Amber Archive Apr 2020: by author

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- [AMBER] miniconda3 AmberTools MMPBSA.py ERROR (Wed Apr 15 2020 - 19:06:02 PDT)
Abdul-Rashid III Sampaco
- Re: [AMBER] Error when installing miniconda through AmberTools19 (Thu Apr 16 2020 - 10:46:16 PDT)
- Re: [AMBER] Acetylated the truncated N- terminal (Thu Apr 09 2020 - 22:16:19 PDT)
ABEL Stephane
- Re: [AMBER] Using tleap tho have the .inpcrd and crd file (Thu Apr 30 2020 - 07:16:53 PDT)
- [AMBER] Using tleap tho have the .inpcrd and crd file (Tue Apr 28 2020 - 04:51:39 PDT)
- Re: [AMBER] protein-protein complex dissociation (Thu Apr 16 2020 - 06:31:34 PDT)
- Re: [AMBER] Amber force field for SDS and DPC detergents (Fri Apr 03 2020 - 03:25:33 PDT)
Abhilash J
- Re: [AMBER] Question about PCA tutorial (Thu Apr 30 2020 - 16:03:54 PDT)
- [AMBER] Question about PCA tutorial (Wed Apr 29 2020 - 14:07:27 PDT)
- Re: [AMBER] Unavailability of AMBER tutorial on PCA (Wed Apr 29 2020 - 10:17:57 PDT)
- [AMBER] Unavailability of AMBER tutorial on PCA (Tue Apr 28 2020 - 13:52:59 PDT)
accuratefreeenergy.gmail.com
- Re: [AMBER] Amber18, tools19, cuda 10.2 (Thu Apr 23 2020 - 06:56:44 PDT)
Ahmed Elrashedy
- Re: [AMBER] Remove restraint (Wed Apr 01 2020 - 05:57:23 PDT)
Anna Sekuła
- [AMBER] Run Amber as a job array (Thu Apr 23 2020 - 07:32:56 PDT)
Antoine MARION
- Re: [AMBER] thanks for the GB/SA section of the manual (Fri Apr 17 2020 - 07:51:18 PDT)
- [AMBER] thanks for the GB/SA section of the manual (Fri Apr 17 2020 - 07:46:10 PDT)
Arnaud Bondon
- Re: [AMBER] wrong geometry amide nitrogen (Thu Apr 30 2020 - 01:17:37 PDT)
- Re: [AMBER] wrong geometry amide nitrogen (Wed Apr 29 2020 - 09:51:08 PDT)
- Re: [AMBER] wrong geometry amide nitrogen (Wed Apr 29 2020 - 08:22:00 PDT)
- Re: [AMBER] wrong geometry amide nitrogen (Wed Apr 29 2020 - 08:13:59 PDT)
- Re: [AMBER] wrong geometry amide nitrogen (Wed Apr 29 2020 - 07:52:01 PDT)
- Re: [AMBER] wrong geometry amide nitrogen (Wed Apr 29 2020 - 01:43:53 PDT)
- [AMBER] wrong geometry amide nitrogen (Fri Apr 24 2020 - 06:56:37 PDT)
- [AMBER] wrong geometry amide nitrogen (Fri Apr 24 2020 - 04:40:58 PDT)
- [AMBER] pyramidal amide nitrogen (Thu Apr 02 2020 - 11:17:38 PDT)
Billiot, Eugene
- [AMBER] examination of ligand binding energy as a function of simulation time with MMPBSA calculations (Sat Apr 11 2020 - 07:48:27 PDT)
Brian Radak
- Re: [AMBER] Ligand leaving binding site at high lambdas using TI softcore (Sat Apr 11 2020 - 08:13:03 PDT)
Carlos Simmerling
- Re: [AMBER] SHAKE ALgorithm and frcmod file (Thu Apr 30 2020 - 14:18:27 PDT)
- Re: [AMBER] tMD and pmemd (Wed Apr 29 2020 - 17:42:35 PDT)
- Re: [AMBER] Recurring problem: Ligand lose planarity (Sun Apr 26 2020 - 11:24:05 PDT)
- Re: [AMBER] Recurring problem: Ligand lose planarity (Sun Apr 26 2020 - 10:23:54 PDT)
- Re: [AMBER] Recurring problem: Ligand lose planarity (Sun Apr 26 2020 - 08:49:49 PDT)
- Re: [AMBER] minimizing a pyridine in water (Sat Apr 25 2020 - 06:18:38 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Wed Apr 22 2020 - 15:19:29 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Wed Apr 22 2020 - 09:48:25 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Wed Apr 22 2020 - 09:39:34 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Wed Apr 22 2020 - 08:52:00 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Wed Apr 22 2020 - 08:27:40 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Tue Apr 21 2020 - 11:59:06 PDT)
- Re: [AMBER] FRCMOD file (Sat Apr 18 2020 - 07:26:57 PDT)
- Re: [AMBER] thanks for the GB/SA section of the manual (Fri Apr 17 2020 - 07:48:59 PDT)
- Re: [AMBER] Force Field for small molecule ligands (Fri Apr 17 2020 - 05:20:29 PDT)
- Re: [AMBER] protein-protein complex dissociation (Thu Apr 16 2020 - 10:12:23 PDT)
- Re: [AMBER] protein-protein complex dissociation (Thu Apr 16 2020 - 09:51:15 PDT)
- Re: [AMBER] protein-protein complex dissociation (Thu Apr 16 2020 - 07:09:03 PDT)
- Re: [AMBER] protein-protein complex dissociation (Thu Apr 16 2020 - 06:21:13 PDT)
- Re: [AMBER] Help for building lignin chain (Wed Apr 15 2020 - 03:54:11 PDT)
- Re: [AMBER] RST File Corrupt (Tue Apr 14 2020 - 11:03:08 PDT)
- Re: [AMBER] integration algorithm of sander? And reference of sander? (Mon Apr 13 2020 - 10:27:20 PDT)
- Re: [AMBER] integration algorithm of sander? And reference of sander? (Mon Apr 13 2020 - 09:18:54 PDT)
- Re: [AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. (Mon Apr 06 2020 - 03:52:38 PDT)
- Re: [AMBER] NPT equilibration is crashing (Sun Apr 05 2020 - 04:41:13 PDT)
- Re: [AMBER] NPT equilibration is crashing (Sat Apr 04 2020 - 11:30:29 PDT)
- Re: [AMBER] NPT equilibration is crashing (Wed Apr 01 2020 - 10:01:49 PDT)
- Re: [AMBER] NPT equilibration is crashing (Wed Apr 01 2020 - 06:14:04 PDT)
Casalini Tommaso
- [AMBER] Simulating magnetite surfaces with AMBER (Tue Apr 14 2020 - 02:44:23 PDT)
ChenXingqiang
- Re: [AMBER] AMBER 18 cuda installation (Sat Apr 11 2020 - 22:55:56 PDT)
- Re: [AMBER] AMBER 18 cuda installation (Sat Apr 11 2020 - 08:11:42 PDT)
- [AMBER] Amber install CUDA truble (Sat Apr 11 2020 - 08:04:44 PDT)
Christina Bergonzo
- Re: [AMBER] Abasic Site and Leap Polymerization (Sun Apr 05 2020 - 12:43:27 PDT)
- Re: [AMBER] Abasic Site and Leap Polymerization (Sat Apr 04 2020 - 14:37:10 PDT)
- Re: [AMBER] Abasic Site and Leap Polymerization (Sat Apr 04 2020 - 09:42:11 PDT)
Christopher Benjamin Coffey
- [AMBER] unsubscribe (Fri Apr 24 2020 - 08:19:20 PDT)
- Re: [AMBER] Amber18, tools19, cuda 10.2 (Thu Apr 23 2020 - 08:13:06 PDT)
- [AMBER] Amber18, tools19, cuda 10.2 (Wed Apr 22 2020 - 11:16:55 PDT)
Cong Liu
- Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests (Tue Apr 14 2020 - 11:04:08 PDT)
- Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests (Tue Apr 14 2020 - 08:24:37 PDT)
- Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests (Sat Apr 11 2020 - 07:25:07 PDT)
- [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests (Fri Apr 10 2020 - 16:52:16 PDT)
Czarny,Ryan
- Re: [AMBER] RST File Corrupt (Tue Apr 14 2020 - 12:05:26 PDT)
- [AMBER] RST File Corrupt (Tue Apr 14 2020 - 10:54:45 PDT)
Daniel Roe
- Re: [AMBER] Restraint on certain atoms during MD (Wed Apr 22 2020 - 14:00:03 PDT)
- Re: [AMBER] Probable bug in tleap. (Fri Apr 17 2020 - 11:47:42 PDT)
David A Case
- Re: [AMBER] Using tleap tho have the .inpcrd and crd file (Wed Apr 29 2020 - 04:20:58 PDT)
- Re: [AMBER] adding hydrogen to pdbqt ligand files (Tue Apr 28 2020 - 16:40:40 PDT)
- Re: [AMBER] Recurring problem: Ligand lose planarity (Mon Apr 27 2020 - 11:24:47 PDT)
- Re: [AMBER] Recurring problem: Ligand lose planarity (Mon Apr 27 2020 - 11:23:18 PDT)
- Re: [AMBER] NAB to create DNA/RNA hybrid? (Mon Apr 27 2020 - 11:18:24 PDT)
- Re: [AMBER] minimizing a pyridine in water (Sat Apr 25 2020 - 10:29:12 PDT)
- Re: [AMBER] wrong geometry amide nitrogen (Fri Apr 24 2020 - 08:01:49 PDT)
- Re: [AMBER] Amber18, tools19, cuda 10.2 (Thu Apr 23 2020 - 05:49:46 PDT)
- Re: [AMBER] FATAL: allocation failure in ivector() error while running 3D-RISM calculations (Thu Apr 23 2020 - 05:54:19 PDT)
- Re: [AMBER] How to change charge value for 1 residue for MD simulation? (Thu Apr 23 2020 - 05:51:52 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Wed Apr 22 2020 - 10:42:06 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Tue Apr 21 2020 - 11:54:45 PDT)
- Re: [AMBER] restraining many individual atoms (Mon Apr 20 2020 - 12:55:38 PDT)
- Re: [AMBER] pytraj error (Mon Apr 20 2020 - 05:05:58 PDT)
- Re: [AMBER] Request for help in solving installation errors of Amber (Mon Apr 20 2020 - 04:59:52 PDT)
- Re: [AMBER] Amber18 PIMD tutorial (Sat Apr 18 2020 - 05:53:07 PDT)
- Re: [AMBER] Error when installing miniconda through AmberTools19 (Thu Apr 16 2020 - 12:02:25 PDT)
- Re: [AMBER] protein-protein complex dissociation (Thu Apr 16 2020 - 11:54:03 PDT)
- Re: [AMBER] Generating an asymmetric box for Steered MD (Thu Apr 16 2020 - 04:54:56 PDT)
- Re: [AMBER] integration algorithm of sander? And reference of sander? (Mon Apr 13 2020 - 12:21:55 PDT)
- Re: [AMBER] Reg:MMPB(GB)SA Error (Mon Apr 13 2020 - 12:16:12 PDT)
- Re: [AMBER] Antechamber/acpype for ligand parametrization and usage of yasara autosmiles (Sun Apr 12 2020 - 05:49:59 PDT)
- Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests (Sat Apr 11 2020 - 05:03:34 PDT)
- Re: [AMBER] Very low MMPBSA result (Sat Apr 11 2020 - 05:00:25 PDT)
- Re: [AMBER] ImportError: Could not import Amber Python modules (Thu Apr 09 2020 - 19:02:32 PDT)
- Re: [AMBER] peek_ewald_inpcrd: Box info not found in inpcrd (Thu Apr 09 2020 - 08:24:56 PDT)
- Re: [AMBER] peek_ewald_inpcrd: Box info not found in inpcrd (Thu Apr 09 2020 - 04:47:22 PDT)
- Re: [AMBER] topology problems (Wed Apr 08 2020 - 04:37:08 PDT)
- Re: [AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. (Mon Apr 06 2020 - 05:03:59 PDT)
- Re: [AMBER] Installation of ambertools on 32 bit linux system (Mon Apr 06 2020 - 05:00:59 PDT)
- Re: [AMBER] PrmtopError: Inconsistent charge definition for atom (Sun Apr 05 2020 - 18:06:14 PDT)
- Re: [AMBER] cellulose chain (Sun Apr 05 2020 - 10:20:28 PDT)
- Re: [AMBER] Differences in Lennard-Jones interactions in CPU vs GPU pmemd? (Sun Apr 05 2020 - 10:15:15 PDT)
- Re: [AMBER] nmode entropy calculations gets stuck way too often (Sat Apr 04 2020 - 10:30:24 PDT)
- Re: [AMBER] ff_amber_to_viparr.py Error (Sat Apr 04 2020 - 10:22:49 PDT)
- Re: [AMBER] Problem in configuring (Thu Apr 02 2020 - 04:50:43 PDT)
- Re: [AMBER] Remove restraint (Wed Apr 01 2020 - 07:02:20 PDT)
David Cerutti
- Re: [AMBER] Can I use paramfit for MM scan? (Wed Apr 15 2020 - 14:44:04 PDT)
- Re: [AMBER] Can I use paramfit for MM scan? (Sun Apr 12 2020 - 23:20:11 PDT)
- Re: [AMBER] Can I use paramfit for MM scan? (Sat Apr 11 2020 - 03:53:15 PDT)
- Re: [AMBER] AMBER 18 cuda installation: error: redefinition of ???simulationConst cSim??? (Sat Apr 04 2020 - 20:54:23 PDT)
David Sáez
- Re: [AMBER] Acetylated the truncated N- terminal (Thu Apr 09 2020 - 23:11:33 PDT)
- Re: [AMBER] Acetylated the truncated N- terminal (Thu Apr 09 2020 - 22:02:24 PDT)
- Re: [AMBER] NPT equilibration is crashing (Fri Apr 03 2020 - 18:56:44 PDT)
- Re: [AMBER] NPT equilibration is crashing (Wed Apr 01 2020 - 06:44:25 PDT)
Debarati DasGupta
- [AMBER] TI simulations (Thu Apr 30 2020 - 12:09:58 PDT)
- Re: [AMBER] minimizing a pyridine in water (Mon Apr 27 2020 - 11:53:48 PDT)
- Re: [AMBER] minimizing a pyridine in water (Sat Apr 25 2020 - 11:32:40 PDT)
- Re: [AMBER] minimizing a pyridine in water (Sat Apr 25 2020 - 10:35:48 PDT)
- Re: [AMBER] minimizing a pyridine in water (Sat Apr 25 2020 - 08:38:29 PDT)
- [AMBER] minimizing a pyridine in water (Sat Apr 25 2020 - 06:10:52 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Wed Apr 22 2020 - 15:10:04 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Wed Apr 22 2020 - 15:22:03 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Wed Apr 22 2020 - 15:07:16 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Wed Apr 22 2020 - 10:05:59 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Wed Apr 22 2020 - 10:04:17 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Wed Apr 22 2020 - 09:45:20 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Wed Apr 22 2020 - 09:33:19 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Wed Apr 22 2020 - 08:41:28 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Wed Apr 22 2020 - 08:34:38 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Tue Apr 21 2020 - 12:02:11 PDT)
- Re: [AMBER] Restraint on certain atoms during MD (Tue Apr 21 2020 - 11:56:46 PDT)
- [AMBER] Restraint on certain atoms during MD (Tue Apr 21 2020 - 05:45:15 PDT)
- Re: [AMBER] Clustering analysis (Wed Apr 15 2020 - 07:38:37 PDT)
- Re: [AMBER] Ligand leaving binding site at high lambdas using TI softcore (Fri Apr 10 2020 - 08:46:19 PDT)
- Re: [AMBER] Ligand leaving binding site at high lambdas using TI softcore (Fri Apr 10 2020 - 05:13:35 PDT)
Devashish_Das
- [AMBER] How to change charge value for 1 residue for MD simulation? (Thu Apr 23 2020 - 00:59:57 PDT)
DHEERAJ CHITARA
- [AMBER] PrmtopError: Inconsistent charge definition for atom (Sun Apr 05 2020 - 10:20:23 PDT)
dhruvi.iiar.res.in
- Re: [AMBER] Request for help in solving installation errors of Amber (Sun Apr 19 2020 - 23:57:48 PDT)
- [AMBER] Request for help in solving installation errors of Amber (Sat Apr 18 2020 - 06:13:11 PDT)
- [AMBER] Request for help in solving installation errors of Amber (Fri Apr 17 2020 - 04:20:54 PDT)
Dickson, Callum
- Re: [AMBER] Ligand leaving binding site at high lambdas using TI softcore (Thu Apr 09 2020 - 12:00:30 PDT)
Dow Hurst
- Re: [AMBER] RTX 2020 Super GPU Random Memory Errors (Mon Apr 20 2020 - 10:30:53 PDT)
Dr. Anselm Horn
- Re: [AMBER] Interaction of cellulose-hemicellulose (Mon Apr 27 2020 - 07:04:57 PDT)
- Re: [AMBER] protein-protein complex dissociation (Fri Apr 17 2020 - 01:10:00 PDT)
Eduardo R. Almeida
- [AMBER] Tsolute and Tsolvent (Mon Apr 27 2020 - 08:00:45 PDT)
- [AMBER] Energy values from mdout files (excluding solvent molecules) (Thu Apr 23 2020 - 06:01:19 PDT)
- [AMBER] Energy values from mdout (excluding solvent molecules) (Mon Apr 20 2020 - 20:57:48 PDT)
Elif Çiğdem Calvin
- [AMBER] Can I use paramfit for MM scan? (Fri Apr 10 2020 - 18:31:06 PDT)
Elvis Martis
- Re: [AMBER] CPPtraj PCA error (Tue Apr 14 2020 - 11:18:39 PDT)
- Re: [AMBER] Reg:MMPB(GB)SA Error (Mon Apr 13 2020 - 11:58:21 PDT)
Erdem Yeler
- Re: [AMBER] Can I use paramfit for MM scan? (Wed Apr 15 2020 - 14:26:08 PDT)
- Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? (Wed Apr 15 2020 - 13:59:10 PDT)
- Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? (Tue Apr 14 2020 - 13:01:14 PDT)
- Re: [AMBER] integration algorithm of sander? And reference of sander? (Tue Apr 14 2020 - 12:56:50 PDT)
- Re: [AMBER] integration algorithm of sander? And reference of sander? (Mon Apr 13 2020 - 10:45:26 PDT)
- Re: [AMBER] integration algorithm of sander? And reference of sander? (Mon Apr 13 2020 - 10:17:35 PDT)
- [AMBER] integration algorithm of sander? And reference of sander? (Mon Apr 13 2020 - 09:12:12 PDT)
- Re: [AMBER] Can I use paramfit for MM scan? (Mon Apr 13 2020 - 04:37:52 PDT)
- Re: [AMBER] Can I use paramfit for MM scan? (Sat Apr 11 2020 - 21:35:13 PDT)
- [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? (Fri Apr 10 2020 - 16:01:59 PDT)
Eugene.Billiot.tamucc.edu
- Re: [AMBER] examination of ligand binding energy as a function of simulation time with MMPBSA calculations (Fri Apr 17 2020 - 11:54:15 PDT)
- Re: [AMBER] examination of ligand binding energy as a function of simulation time with MMPBSA calculations (Fri Apr 17 2020 - 08:09:42 PDT)
Fabian Glaser
- [AMBER] implicit water (Wed Apr 22 2020 - 11:53:45 PDT)
Francesco Gentile
- [AMBER] tMD and pmemd (Wed Apr 29 2020 - 17:00:17 PDT)
Gallo, Angelo
- [AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. (Mon Apr 06 2020 - 02:12:26 PDT)
Gardezi,Shahbaz
- Re: [AMBER] Error when installing miniconda through AmberTools19 (Thu Apr 16 2020 - 13:28:20 PDT)
- Re: [AMBER] Error when installing miniconda through AmberTools19 (Thu Apr 16 2020 - 10:51:54 PDT)
- [AMBER] Error when installing miniconda through AmberTools19 (Thu Apr 16 2020 - 10:40:06 PDT)
Gerardo Zerbetto De Palma
- Re: [AMBER] Running Steered MD Simulations using GPU (Wed Apr 01 2020 - 08:51:51 PDT)
Gini
- [AMBER] Sander can not calculate Mbar energy (Wed Apr 22 2020 - 17:21:53 PDT)
Giorgos Lambrinidis
- Re: [AMBER] RTX 2020 Super GPU Random Memory Errors (Wed Apr 01 2020 - 00:21:50 PDT)
Gustavo Seabra
- Re: [AMBER] nativecontacts (Wed Apr 29 2020 - 05:56:19 PDT)
- Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? (Tue Apr 14 2020 - 07:28:12 PDT)
Hai Nguyen
- Re: [AMBER] pytraj error (Tue Apr 21 2020 - 06:55:52 PDT)
- Re: [AMBER] pytraj error (Mon Apr 20 2020 - 20:56:58 PDT)
- Re: [AMBER] Request for help in solving installation errors of Amber (Sat Apr 18 2020 - 18:42:38 PDT)
- Re: [AMBER] Request for help in solving installation errors of Amber (Sat Apr 18 2020 - 18:27:50 PDT)
- Re: [AMBER] Installing nglview (Fri Apr 10 2020 - 17:45:08 PDT)
- Re: [AMBER] Installing nglview (Fri Apr 10 2020 - 17:11:17 PDT)
Hector A. Baldoni
- [AMBER] Targeted MD (Tue Apr 21 2020 - 17:53:36 PDT)
- [AMBER] Probable bug in tleap. (Fri Apr 17 2020 - 11:38:41 PDT)
- Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? (Tue Apr 14 2020 - 07:47:13 PDT)
- Re: [AMBER] Sequence command to build the 4 - O glucuronuxylans chain (Sun Apr 05 2020 - 11:52:44 PDT)
Ignacio General
- [AMBER] restraining many individual atoms (Mon Apr 20 2020 - 11:06:01 PDT)
Ignacio J. General
- Re: [AMBER] restraining many individual atoms (Mon Apr 20 2020 - 13:31:21 PDT)
- Re: [AMBER] restraining many individual atoms (Mon Apr 20 2020 - 12:48:36 PDT)
Ilyas Yildirim
- Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? (Fri Apr 10 2020 - 16:15:46 PDT)
iraklis litinas
- [AMBER] ff_amber_to_viparr.py Error (Sat Apr 04 2020 - 02:04:58 PDT)
James Kress
- Re: [AMBER] Unavailability of AMBER tutorial on PCA (Tue Apr 28 2020 - 15:38:23 PDT)
- Re: [AMBER] minimizing a pyridine in water (Sat Apr 25 2020 - 16:39:37 PDT)
- Re: [AMBER] restraining many individual atoms (Mon Apr 20 2020 - 12:37:44 PDT)
Jatin Kashyap
- Re: [AMBER] Installing nglview (Fri Apr 10 2020 - 17:30:48 PDT)
- [AMBER] Installing nglview (Thu Apr 09 2020 - 20:18:53 PDT)
Jenny 148
- Re: [AMBER] Recurring problem: Ligand lose planarity (Mon Apr 27 2020 - 11:51:53 PDT)
- Re: [AMBER] Recurring problem: Ligand lose planarity (Sun Apr 26 2020 - 14:15:22 PDT)
- Re: [AMBER] Recurring problem: Ligand lose planarity (Sun Apr 26 2020 - 11:28:39 PDT)
- Re: [AMBER] Recurring problem: Ligand lose planarity (Sun Apr 26 2020 - 11:04:32 PDT)
- Re: [AMBER] Recurring problem: Ligand lose planarity (Sun Apr 26 2020 - 09:33:51 PDT)
- [AMBER] Recurring problem: Ligand lose planarity (Sat Apr 25 2020 - 21:49:45 PDT)
- [AMBER] Ligand lose planarity (Sat Apr 25 2020 - 08:09:45 PDT)
Jisha B
- [AMBER] Mutations in existing DNA PDB file (Thu Apr 30 2020 - 09:36:38 PDT)
- [AMBER] NAB to create DNA/RNA hybrid? (Sat Apr 25 2020 - 23:21:24 PDT)
Junmei Wang
- Re: [AMBER] wrong geometry amide nitrogen (Thu Apr 30 2020 - 20:15:53 PDT)
- Re: [AMBER] wrong geometry amide nitrogen (Wed Apr 29 2020 - 21:45:25 PDT)
- Re: [AMBER] wrong geometry amide nitrogen (Wed Apr 29 2020 - 08:09:26 PDT)
- Re: [AMBER] wrong geometry amide nitrogen (Wed Apr 29 2020 - 07:36:21 PDT)
- Re: [AMBER] wrong geometry amide nitrogen (Wed Apr 29 2020 - 07:12:46 PDT)
- Re: [AMBER] wrong geometry amide nitrogen (Tue Apr 28 2020 - 14:02:10 PDT)
Juraj Dobias
- Re: [AMBER] Ligand leaving binding site at high lambdas using TI softcore (Sat Apr 11 2020 - 02:22:55 PDT)
- Re: [AMBER] Ligand leaving binding site at high lambdas using TI softcore (Thu Apr 09 2020 - 13:34:11 PDT)
- Re: [AMBER] Ligand leaving binding site at high lambdas using TI softcore (Thu Apr 09 2020 - 10:30:07 PDT)
- [AMBER] Ligand leaving binding site at high lambdas using TI softcore (Wed Apr 08 2020 - 13:39:52 PDT)
Karl Kirschner
- Re: [AMBER] Help for building lignin chain (Sat Apr 11 2020 - 01:23:49 PDT)
- Re: [AMBER] Sequence command to build the 4 - O glucuronuxylans chain (Sun Apr 05 2020 - 01:17:37 PDT)
Kellon Belfon
- Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests (Tue Apr 14 2020 - 10:36:48 PDT)
Lachele Foley
- Re: [AMBER] Interaction of cellulose-hemicellulose (Wed Apr 29 2020 - 18:01:59 PDT)
- Re: [AMBER] tlea (Wed Apr 29 2020 - 17:46:37 PDT)
- Re: [AMBER] Interaction of cellulose-hemicellulose (Fri Apr 24 2020 - 04:33:24 PDT)
- Re: [AMBER] Interaction of cellulose-hemicellulose (Sun Apr 19 2020 - 23:48:13 PDT)
- Re: [AMBER] Interaction of cellulose-hemicellulose (Sat Apr 18 2020 - 00:21:21 PDT)
- Re: [AMBER] Interaction of cellulose-hemicellulose (Thu Apr 16 2020 - 23:06:01 PDT)
- Re: [AMBER] Interaction of cellulose-hemicellulose (Thu Apr 16 2020 - 01:22:43 PDT)
- Re: [AMBER] 1 chain-1chain interactions between carbohydrates (Thu Apr 16 2020 - 01:20:50 PDT)
Lara rajam
- [AMBER] Reg:MMPB(GB)SA Error (Mon Apr 13 2020 - 11:26:06 PDT)
Leena Aggarwal
- [AMBER] Fwd: FATAL: allocation failure in ivector() error while running 3D-RISM calculations (Thu Apr 23 2020 - 11:25:47 PDT)
- [AMBER] FATAL: allocation failure in ivector() error while running 3D-RISM calculations (Thu Apr 23 2020 - 04:32:16 PDT)
Lenka
- Re: [AMBER] sum of charges from parm file (Tue Mar 31 2020 - 15:47:47 PDT)
- [AMBER] sum of charges from parm file (Tue Mar 31 2020 - 15:27:36 PDT)
Liao
- Re: [AMBER] nmode entropy calculations gets stuck way too often (Sat Apr 11 2020 - 21:30:57 PDT)
- Re: [AMBER] nmode entropy calculations gets stuck way too often (Sat Apr 04 2020 - 12:26:25 PDT)
- Re: [AMBER] nmode entropy calculations gets stuck way too often (Fri Apr 03 2020 - 18:44:22 PDT)
- [AMBER] nmode entropy calculations gets stuck way too often (Fri Apr 03 2020 - 16:42:58 PDT)
Lod King
- [AMBER] Partial charge for ligand (Fri Apr 10 2020 - 17:00:05 PDT)
- Re: [AMBER] Acetylated the truncated N- terminal (Thu Apr 09 2020 - 23:14:53 PDT)
- Re: [AMBER] Acetylated the truncated N- terminal (Thu Apr 09 2020 - 22:10:03 PDT)
- [AMBER] Acetylated the truncated N- terminal (Thu Apr 09 2020 - 20:47:27 PDT)
Lorenzo Gontrani
- Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? (Sun Apr 12 2020 - 08:11:02 PDT)
Marawan Hussien
- [AMBER] adding hydrogen to pdbqt ligand files (Tue Apr 28 2020 - 14:15:36 PDT)
mark.bergman.uphs.upenn.edu
- Re: [AMBER] [External] Re: AmberTools19 update.8 fails to install (Thu Apr 02 2020 - 08:29:23 PDT)
Matias Machado
- Re: [AMBER] topology problems (Tue Apr 07 2020 - 12:28:09 PDT)
mohamed marzouk
- [AMBER] nativecontacts (Tue Apr 28 2020 - 23:35:04 PDT)
- Re: [AMBER] cylindrical Simulation (Tue Apr 28 2020 - 23:26:17 PDT)
- [AMBER] cylindrical Simulation (Sun Apr 26 2020 - 18:47:12 PDT)
- [AMBER] Remove restraint (Wed Apr 01 2020 - 05:50:33 PDT)
MYRIAN TORRES RICO
- Re: [AMBER] tlea (Thu Apr 30 2020 - 00:55:31 PDT)
- [AMBER] tleap error (Wed Apr 29 2020 - 03:23:30 PDT)
- [AMBER] tlea (Tue Apr 28 2020 - 02:25:58 PDT)
- [AMBER] error tleap (Tue Apr 28 2020 - 02:24:47 PDT)
Nada Afiva
- Re: [AMBER] Very low MMPBSA result (Wed Apr 15 2020 - 12:36:01 PDT)
- Re: [AMBER] Very low MMPBSA result (Mon Apr 13 2020 - 18:41:59 PDT)
- Re: [AMBER] Very low MMPBSA result (Mon Apr 13 2020 - 03:44:44 PDT)
- Re: [AMBER] Very low MMPBSA result (Sat Apr 11 2020 - 23:10:28 PDT)
- Re: [AMBER] Very low MMPBSA result (Sat Apr 11 2020 - 02:16:13 PDT)
- Re: [AMBER] Very low MMPBSA result (Fri Apr 10 2020 - 17:54:22 PDT)
- Re: [AMBER] Very low MMPBSA result (Fri Apr 10 2020 - 16:46:09 PDT)
- [AMBER] Very low MMPBSA result (Fri Apr 10 2020 - 14:18:47 PDT)
Núbia Toman
- Re: [AMBER] protein-protein complex dissociation (Fri Apr 17 2020 - 01:50:34 PDT)
- Re: [AMBER] protein-protein complex dissociation (Thu Apr 16 2020 - 10:58:14 PDT)
- Re: [AMBER] protein-protein complex dissociation (Thu Apr 16 2020 - 10:03:52 PDT)
- Re: [AMBER] protein-protein complex dissociation (Thu Apr 16 2020 - 09:48:20 PDT)
- Re: [AMBER] protein-protein complex dissociation (Thu Apr 16 2020 - 06:42:45 PDT)
- Re: [AMBER] protein-protein complex dissociation (Thu Apr 16 2020 - 06:36:13 PDT)
- [AMBER] protein-protein complex dissociation (Thu Apr 16 2020 - 06:17:53 PDT)
Paulius Kantakevicius
- [AMBER] 12-6-4LJ for thermodynamic integration on PMEMD engine (Sat Apr 04 2020 - 12:01:13 PDT)
Pengfei Li
- Re: [AMBER] tleap for Mg2+ data type (Thu Apr 09 2020 - 09:19:19 PDT)
- Re: [AMBER] sum of charges from parm file (Thu Apr 09 2020 - 09:12:11 PDT)
- Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial (Thu Apr 09 2020 - 08:24:20 PDT)
- Re: [AMBER] 12-6-4LJ for thermodynamic integration on PMEMD engine (Thu Apr 09 2020 - 08:22:55 PDT)
Pinky Mazumder
- Re: [AMBER] Interaction of cellulose-hemicellulose (Sun Apr 26 2020 - 20:59:07 PDT)
- Re: [AMBER] Interaction of cellulose-hemicellulose (Fri Apr 24 2020 - 00:30:36 PDT)
- Re: [AMBER] Interaction of cellulose-hemicellulose (Mon Apr 20 2020 - 18:30:07 PDT)
- Re: [AMBER] Interaction of cellulose-hemicellulose (Sun Apr 19 2020 - 22:05:17 PDT)
- Re: [AMBER] Interaction of cellulose-hemicellulose (Fri Apr 17 2020 - 14:28:20 PDT)
- Re: [AMBER] Interaction of cellulose-hemicellulose (Fri Apr 17 2020 - 07:59:54 PDT)
- Re: [AMBER] Interaction of cellulose-hemicellulose (Fri Apr 17 2020 - 00:45:28 PDT)
- Re: [AMBER] Interaction of cellulose-hemicellulose (Thu Apr 16 2020 - 22:58:54 PDT)
- [AMBER] Interaction of cellulose-hemicellulose (Wed Apr 15 2020 - 20:13:45 PDT)
- Re: [AMBER] Help for building lignin chain (Tue Apr 14 2020 - 20:39:45 PDT)
- [AMBER] 1 chain-1chain interactions between carbohydrates (Tue Apr 14 2020 - 20:36:31 PDT)
- [AMBER] Help for building lignin chain (Sat Apr 11 2020 - 00:21:32 PDT)
- [AMBER] command for building composite of cellulose microfibrils and hemicelullose (Mon Apr 06 2020 - 15:05:16 PDT)
- Re: [AMBER] Sequence command to build the 4 - O glucuronuxylans chain (Sun Apr 05 2020 - 15:46:10 PDT)
- Re: [AMBER] Sequence command to build the 4 - O glucuronuxylans chain (Sun Apr 05 2020 - 15:00:22 PDT)
- [AMBER] Help for the sequence of residue name (Sun Apr 05 2020 - 00:09:15 PDT)
- [AMBER] Sequence command to build the 4 - O glucuronuxylans chain (Sat Apr 04 2020 - 19:26:03 PDT)
- Re: [AMBER] Contents of Amber Digest (Sat Apr 04 2020 - 01:14:02 PDT)
- [AMBER] cellulose chain (Thu Apr 02 2020 - 12:09:59 PDT)
Prasanth G, Research Scholar
- [AMBER] Antechamber/acpype for ligand parametrization and usage of yasara autosmiles (Sat Apr 11 2020 - 10:37:10 PDT)
- [AMBER] Installation of ambertools on 32 bit linux system (Sun Apr 05 2020 - 22:12:12 PDT)
Prathit Chatterjee
- [AMBER] Problem in calculating pairwise interaction with CPPTRAJ (Tue Apr 21 2020 - 02:47:42 PDT)
Preeti Pandey
- Re: [AMBER] examination of ligand binding energy as a function of simulation time with MMPBSA calculations (Fri Apr 17 2020 - 11:43:14 PDT)
Qinghua Liao
- Re: [AMBER] Ligand leaving binding site at high lambdas using TI softcore (Fri Apr 10 2020 - 05:44:08 PDT)
Raman Preet Singh
- Re: [AMBER] cellulose chain (Sun Apr 05 2020 - 10:30:40 PDT)
Rana Rehan Khalid
- Re: [AMBER] CPPtraj PCA error (Tue Apr 14 2020 - 11:36:24 PDT)
- [AMBER] CPPtraj PCA error (Tue Apr 14 2020 - 10:57:54 PDT)
Ravi Abrol
- Re: [AMBER] pytraj error (Tue Apr 21 2020 - 14:21:36 PDT)
- Re: [AMBER] pytraj error (Tue Apr 21 2020 - 04:02:03 PDT)
- Re: [AMBER] pytraj error (Mon Apr 20 2020 - 14:03:47 PDT)
- [AMBER] pytraj error (Mon Apr 20 2020 - 00:06:35 PDT)
Ray Luo
- Re: [AMBER] Very low MMPBSA result (Mon Apr 13 2020 - 13:21:22 PDT)
- Re: [AMBER] examination of ligand binding energy as a function of simulation time with MMPBSA calculations (Sun Apr 12 2020 - 19:33:47 PDT)
- Re: [AMBER] Very low MMPBSA result (Sun Apr 12 2020 - 09:01:23 PDT)
- Re: [AMBER] AMBER 18 cuda installation (Sat Apr 11 2020 - 09:59:12 PDT)
- Re: [AMBER] Very low MMPBSA result (Fri Apr 10 2020 - 18:42:27 PDT)
- Re: [AMBER] Very low MMPBSA result (Fri Apr 10 2020 - 15:37:31 PDT)
Renato Araujo
- [AMBER] ImportError: Could not import Amber Python modules (Thu Apr 09 2020 - 10:24:18 PDT)
Ricky Nencini
- Re: [AMBER] Amber force field for SDS and DPC detergents (Fri Apr 03 2020 - 10:06:29 PDT)
- [AMBER] Amber force field for SDS and DPC detergents (Fri Apr 03 2020 - 03:17:27 PDT)
Robert Molt
- Re: [AMBER] Abasic Site and Leap Polymerization (Sun Apr 05 2020 - 10:22:40 PDT)
- Re: [AMBER] Abasic Site and Leap Polymerization (Sat Apr 04 2020 - 13:01:13 PDT)
- Re: [AMBER] Abasic Site and Leap Polymerization (Sat Apr 04 2020 - 08:56:33 PDT)
Rodrigo Galindo-Murillo
- Re: [AMBER] Unavailability of AMBER tutorial on PCA (Wed Apr 29 2020 - 10:27:10 PDT)
Roitberg,Adrian E
- Re: [AMBER] nmode entropy calculations gets stuck way too often (Fri Apr 03 2020 - 16:55:14 PDT)
Rosellen, Martin
- Re: [AMBER] Error: Could not find angle parameter (Fri Apr 03 2020 - 01:04:51 PDT)
Sapna Shedge
- Re: [AMBER] Amber18 PIMD tutorial (Sat Apr 18 2020 - 15:56:58 PDT)
- [AMBER] Amber18 PIMD tutorial (Fri Apr 17 2020 - 23:16:19 PDT)
- Re: [AMBER] Amber install CUDA truble (Mon Apr 13 2020 - 17:55:02 PDT)
- [AMBER] AMBER 18 cuda installation: error: redefinition of ‘simulationConst cSim’ (Thu Apr 02 2020 - 10:58:23 PDT)
- [AMBER] Problem in configuring (Wed Apr 01 2020 - 21:34:48 PDT)
Satyaseelan C
- Re: [AMBER] NAB to create DNA/RNA hybrid? (Mon Apr 27 2020 - 20:38:27 PDT)
- Re: [AMBER] DNA-RNA duplex (Mon Apr 27 2020 - 20:37:35 PDT)
Scott Brozell
- Re: [AMBER] Probable bug in tleap. (Fri Apr 17 2020 - 11:46:17 PDT)
- Re: [AMBER] AMBER 18 cuda installation: error: redefinition of ???simulationConst cSim??? (Sat Apr 04 2020 - 18:09:42 PDT)
Seibold, Steve Allan
- [AMBER] topology problems (Tue Apr 07 2020 - 09:58:59 PDT)
Shum, Ho Hin
- [AMBER] Incorrect results when running MMPBSA example. (Thu Apr 02 2020 - 21:48:38 PDT)
Siddharth marwaha
- [AMBER] AMBER leap issues constructing non-standard residue (Mon Apr 27 2020 - 11:50:30 PDT)
Song Hu
- [AMBER] geometry of amino (Mon Apr 13 2020 - 22:59:00 PDT)
Song, Lin
- Re: [AMBER] 12-6-4LJ for thermodynamic integration on PMEMD engine (Thu Apr 09 2020 - 08:34:22 PDT)
Souvik Dey
- Re: [AMBER] Generating an asymmetric box for Steered MD (Fri Apr 17 2020 - 00:03:52 PDT)
- Re: [AMBER] Generating an asymmetric box for Steered MD (Thu Apr 16 2020 - 12:33:36 PDT)
- [AMBER] Generating an asymmetric box for Steered MD (Wed Apr 15 2020 - 15:43:01 PDT)
- [AMBER] Running Steered MD Simulations using GPU (Wed Apr 01 2020 - 08:48:18 PDT)
Sruthi Sudhakar
- Re: [AMBER] Recurring problem: Ligand lose planarity (Sun Apr 26 2020 - 08:33:44 PDT)
- [AMBER] DNA-RNA duplex (Sat Apr 25 2020 - 07:34:30 PDT)
- [AMBER] FRCMOD file (Sat Apr 18 2020 - 07:01:46 PDT)
- Re: [AMBER] Force Field for small molecule ligands (Fri Apr 17 2020 - 06:06:07 PDT)
- [AMBER] Force Field for small molecule ligands (Fri Apr 17 2020 - 05:17:35 PDT)
- [AMBER] Penalty score in frcmod file (Mon Apr 06 2020 - 23:24:47 PDT)
Steven M. Graham
- Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? (Tue Apr 14 2020 - 07:35:51 PDT)
SUNITA MUDULI
- [AMBER] How to get the eigenvalues from PCA (Mon Apr 27 2020 - 13:31:40 PDT)
Sunita Patel
- Re: [AMBER] peek_ewald_inpcrd: Box info not found in inpcrd (Fri Apr 10 2020 - 19:49:08 PDT)
- Re: [AMBER] tleap for Mg2+ data type (Thu Apr 09 2020 - 19:39:05 PDT)
- Re: [AMBER] peek_ewald_inpcrd: Box info not found in inpcrd (Thu Apr 09 2020 - 06:31:14 PDT)
- [AMBER] peek_ewald_inpcrd: Box info not found in inpcrd (Wed Apr 08 2020 - 21:01:18 PDT)
- Re: [AMBER] NPT equilibration is crashing (Sat Apr 04 2020 - 19:53:31 PDT)
- Re: [AMBER] NPT equilibration is crashing (Sat Apr 04 2020 - 11:22:13 PDT)
- Re: [AMBER] NPT equilibration is crashing (Fri Apr 03 2020 - 18:23:34 PDT)
- Re: [AMBER] NPT equilibration is crashing (Wed Apr 01 2020 - 09:41:43 PDT)
- Re: [AMBER] NPT equilibration is crashing (Wed Apr 01 2020 - 05:45:40 PDT)
swjjin0015.163.com
- [AMBER] Sander can't calculate Mbar energy (Tue Apr 21 2020 - 17:11:48 PDT)
- [AMBER] Sander can't calculate MBAR energy (Mon Apr 20 2020 - 18:31:19 PDT)
Thomas Cheatham
- Re: [AMBER] Question about PCA tutorial (Wed Apr 29 2020 - 20:24:07 PDT)
ttz
- [AMBER] questions about paramfit (Thu Apr 09 2020 - 21:54:12 PDT)
Vlad Cojocaru
- Re: [AMBER] simulations of proteins with 2 domains connected by a linker (Thu Apr 16 2020 - 02:35:57 PDT)

Amber Archive Apr 2020 by author