] Free energy of solvation using polarizable force fields
(Sat May 23 2020 - 09:31:35 PDT)
Re: [AMBER] Amber18 with AmberTools20 test.serial FAILURES and ERRORS
(Sat May 23 2020 - 09:12:29 PDT)
Re: [AMBER] QM/MM MD: Error reading box
(Fri May 22 2020 - 05:32:37 PDT)
Re: [AMBER] QM/MM MD: Error reading box
(Thu May 21 2020 - 11:05:06 PDT)
Re: [AMBER] Amber20 serial make test FAILUREs on IBM Power9
(Thu May 21 2020 - 11:00:41 PDT)
Re: [AMBER] How to use set pert=true
(Wed May 20 2020 - 18:15:53 PDT)
Re: [AMBER] How to use set pert=true
(Wed May 20 2020 - 10:43:27 PDT)
Re: [AMBER] how to compute the protein interaction surface with the ligand
(Wed May 20 2020 - 10:31:03 PDT)
Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer
(Tue May 19 2020 - 18:25:15 PDT)
Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer
(Tue May 19 2020 - 05:02:32 PDT)
Re: [AMBER] parameter for modified residue
(Tue May 19 2020 - 04:43:40 PDT)
Re: [AMBER] Amber20 pmemd.cuda installation
(Sun May 17 2020 - 17:34:56 PDT)
Re: [AMBER] Amber20 MPICH location problem
(Sun May 17 2020 - 05:46:08 PDT)
Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer
(Sat May 16 2020 - 18:48:47 PDT)
Re: [AMBER] Amber20 MPIC location problem
(Sat May 16 2020 - 05:46:43 PDT)
Re: [AMBER] upgrade to 19
(Sat May 16 2020 - 05:29:36 PDT)
Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer
(Sat May 16 2020 - 05:05:07 PDT)
Re: [AMBER] Fwd: Fw: Amber18 - MPI version error on HPC Cluster
(Fri May 15 2020 - 07:46:18 PDT)
Re: [AMBER] updating to ambertools 20 from version 19
(Fri May 15 2020 - 07:42:04 PDT)
Re: [AMBER] Installation error
(Fri May 15 2020 - 07:38:38 PDT)
Re: [AMBER] help
(Thu May 14 2020 - 18:31:31 PDT)
Re: [AMBER] differences in EGB energies sander vs. pmemd
(Thu May 14 2020 - 18:28:36 PDT)
Re: [AMBER] installation problem
(Thu May 14 2020 - 03:56:51 PDT)
Re: [AMBER] OHE residue and crashing
(Wed May 13 2020 - 13:18:59 PDT)
Re: [AMBER] Topology and parameters for the T4 - Thyroxine
(Tue May 12 2020 - 18:51:17 PDT)
Re: [AMBER] 2 aminpurine parameter from Bryce reference?
(Tue May 12 2020 - 18:47:22 PDT)
Re: [AMBER] help
(Tue May 12 2020 - 18:34:27 PDT)
Re: [AMBER] Amber20 sander speed difference between cmake and old configure method
(Tue May 12 2020 - 05:25:39 PDT)
Re: [AMBER] OHE residue and crashing
(Tue May 12 2020 - 05:21:38 PDT)
Re: [AMBER] 2 aminpurine parameter from Bryce reference?
(Mon May 11 2020 - 18:12:43 PDT)
Re: [AMBER] MMPBSA - Ternary System = protein-ligand-1-ligand-2
(Mon May 11 2020 - 04:55:47 PDT)
Re: [AMBER] error MMPBSA
(Mon May 11 2020 - 04:51:49 PDT)
Re: [AMBER] Ewald grid size question
(Sun May 10 2020 - 18:05:03 PDT)
Re: [AMBER] OHE residue and crashing
(Sun May 10 2020 - 11:28:15 PDT)
Re: [AMBER] Neutralizing a system
(Sun May 10 2020 - 11:17:53 PDT)
Re: [AMBER] the error from make test.serial
(Sun May 10 2020 - 11:17:28 PDT)
Re: [AMBER] the error from make test.serial
(Sun May 10 2020 - 06:19:42 PDT)
Re: [AMBER] GPU based TI runs
(Sat May 09 2020 - 06:10:19 PDT)
Re: [AMBER] Temperature and total energy keeps dropping with NVE ensemble
(Sat May 09 2020 - 06:03:05 PDT)
Re: [AMBER] Xmin minimisation
(Sat May 09 2020 - 05:59:17 PDT)
Re: [AMBER] [BULK] Re: MM-PBSA calculation error
(Wed May 06 2020 - 09:32:42 PDT)
Re: [AMBER] Amber20 sander speed difference between cmake and old configure method
(Wed May 06 2020 - 09:22:33 PDT)
Re: [AMBER] MM-PBSA calculation error
(Wed May 06 2020 - 05:36:48 PDT)
Re: [AMBER] AmberTools20 comilation on macOS
(Wed May 06 2020 - 05:31:52 PDT)
Re: [AMBER] AmberTools20 comilation on macOS
(Tue May 05 2020 - 13:44:18 PDT)
Re: [AMBER] The lipid section in the 2020 manual require updating
(Tue May 05 2020 - 06:09:05 PDT)
Re: [AMBER] AmberTools20 comilation on macOS
(Tue May 05 2020 - 05:58:58 PDT)
Re: [AMBER] Abasic Site and Errant OH Group on Sugar
(Mon May 04 2020 - 07:44:58 PDT)
Re: [AMBER] Release of Amber20 and AmberTools20
(Mon May 04 2020 - 07:40:01 PDT)
Re: [AMBER] Simulation stops during NPT
(Mon May 04 2020 - 05:38:24 PDT)
[AMBER] Release of Amber20 and AmberTools20
(Mon May 04 2020 - 05:34:13 PDT)
Re: [AMBER] timestep dt for higher temperatures
(Fri May 01 2020 - 05:36:33 PDT)
Re: [AMBER] SHAKE ALgorithm and frcmod file
(Fri May 01 2020 - 05:34:04 PDT)
David Cerutti
Re: [AMBER] AMBER Digest, Vol 3017, Issue 1
(Sat May 30 2020 - 20:59:36 PDT)
Re: [AMBER] amber20 output header
(Sat May 30 2020 - 20:56:46 PDT)
Re: [AMBER] questions for mdgx-virtual site
(Fri May 29 2020 - 02:49:46 PDT)
Re: [AMBER] questions for mdgx-virtual site
(Fri May 29 2020 - 02:42:42 PDT)
[AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming
(Thu May 28 2020 - 23:30:20 PDT)
Re: [AMBER] Amber20 pmemd.cuda installation and performance problems
(Thu May 28 2020 - 15:51:16 PDT)
Re: [AMBER] Amber20 pmemd.cuda performance problems (especially on Turing-based GPUs)
(Thu May 28 2020 - 08:34:25 PDT)
Re: [AMBER] Amber20 pmemd.cuda installation and performance problems
(Wed May 27 2020 - 04:54:32 PDT)
Re: [AMBER] Amber20 pmemd.cuda performance problems (especially on Turing-based GPUs)
(Mon May 25 2020 - 02:40:35 PDT)
Re: [AMBER] Amber20 pmemd.cuda installation and performance problems
(Tue May 19 2020 - 12:39:50 PDT)
Re: [AMBER] pmemd simulation
(Tue May 12 2020 - 23:52:06 PDT)
Re: [AMBER] How to perameterize peptide like compound
(Tue May 12 2020 - 08:39:01 PDT)
Re: [AMBER] Temperature and total energy keeps dropping with NVE ensemble
(Sun May 10 2020 - 22:23:53 PDT)
Re: [AMBER] Ewald grid size question
(Sun May 10 2020 - 21:40:13 PDT)
Re: [AMBER] tlea
(Sun May 10 2020 - 12:19:38 PDT)
Dawid das
Re: [AMBER] How to use set pert=true
(Fri May 22 2020 - 07:34:35 PDT)
Re: [AMBER] How to use set pert=true
(Wed May 20 2020 - 12:07:10 PDT)
[AMBER] How to use set pert=true
(Wed May 20 2020 - 09:32:27 PDT)
Debarati DasGupta
[AMBER] Simulating pyridine in water TIP3P
(Thu May 28 2020 - 09:22:57 PDT)
[AMBER] TI production runs(20ns) NVT query
(Thu May 21 2020 - 07:05:42 PDT)
Re: [AMBER] GPU based TI runs
(Sat May 09 2020 - 10:40:39 PDT)
Re: [AMBER] GPU based TI runs
(Sat May 09 2020 - 08:57:13 PDT)
Re: [AMBER] GPU based TI runs
(Sat May 09 2020 - 07:00:52 PDT)
[AMBER] GPU based TI runs
(Sat May 09 2020 - 04:56:04 PDT)
[AMBER] NPT 2 ns of equilibration
(Sat May 02 2020 - 11:27:21 PDT)
Re: [AMBER] TI simulations
(Fri May 01 2020 - 05:27:21 PDT)
DHEERAJ CHITARA
[AMBER] Query regarding calculating RMSF.
(Thu May 14 2020 - 23:51:19 PDT)
Eduardo Mayo
Re: [AMBER] adding hydrogen to pdbqt ligand files
(Thu May 28 2020 - 23:25:00 PDT)
Eduardo R. Almeida
[AMBER] Open a hole into an equilibrated lipid bilayer
(Tue May 12 2020 - 19:44:54 PDT)
Elif Çiğdem Calvin
Re: [AMBER] SHAKE ALgorithm and frcmod file
(Fri May 01 2020 - 05:52:30 PDT)
Re: [AMBER] SHAKE ALgorithm and frcmod file
(Fri May 01 2020 - 05:27:35 PDT)
Re: [AMBER] SHAKE ALgorithm and frcmod file
(Fri May 01 2020 - 05:22:51 PDT)
[AMBER] SHAKE ALgorithm and frcmod file
(Thu Apr 30 2020 - 14:14:10 PDT)
Elvis Martis
Re: [AMBER] error MMPBSA
(Mon May 11 2020 - 05:53:01 PDT)
Re: [AMBER] error MMPBSA
(Mon May 11 2020 - 03:59:26 PDT)
Re: [AMBER] MMGBSA-DECOM calculation
(Wed May 06 2020 - 06:32:28 PDT)
Re: [AMBER] MMGBSA-DECOM calculation
(Wed May 06 2020 - 05:25:52 PDT)
emanuele falbo
Re: [AMBER] QM/MM MD: Error reading box
(Mon May 25 2020 - 02:39:39 PDT)
Re: [AMBER] QM/MM MD: Error reading box
(Sun May 24 2020 - 02:37:03 PDT)
Re: [AMBER] QM/MM MD: Error reading box
(Fri May 22 2020 - 06:58:27 PDT)
Re: [AMBER] QM/MM MD: Error reading box
(Fri May 22 2020 - 01:23:23 PDT)
[AMBER] QM/MM MD: Error reading box
(Thu May 21 2020 - 07:42:33 PDT)
[AMBER] CPPTRAJ: distance between atoms
(Mon May 04 2020 - 03:55:27 PDT)
Erdem Yeler
Re: [AMBER] paramfit - negative energy for 1 of the 2 term
(Sat May 23 2020 - 08:17:55 PDT)
[AMBER] paramfit - negative energy for 1 of the 2 term
(Thu May 21 2020 - 05:26:07 PDT)
Feng Pan
Re: [AMBER] Steered MD with COM_ANGLE
(Mon May 18 2020 - 06:35:27 PDT)
Filip Fratev
Re: [AMBER] Amber20 pmemd.cuda installation and performance problems
(Wed May 27 2020 - 03:12:46 PDT)
Re: [AMBER] Amber20 pmemd.cuda installation and performance problems
(Wed May 27 2020 - 03:00:36 PDT)
[AMBER] Amber20 pmemd.cuda installation and performance problems
(Sun May 17 2020 - 01:43:26 PDT)
Re: [AMBER] Amber20 MPICH location problem
(Sun May 17 2020 - 01:25:51 PDT)
Re: [AMBER] Amber20 MPICH location problem
(Sat May 16 2020 - 02:57:29 PDT)
[AMBER] Amber20 MPIC location problem
(Fri May 15 2020 - 20:54:11 PDT)
Francesco Pietra
[AMBER] about charmmgen
(Wed May 06 2020 - 09:28:01 PDT)
fratev.biomed.bas.bg
Re: [AMBER] Amber20 MPICH location problem
(Sat May 16 2020 - 20:13:19 PDT)
Gao J
Re: [AMBER] AMBER Digest, Vol 3017, Issue 1
(Sat May 30 2020 - 19:18:36 PDT)
[AMBER] questions for mdgx-virtual site
(Fri May 29 2020 - 01:29:44 PDT)
Gerald Monard
Re: [AMBER] Amber20 MPIC location problem
(Sun May 17 2020 - 07:26:29 PDT)
Gould, Ian R
Re: [AMBER] The lipid section in the 2020 manual require updating
(Tue May 05 2020 - 07:19:50 PDT)
Gustaf Olsson
Re: [AMBER] Small molecules paramters
(Thu May 28 2020 - 22:53:03 PDT)
Re: [AMBER] Fwd: Fw: Amber18 - MPI version error on HPC Cluster
(Thu May 14 2020 - 22:34:46 PDT)
Re: [AMBER] AmberTools20 comilation on macOS
(Wed May 06 2020 - 06:38:14 PDT)
Re: [AMBER] FRCMOD FILE DATABASE
(Tue May 05 2020 - 22:43:24 PDT)
Re: [AMBER] AmberTools20 comilation on macOS
(Tue May 05 2020 - 22:33:59 PDT)
Re: [AMBER] AmberTools20 comilation on macOS
(Tue May 05 2020 - 10:03:52 PDT)
Re: [AMBER] AmberTools20 comilation on macOS
(Tue May 05 2020 - 09:22:03 PDT)
Re: [AMBER] AmberTools20 comilation on macOS
(Tue May 05 2020 - 02:33:42 PDT)
Re: [AMBER] AmberTools20 comilation on macOS
(Tue May 05 2020 - 01:38:13 PDT)
Re: [AMBER] AmberTools20 comilation on macOS
(Tue May 05 2020 - 01:22:42 PDT)
[AMBER] AmberTools20 comilation on macOS
(Tue May 05 2020 - 01:07:11 PDT)
Gustavo Seabra
Re: [AMBER] Small molecules paramters
(Fri May 29 2020 - 09:20:56 PDT)
Re: [AMBER] Amber99SB force field
(Thu May 28 2020 - 06:56:08 PDT)
Hai Nguyen
Re: [AMBER] Using pytraj with jupyter notebook
(Sun May 31 2020 - 16:43:39 PDT)
Harald Lanig
[AMBER] Galactosylation of 5-Hydroxylysine
(Thu May 14 2020 - 09:05:08 PDT)
Hector A. Baldoni
Re: [AMBER] autoimage waters
(Wed May 13 2020 - 16:40:35 PDT)
[AMBER] autoimage waters
(Wed May 13 2020 - 12:46:38 PDT)
Homeo Morphism
[AMBER] updating to ambertools 20 from version 19
(Fri May 15 2020 - 03:57:48 PDT)
Hrishikesh Dhondge
Re: [AMBER] Installation error
(Sat May 16 2020 - 03:14:40 PDT)
[AMBER] Installation Error while linking C executable xaLeap
(Fri May 15 2020 - 06:33:14 PDT)
[AMBER] Installation error
(Fri May 15 2020 - 03:09:44 PDT)
Ignjat Filipović
[AMBER] Questions about QM
(Mon May 25 2020 - 07:23:45 PDT)
James Kress
Re: [AMBER] addions
(Sat May 09 2020 - 19:47:47 PDT)
Re: [AMBER] addions
(Sat May 09 2020 - 14:56:37 PDT)
Jan Mičan
[AMBER] What would you like to see in visualization of chemical data?
(Tue May 26 2020 - 09:59:39 PDT)
janardhanan c
Re: [AMBER] Leaprc error
(Sun May 03 2020 - 02:58:54 PDT)
[AMBER] Leaprc error
(Sat May 02 2020 - 03:11:07 PDT)
Jenny 148
[AMBER] Neutralizing a system
(Sun May 10 2020 - 05:56:45 PDT)
[AMBER] FRCMOD FILE DATABASE
(Tue May 05 2020 - 22:33:20 PDT)
Jisha B
[AMBER] Could not find control namelist error
(Sat May 16 2020 - 04:31:11 PDT)
[AMBER] addions
(Wed May 06 2020 - 08:55:28 PDT)
Josh Berryman
Re: [AMBER] Amber18 with AmberTools20 test.serial FAILURES and ERRORS
(Sat May 23 2020 - 09:03:57 PDT)
José Daniel Martinez
Re: [AMBER] Different LJ parameters in .dat file and 'atominfo' output
(Wed May 27 2020 - 01:25:01 PDT)
[AMBER] Different LJ parameters in .dat file and 'atominfo' output
(Sat May 23 2020 - 05:17:50 PDT)
Junmei Wang
Re: [AMBER] wrong geometry amide nitrogen
(Fri May 01 2020 - 12:50:30 PDT)
Karl Kirschner
Re: [AMBER] creating parameters for a thioglycoside
(Mon May 04 2020 - 11:28:22 PDT)
Kat G
[AMBER] Questions about PCA
(Thu May 14 2020 - 21:27:24 PDT)
Kellon Belfon
Re: [AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model
(Sat May 23 2020 - 22:46:50 PDT)
Re: [AMBER] AMBER Tools 20: Bug in libraries of modified amino acids prevents force field load
(Wed May 20 2020 - 14:13:51 PDT)
Re: [AMBER] Steered MD with COM_ANGLE
(Thu May 14 2020 - 12:04:04 PDT)
Re: [AMBER] Steered MD with COM_ANGLE
(Wed May 13 2020 - 19:34:31 PDT)
Kenneth Huang
Re: [AMBER] Tool to calculate CSP and NOE for DNA trajectory?
(Thu May 28 2020 - 20:57:59 PDT)
[AMBER] Tool to calculate CSP and NOE for DNA trajectory?
(Wed May 27 2020 - 16:47:41 PDT)
Re: [AMBER] 2 aminpurine parameter from Bryce reference?
(Tue May 12 2020 - 14:06:34 PDT)
[AMBER] 2 aminpurine parameter from Bryce reference?
(Mon May 11 2020 - 13:31:37 PDT)
[AMBER] 2 aminpurine parameter from Bryce reference?
(Mon May 11 2020 - 13:15:55 PDT)
Kodituwakku,Dimuthu Nirmani
[AMBER] Similar RESP1 and RESP2 fitting outputs
(Fri May 15 2020 - 07:16:21 PDT)
Lachele Foley
Re: [AMBER] Galactosylation of 5-Hydroxylysine
(Tue May 19 2020 - 13:21:50 PDT)
Re: [AMBER] cellulose chain
(Sat May 16 2020 - 02:33:03 PDT)
Re: [AMBER] cellulose chain
(Fri May 15 2020 - 20:09:26 PDT)
Re: [AMBER] How to merge GLYCAM06 and lipid17 to generate force field for simple g; ycolipids?
(Sun May 10 2020 - 11:31:33 PDT)
Re: [AMBER] tlea
(Sun May 10 2020 - 11:14:40 PDT)
Liao
Re: [AMBER] AMBER 18 GPU
(Thu May 14 2020 - 11:02:21 PDT)
Re: [AMBER] How to perameterize peptide like compound
(Wed May 13 2020 - 00:00:47 PDT)
[AMBER] Temperature and total energy keeps dropping with NVE ensemble
(Fri May 08 2020 - 21:38:15 PDT)
[AMBER] timestep dt for higher temperatures
(Fri May 01 2020 - 00:41:54 PDT)
Lod King
Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer
(Tue May 19 2020 - 10:53:07 PDT)
Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer
(Sun May 17 2020 - 06:40:47 PDT)
Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer
(Sat May 16 2020 - 19:00:01 PDT)
Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer
(Sat May 16 2020 - 13:16:25 PDT)
Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer
(Fri May 15 2020 - 21:09:20 PDT)
[AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer
(Fri May 15 2020 - 08:36:08 PDT)
Marcelo Andrade Chagas
[AMBER] Topology and parameters for the T4 - Thyroxine
(Tue May 12 2020 - 15:08:35 PDT)
[AMBER] MMPBSA - Ternary System = protein-ligand-1-ligand-2
(Mon May 11 2020 - 04:17:38 PDT)
Martin Mielke
Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible?
(Fri May 08 2020 - 03:06:43 PDT)
Re: [AMBER] Minimum recommended hardware specs for AmberTools20 and Amber20
(Thu May 07 2020 - 00:41:16 PDT)
Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible?
(Wed May 06 2020 - 06:28:27 PDT)
Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible?
(Tue May 05 2020 - 14:26:57 PDT)
[AMBER] Mass-weighted RMSD one-liner with cpptraj - possible?
(Mon May 04 2020 - 06:23:09 PDT)
Matias Machado
[AMBER] AMBER Tools 20: Bug in libraries of modified amino acids prevents force field load
(Wed May 20 2020 - 10:13:34 PDT)
Re: [AMBER] addions
(Sat May 09 2020 - 16:04:02 PDT)
Re: [AMBER] [EXTERNAL] addions
(Wed May 06 2020 - 10:45:46 PDT)
Md Fulbabu Sk
Re: [AMBER] Query regarding calculating RMSF.
(Fri May 15 2020 - 04:57:32 PDT)
mohamed marzouk
[AMBER] COM position
(Tue May 19 2020 - 02:41:30 PDT)
MYRIAN TORRES RICO
Re: [AMBER] help
(Fri May 15 2020 - 01:58:37 PDT)
Re: [AMBER] help
(Wed May 13 2020 - 10:27:53 PDT)
[AMBER] help
(Tue May 12 2020 - 09:21:29 PDT)
Re: [AMBER] error MMPBSA
(Mon May 11 2020 - 04:49:04 PDT)
[AMBER] error MMPBSA
(Mon May 11 2020 - 03:12:38 PDT)
[AMBER] MD and MD-tar restrictions
(Fri May 08 2020 - 03:53:54 PDT)
Niransha Kumarachchi
[AMBER] differences in EGB energies sander vs. pmemd
(Thu May 14 2020 - 16:20:28 PDT)
Oleksandr Kravchenko
[AMBER] Missing bond parameters after MCPB.py
(Wed May 27 2020 - 03:29:31 PDT)
Piia Kokkonen
Re: [AMBER] OHE residue and crashing
(Wed May 13 2020 - 05:46:18 PDT)
Re: [AMBER] OHE residue and crashing
(Mon May 11 2020 - 23:04:31 PDT)
[AMBER] OHE residue and crashing
(Fri May 08 2020 - 06:49:50 PDT)
Pinky Mazumder
Re: [AMBER] cellulose chain
(Fri May 29 2020 - 07:46:58 PDT)
Re: [AMBER] cellulose chain
(Fri May 15 2020 - 20:53:27 PDT)
Re: [AMBER] cellulose chain
(Fri May 15 2020 - 20:51:30 PDT)
Re: [AMBER] cellulose chain
(Fri May 15 2020 - 10:00:57 PDT)
Prajwal Nandekar
Re: [AMBER] how to identify lipids around a protein
(Fri May 29 2020 - 18:22:43 PDT)
Prapasiri Pongprayoon
[AMBER] Help with Acpype in AmberTools19
(Sun May 24 2020 - 23:07:32 PDT)
[AMBER] Help with Acpype on AMberTools19
(Sun May 24 2020 - 23:02:50 PDT)
Prasanth G, Research Scholar
Re: [AMBER] MMPBSA - per residue decomposition
(Fri May 22 2020 - 23:50:47 PDT)
[AMBER] MMPBSA - per residue decomposition
(Thu May 21 2020 - 01:09:47 PDT)
Pratul Agarwal
[AMBER] QM/MM with finite temperature string
(Fri May 01 2020 - 11:17:57 PDT)
Rana Rehan Khalid
[AMBER] How to perameterize peptide like compound
(Tue May 12 2020 - 05:38:00 PDT)
Rangarajan, Amith
Re: [AMBER] Using pytraj with jupyter notebook
(Sun May 31 2020 - 12:44:17 PDT)
Ranim Maaieh
[AMBER] clustering parameter files
(Mon May 25 2020 - 07:36:39 PDT)
Renato Araujo
Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer
(Sun May 17 2020 - 07:31:37 PDT)
Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer
(Sun May 17 2020 - 06:12:50 PDT)
Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer
(Fri May 15 2020 - 16:01:40 PDT)
[AMBER] AMBER 18 GPU
(Thu May 14 2020 - 09:53:40 PDT)
Re: [AMBER] MMGBSA-DECOM calculation
(Wed May 06 2020 - 06:27:05 PDT)
Re: [AMBER] MMGBSA-DECOM calculation
(Wed May 06 2020 - 06:15:39 PDT)
[AMBER] MMGBSA-DECOM calculation
(Wed May 06 2020 - 04:17:46 PDT)
Robert Molt
Re: [AMBER] addions
(Sat May 09 2020 - 17:20:10 PDT)
Re: [AMBER] addions
(Sat May 09 2020 - 15:13:44 PDT)
Re: [AMBER] addions
(Sat May 09 2020 - 14:35:24 PDT)
Re: [AMBER] Release of Amber20 and AmberTools20
(Mon May 04 2020 - 05:42:25 PDT)
[AMBER] Abasic Site and Errant OH Group on Sugar
(Mon May 04 2020 - 05:40:40 PDT)
Robin Betz
Re: [AMBER] paramfit - negative energy for 1 of the 2 term
(Thu May 21 2020 - 14:51:02 PDT)
rosaester.forgione.unina.it
Re: [AMBER] creating parameters for a thioglycoside
(Mon May 11 2020 - 03:27:48 PDT)
[AMBER] creating parameters for a thioglycoside
(Mon May 04 2020 - 09:59:39 PDT)
Ross Walker
Re: [AMBER] The lipid section in the 2020 manual require updating
(Tue May 05 2020 - 07:30:23 PDT)
Sadaf Rani
[AMBER] Absolute free energy calculation-GitHub
(Sat May 16 2020 - 17:03:00 PDT)
Re: [AMBER] Free energy calculation and system crash
(Mon May 04 2020 - 06:08:01 PDT)
Re: [AMBER] Free energy calculation and system crash
(Sat May 02 2020 - 17:29:43 PDT)
[AMBER] Free energy calculation and system crash
(Sat May 02 2020 - 15:54:14 PDT)
Sally Pias
[AMBER] how to identify lipids around a protein
(Fri May 29 2020 - 17:53:48 PDT)
Samanta M
Re: [AMBER] Amber18 with AmberTools20 test.serial FAILURES and ERRORS
(Sat May 23 2020 - 11:07:50 PDT)
[AMBER] Amber18 with AmberTools20 test.serial FAILURES and ERRORS
(Sat May 23 2020 - 07:02:03 PDT)
sangita kachhap
Re: [AMBER] parameter for modified residue
(Tue May 19 2020 - 12:56:35 PDT)
[AMBER] parameter for modified residue
(Mon May 18 2020 - 09:32:01 PDT)
sbojarowski.chem.uw.edu.pl
[AMBER] C4 parameters for Au0 from INTERFACE FF
(Tue May 05 2020 - 05:58:34 PDT)
Schröder, David Christopher
Re: [AMBER] cpptraj PCA PC-mode pseudo traj
(Mon May 04 2020 - 13:52:47 PDT)
[AMBER] cpptraj PCA PC-mode pseudo traj
(Mon May 04 2020 - 13:19:23 PDT)
Scott Brozell
[AMBER] upgrade to 19
(Fri May 15 2020 - 15:01:29 PDT)
Re: [AMBER] Xmin minimisation
(Fri May 08 2020 - 17:41:26 PDT)
Seketoulie Keretsu
[AMBER] Amber99SB force field
(Thu May 28 2020 - 05:51:12 PDT)
Serena Vittorio
Re: [AMBER] [BULK] Re: [BULK] Re: MM-PBSA calculation error
(Thu May 07 2020 - 02:26:12 PDT)
Re: [AMBER] [BULK] Re: MM-PBSA calculation error
(Wed May 06 2020 - 08:38:01 PDT)
[AMBER] MM-PBSA calculation error
(Wed May 06 2020 - 02:01:38 PDT)
Sharif Nada
[AMBER] Flags to Turn off Charges in pmemd
(Wed May 06 2020 - 03:44:24 PDT)
SHAUNAK BADANI
[AMBER] Query regarding force fields
(Fri May 15 2020 - 11:10:15 PDT)
Sivanandam Magudeeswaran
[AMBER] Fwd: Fw: Amber18 - MPI version error on HPC Cluster
(Thu May 14 2020 - 21:04:53 PDT)
Smith, Micholas D.
Re: [AMBER] [EXTERNAL] Re: Amber99SB force field
(Thu May 28 2020 - 11:54:46 PDT)
Re: [AMBER] [EXTERNAL] addions
(Wed May 06 2020 - 10:18:27 PDT)
Sofia Vasilakaki
[AMBER] pmemd simulation
(Tue May 12 2020 - 23:01:28 PDT)
Song, Lin
Re: [AMBER] GPU based TI runs
(Sat May 09 2020 - 10:28:51 PDT)
Re: [AMBER] GPU based TI runs
(Sat May 09 2020 - 08:41:54 PDT)
Re: [AMBER] TI simulations
(Thu Apr 30 2020 - 17:18:02 PDT)
Stephan Schott
Re: [AMBER] The lipid section in the 2020 manual require updating
(Tue May 05 2020 - 07:39:53 PDT)
Re: [AMBER] The lipid section in the 2020 manual require updating
(Tue May 05 2020 - 06:45:59 PDT)
Sunita Patel
Re: [AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model
(Sun May 24 2020 - 06:07:07 PDT)
Re: [AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model
(Sat May 23 2020 - 21:05:57 PDT)
[AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model
(Sat May 23 2020 - 07:01:04 PDT)
Re: [AMBER] Simulation stops during NPT
(Sun May 03 2020 - 18:45:07 PDT)
Re: [AMBER] Simulation stops during NPT
(Sun May 03 2020 - 11:52:50 PDT)
Re: [AMBER] Simulation stops during NPT
(Sat May 02 2020 - 23:11:09 PDT)
[AMBER] Simulation stops during NPT
(Sat May 02 2020 - 03:18:09 PDT)
Thomas Evangelidis
Re: [AMBER] how to compute the protein interaction surface with the ligand
(Sat May 23 2020 - 17:11:51 PDT)
Re: [AMBER] how to compute the protein interaction surface with the ligand
(Sat May 23 2020 - 16:32:54 PDT)
Re: [AMBER] how to compute the protein interaction surface with the ligand
(Wed May 20 2020 - 11:26:48 PDT)
Re: [AMBER] how to compute the protein interaction surface with the ligand
(Mon May 18 2020 - 13:56:33 PDT)
[AMBER] how to compute the protein interaction surface with the ligand
(Fri May 08 2020 - 15:57:39 PDT)
Thomas Gaillard
[AMBER] RMSD discontinuity between NPT and NVT with restraints
(Wed May 06 2020 - 08:57:00 PDT)
Thomas Zeiser
Re: [AMBER] Amber20 pmemd.cuda performance problems (especially on Turing-based GPUs)
(Mon May 25 2020 - 02:01:09 PDT)
Timothy Schutt
[AMBER] igb for non-aqueous solvent?
(Fri May 29 2020 - 06:40:59 PDT)
Veenis, Andrew Jay
[AMBER] Thermodynamic integration by parameter interpolation (PI-TI)
(Thu May 07 2020 - 07:01:05 PDT)
Vijay Achari
[AMBER] How to merge GLYCAM06 and lipid17 to generate force field for simple g; ycolipids?
(Thu May 07 2020 - 01:30:37 PDT)
viktor drobot
Re: [AMBER] Amber20 pmemd.cuda installation and performance problems
(Sun May 17 2020 - 01:53:21 PDT)
Wesley Michael Botello-Smith
Re: [AMBER] can i analysis number of water molecules in protein by watershell
(Wed May 20 2020 - 09:39:46 PDT)
Xiaoyong Zhang
[AMBER] AMBER 16 NFE MULTI_RMSD Question on the Output of reaction variable
(Thu May 28 2020 - 08:39:38 PDT)
Yuliana Bosken
Re: [AMBER] Ewald grid size question
(Sun May 10 2020 - 18:10:55 PDT)
[AMBER] Ewald grid size question
(Sun May 10 2020 - 16:10:01 PDT)
Zhiyi Wu
[AMBER] About having an auto-restart keyword for the amber/orca interface.
(Wed May 13 2020 - 14:41:11 PDT)
[AMBER] The lipid section in the 2020 manual require updating
(Tue May 05 2020 - 03:38:05 PDT)
石娜
[AMBER] can i analysis number of water molecules in protein by watershell
(Wed May 06 2020 - 06:21:50 PDT)
谢信锐
Re: [AMBER] the error from make test.serial
(Sun May 10 2020 - 07:00:09 PDT)
[AMBER] the error from make test.serial
(Sun May 10 2020 - 05:28:34 PDT)
马海川
Re: [AMBER] Amber for help
(Sat May 30 2020 - 06:04:02 PDT)
Last message date
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Sun May 31 2020 - 17:00:02 PDT
Archived on
: Wed Dec 25 2024 - 05:55:58 PST
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