Amber Archive Feb 2020 by thread
278 messages
:
Starting
Sat Feb 01 2020 - 11:00:02 PST,
Ending
Sat Feb 29 2020 - 12:30:02 PST
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Re: [AMBER] cpptraj_clucster
Lod King
(Sat Feb 01 2020 - 10:47:56 PST)
Re: [AMBER] cpptraj_clucster
Daniel Roe
(Sat Feb 01 2020 - 11:05:57 PST)
[AMBER] ante-MMPBSA.py
Rui Chen
(Sat Feb 01 2020 - 13:20:17 PST)
Re: [AMBER] ante-MMPBSA.py
Elvis Martis
(Sat Feb 01 2020 - 18:56:38 PST)
Re: [AMBER] ante-MMPBSA.py
Rui Chen
(Sat Feb 01 2020 - 19:02:53 PST)
Re: [AMBER] ante-MMPBSA.py
Elvis Martis
(Sat Feb 01 2020 - 20:15:41 PST)
Re: [AMBER] ante-MMPBSA.py
Elvis Martis
(Sat Feb 01 2020 - 20:16:16 PST)
Re: [AMBER] ante-MMPBSA.py
Rui Chen
(Sat Feb 01 2020 - 20:26:33 PST)
[AMBER] installation of amber 18 failed - CUDA_HOME not set (although not true)
Bisignano, Paola
(Sat Feb 01 2020 - 20:09:08 PST)
Re: [AMBER] installation of amber 18 failed - CUDA_HOME not set (although not true)
Elvis Martis
(Sat Feb 01 2020 - 20:17:56 PST)
Re: [AMBER] installation of amber 18 failed - CUDA_HOME not set (although not true)
Bisignano, Paola
(Sat Feb 01 2020 - 20:19:20 PST)
Re: [AMBER] installation of amber 18 failed - CUDA_HOME not set (although not true)
Gerardo Zerbetto De Palma
(Sat Feb 01 2020 - 20:31:17 PST)
Re: [AMBER] installation of amber 18 failed - CUDA_HOME not set (although not true)
David Case
(Sun Feb 02 2020 - 05:34:52 PST)
[AMBER] "Bad inpcrd file!" when running pmemd.MPI but not pmemd
Johannes Blaschke
(Sun Feb 02 2020 - 09:09:13 PST)
Re: [AMBER] "Bad inpcrd file!" when running pmemd.MPI but not pmemd
Daniel Roe
(Mon Feb 03 2020 - 05:15:30 PST)
Re: [AMBER] "Bad inpcrd file!" when running pmemd.MPI but not pmemd
David A Case
(Mon Feb 03 2020 - 05:17:58 PST)
[AMBER] .crd error
MYRIAN TORRES RICO
(Mon Feb 03 2020 - 01:16:16 PST)
Re: [AMBER] .crd error
Daniel Roe
(Mon Feb 03 2020 - 05:08:08 PST)
Re: [AMBER] .crd error
MYRIAN TORRES RICO
(Tue Feb 04 2020 - 01:12:18 PST)
Re: [AMBER] .crd error
Gustaf Olsson
(Tue Feb 04 2020 - 03:11:51 PST)
Re: [AMBER] .crd error
MYRIAN TORRES RICO
(Tue Feb 04 2020 - 04:57:09 PST)
Re: [AMBER] .crd error
David A Case
(Tue Feb 04 2020 - 05:34:13 PST)
Re: [AMBER] .crd error
MYRIAN TORRES RICO
(Tue Feb 04 2020 - 06:26:53 PST)
Re: [AMBER] .crd error
Carlos Simmerling
(Tue Feb 04 2020 - 07:00:40 PST)
Re: [AMBER] .crd error
MYRIAN TORRES RICO
(Tue Feb 04 2020 - 07:37:17 PST)
Re: [AMBER] .crd error
Gustaf Olsson
(Tue Feb 04 2020 - 06:35:45 PST)
Re: [AMBER] .crd error
Daniel Roe
(Tue Feb 04 2020 - 11:37:04 PST)
Re: [AMBER] .crd error
David A Case
(Mon Feb 03 2020 - 05:24:22 PST)
Re: [AMBER] sulfonamide parameters for correct geometry
Junmei Wang
(Mon Feb 03 2020 - 10:01:45 PST)
Re: [AMBER] sulfonamide parameters for correct geometry
Annachiara TINIVELLA
(Thu Feb 06 2020 - 08:17:36 PST)
[AMBER] Reading Frames from Trajectory File
Catherine Jenifer Rajam Rajendran
(Mon Feb 03 2020 - 10:12:50 PST)
Re: [AMBER] Reading Frames from Trajectory File
Carlos Simmerling
(Mon Feb 03 2020 - 10:39:22 PST)
Re: [AMBER] [External] Re: Reading Frames from Trajectory File
Catherine Jenifer Rajam Rajendran
(Mon Feb 03 2020 - 10:51:00 PST)
Re: [AMBER] [External] Re: Reading Frames from Trajectory File
Carlos Simmerling
(Mon Feb 03 2020 - 10:55:41 PST)
Re: [AMBER] [External] Re: Reading Frames from Trajectory File
Catherine Jenifer Rajam Rajendran
(Mon Feb 03 2020 - 11:03:48 PST)
Re: [AMBER] Reading Frames from Trajectory File
Daniel Roe
(Mon Feb 03 2020 - 11:12:38 PST)
Re: [AMBER] [External] Re: Reading Frames from Trajectory File
Catherine Jenifer Rajam Rajendran
(Mon Feb 03 2020 - 11:45:02 PST)
Re: [AMBER] Help building a model of a 2F-2S protein with MDPB.py
Gustavo Seabra
(Mon Feb 03 2020 - 11:46:12 PST)
Re: [AMBER] Help building a model of a 2F-2S protein with MDPB.py
Pengfei Li
(Mon Feb 03 2020 - 18:02:20 PST)
Re: [AMBER] About utilities to convert Amber input files for MD into the Tinker, NAMD, Genesis, or Desmond input files
Pengfei Li
(Mon Feb 03 2020 - 18:09:05 PST)
Re: [AMBER] parameters for Si3N4
Pengfei Li
(Mon Feb 03 2020 - 18:13:34 PST)
[AMBER] heme B parameter by mcpb
PRAGYA PRIYADARSHINI
(Mon Feb 03 2020 - 20:39:48 PST)
[AMBER] pdb4amber strips atoms
Petro
(Tue Feb 04 2020 - 04:47:23 PST)
Re: [AMBER] pdb4amber strips atoms
Petro
(Tue Feb 04 2020 - 04:58:19 PST)
Re: [AMBER] Resolving overlapping atoms.
Petro
(Tue Feb 04 2020 - 04:50:23 PST)
[AMBER] CPPTRAJ hydrogen bond analysis
Rui Chen
(Tue Feb 04 2020 - 07:21:53 PST)
Re: [AMBER] CPPTRAJ hydrogen bond analysis
Daniel Roe
(Tue Feb 04 2020 - 11:42:26 PST)
Re: [AMBER] CPPTRAJ hydrogen bond analysis
Rui Chen
(Tue Feb 04 2020 - 12:45:54 PST)
Re: [AMBER] CalcError: /truba/sw/centos6.4/app/amber/amber14/bin/sander failed with prmtop gas.complex.prmtop!
Rana Rehan Khalid
(Tue Feb 04 2020 - 12:24:37 PST)
[AMBER] Gas phase simulation for heat of vaporization calculation
wijaya.t.aa.m.titech.ac.jp
(Wed Feb 05 2020 - 00:18:20 PST)
[AMBER] Reg. Periodic Boundary Conditions
DHEERAJ CHITARA
(Wed Feb 05 2020 - 04:20:36 PST)
Re: [AMBER] Reg. Periodic Boundary Conditions
Carlos Simmerling
(Wed Feb 05 2020 - 04:39:26 PST)
Re: [AMBER] Reg. Periodic Boundary Conditions
David A Case
(Wed Feb 05 2020 - 04:52:47 PST)
Re: [AMBER] (no subject)
mirzo
(Wed Feb 05 2020 - 05:11:50 PST)
[AMBER] counterions present in topology files for the MMPSA calculation
Shilpa Gupta
(Wed Feb 05 2020 - 05:43:46 PST)
Re: [AMBER] counterions present in topology files for the MMPSA calculation
Elvis Martis
(Wed Feb 05 2020 - 05:51:33 PST)
[AMBER] Several FAILED tests for AmberTools19 and Amber18
zmatovic.kg.ac.rs
(Wed Feb 05 2020 - 06:12:02 PST)
[AMBER] AQUA-DUCT Summer School 22-25 June, Gliwice, Poland
Markowska
(Wed Feb 05 2020 - 07:08:02 PST)
[AMBER] hiii
ankita mehta
(Wed Feb 05 2020 - 10:27:00 PST)
Re: [AMBER] hiii
David A Case
(Wed Feb 05 2020 - 10:46:28 PST)
Re: [AMBER] hiii
ankita mehta
(Wed Feb 05 2020 - 11:00:02 PST)
Re: [AMBER] hiii
ankita mehta
(Wed Feb 05 2020 - 11:09:51 PST)
Re: [AMBER] hiii
Daniel Roe
(Thu Feb 06 2020 - 05:16:02 PST)
[AMBER] MMPBSA calculations
Baptiste Legrand
(Thu Feb 06 2020 - 03:14:17 PST)
Re: [AMBER] MMPBSA calculations
Elvis Martis
(Thu Feb 06 2020 - 20:54:18 PST)
Re: [AMBER] Shaw DE RNA ff in Amber format
Josh Berryman
(Thu Feb 06 2020 - 05:34:00 PST)
Re: [AMBER] Shaw DE RNA ff in Amber format
Cavender, Chapin
(Thu Feb 06 2020 - 13:23:53 PST)
[AMBER] Question about LSC-IVR keep running without any output information after PIMD sampling
wangjianing_mail
(Thu Feb 06 2020 - 05:51:55 PST)
[AMBER] On QM/MM dummy atom and deprotonated TYR
David Sáez
(Thu Feb 06 2020 - 14:38:55 PST)
Re: [AMBER] On QM/MM dummy atom and deprotonated TYR
Clorice Reinhardt
(Thu Feb 06 2020 - 15:27:38 PST)
Re: [AMBER] On QM/MM dummy atom and deprotonated TYR
David Sáez
(Thu Feb 06 2020 - 18:36:44 PST)
Re: [AMBER] On QM/MM dummy atom and deprotonated TYR
David Sáez
(Tue Feb 11 2020 - 07:28:29 PST)
Re: [AMBER] On QM/MM dummy atom and deprotonated TYR
Clorice Reinhardt
(Tue Feb 11 2020 - 07:34:51 PST)
Re: [AMBER] On QM/MM dummy atom and deprotonated TYR
Clorice Reinhardt
(Tue Feb 11 2020 - 07:47:35 PST)
[AMBER] tleap/xleap performance enhancement
Himanshu Joshi
(Thu Feb 06 2020 - 14:48:58 PST)
Re: [AMBER] tleap/xleap performance enhancement
David A Case
(Fri Feb 07 2020 - 05:00:10 PST)
Re: [AMBER] tleap/xleap performance enhancement
Himanshu Joshi
(Fri Feb 07 2020 - 09:08:39 PST)
Re: [AMBER] tleap/xleap performance enhancement
Himanshu Joshi
(Fri Feb 07 2020 - 12:12:44 PST)
Re: [AMBER] tleap/xleap performance enhancement
Matias Machado
(Mon Feb 10 2020 - 07:35:05 PST)
[AMBER] [LEaP] Atom does not have a type
Johannes Kalliauer
(Fri Feb 07 2020 - 06:09:29 PST)
Re: [AMBER] [LEaP] Atom does not have a type
Gustavo Seabra
(Fri Feb 07 2020 - 08:02:01 PST)
Re: [AMBER] [LEaP] Atom does not have a type
mirzo
(Fri Feb 07 2020 - 08:32:54 PST)
Re: [AMBER] [LEaP] Atom does not have a type
David A Case
(Fri Feb 07 2020 - 15:06:13 PST)
[AMBER] question about pressure and sensible MD trajectories
Gordon Richard Chalmers
(Fri Feb 07 2020 - 19:38:43 PST)
Re: [AMBER] question about pressure and sensible MD trajectories
Gordon Richard Chalmers
(Fri Feb 07 2020 - 19:53:39 PST)
[AMBER] query on a script called getdvdl.py in AMBER TI tutorial section
Debarati DasGupta
(Sat Feb 08 2020 - 06:50:39 PST)
[AMBER] Regarding RMSD calculation and Clustering
Manish Kumar Mohanty
(Sat Feb 08 2020 - 21:10:09 PST)
[AMBER] TI on pmemd CUDA, AMBER18
Hosein Geraili Daronkola
(Mon Feb 10 2020 - 02:13:48 PST)
Re: [AMBER] TI on pmemd CUDA, AMBER18
Taisung Lee
(Tue Feb 11 2020 - 06:39:33 PST)
Re: [AMBER] TI on pmemd CUDA, AMBER18
Hosein Geraili Daronkola
(Fri Feb 21 2020 - 01:57:41 PST)
[AMBER] DOCKED LIGAND CONFORMATION INTO AMBER MD
Sruthi Sudhakar
(Mon Feb 10 2020 - 02:56:43 PST)
Re: [AMBER] DOCKED LIGAND CONFORMATION INTO AMBER MD
Elvis Martis
(Mon Feb 10 2020 - 04:13:14 PST)
[AMBER] kindly guide me.
ALAMGIR KHAN
(Mon Feb 10 2020 - 21:25:00 PST)
Re: [AMBER] kindly guide me.
David A Case
(Tue Feb 11 2020 - 04:49:07 PST)
[AMBER] how to treat capped non-standard AA residue
Vaibhav Dixit
(Tue Feb 11 2020 - 02:07:04 PST)
[AMBER] pmemd.cuda installation
Bacaita Simona
(Tue Feb 11 2020 - 11:40:44 PST)
Re: [AMBER] pmemd.cuda installation
David A Case
(Wed Feb 12 2020 - 06:08:46 PST)
[AMBER] AMBER 18 installation issue
Abhilash J
(Tue Feb 11 2020 - 17:09:56 PST)
Re: [AMBER] AMBER 18 installation issue
David A Case
(Wed Feb 12 2020 - 06:16:36 PST)
Re: [AMBER] AMBER 18 installation issue
Abhilash J
(Wed Feb 12 2020 - 08:44:32 PST)
[AMBER] Query regarding 3DRISM in Amber with CHARMM force field
Rakesh Srivastava
(Tue Feb 11 2020 - 22:46:07 PST)
Re: [AMBER] Query regarding 3DRISM in Amber with CHARMM force field
Tyler Luchko (Lists)
(Wed Feb 12 2020 - 10:05:06 PST)
Re: [AMBER] Amber install error
David A Case
(Wed Feb 12 2020 - 06:11:53 PST)
[AMBER] Simulation of an asymmetric membrane model
Eduardo R. Almeida
(Wed Feb 12 2020 - 11:38:07 PST)
Re: [AMBER] Simulation of an asymmetric membrane model
ABEL Stephane
(Thu Feb 13 2020 - 01:37:43 PST)
Re: [AMBER] Simulation of an asymmetric membrane model
Matias Machado
(Thu Feb 13 2020 - 11:37:33 PST)
[AMBER] Representative structures from `clusterdihedral`?
Gustavo Seabra
(Wed Feb 12 2020 - 13:43:52 PST)
[AMBER] BMRB Chemical shift values
Lod King
(Wed Feb 12 2020 - 15:21:29 PST)
Re: [AMBER] BMRB Chemical shift values
Christina Bergonzo
(Thu Feb 13 2020 - 05:50:58 PST)
Re: [AMBER] BMRB Chemical shift values
Gordon Richard Chalmers
(Thu Feb 13 2020 - 07:07:49 PST)
Re: [AMBER] BMRB Chemical shift values
Lod King
(Thu Feb 13 2020 - 08:05:15 PST)
Re: [AMBER] BMRB Chemical shift values
Adrian Roitberg
(Thu Feb 13 2020 - 08:29:02 PST)
[AMBER] counter ions in TI calculations
Maier, Sarah
(Wed Feb 12 2020 - 16:03:49 PST)
Re: [AMBER] counter ions in TI calculations
Josh Berryman
(Wed Feb 12 2020 - 23:45:58 PST)
[AMBER] QM/MM AMBER/ORCA: output
emanuele falbo
(Thu Feb 13 2020 - 01:21:40 PST)
Re: [AMBER] QM/MM AMBER/ORCA: output
Goetz, Andreas
(Thu Feb 13 2020 - 02:20:45 PST)
Re: [AMBER] QM/MM AMBER/ORCA: output
emanuele falbo
(Thu Feb 13 2020 - 06:25:39 PST)
Re: [AMBER] QM/MM AMBER/ORCA: output
Goetz, Andreas
(Thu Feb 13 2020 - 23:07:09 PST)
Re: [AMBER] QM/MM AMBER/ORCA: output
emanuele falbo
(Wed Feb 19 2020 - 08:27:15 PST)
Re: [AMBER] QM/MM AMBER/ORCA: output
Goetz, Andreas
(Wed Feb 19 2020 - 09:11:20 PST)
[AMBER] Compatibility issue of Atom type naming in AMBER
Lod King
(Thu Feb 13 2020 - 14:57:38 PST)
Re: [AMBER] Compatibility issue of Atom type naming in AMBER
David A Case
(Fri Feb 14 2020 - 04:36:48 PST)
[AMBER] H++ processing non-standard amino acids: Atom does not have a type
Wei-Tse Hsu
(Thu Feb 13 2020 - 21:16:35 PST)
Re: [AMBER] H++ processing non-standard amino acids: Atom does not have a type
Ramu Anandakrishnan
(Fri Feb 14 2020 - 05:27:16 PST)
[AMBER] combination of MD simulations with NMR
Vlad Cojocaru
(Fri Feb 14 2020 - 01:07:33 PST)
[AMBER] Production run in NVT ensemble
Baptiste Legrand
(Fri Feb 14 2020 - 03:04:18 PST)
Re: [AMBER] Production run in NVT ensemble
Carlos Simmerling
(Fri Feb 14 2020 - 03:34:51 PST)
Re: [AMBER] Production run in NVT ensemble
Baptiste Legrand
(Wed Feb 19 2020 - 00:13:03 PST)
[AMBER] how to locate all parameters for specific AA in parm directory
Vaibhav Dixit
(Thu Feb 13 2020 - 23:41:12 PST)
Re: [AMBER] how to locate all parameters for specific AA in parm directory
Carlos Simmerling
(Fri Feb 14 2020 - 03:31:18 PST)
Re: [AMBER] how to locate all parameters for specific AA in parm directory
Vaibhav Dixit
(Fri Feb 14 2020 - 00:38:11 PST)
Re: [AMBER] how to locate all parameters for specific AA in parm directory
Vaibhav Dixit
(Fri Feb 14 2020 - 08:21:20 PST)
Re: [AMBER] how to locate all parameters for specific AA in parm directory
Carlos Simmerling
(Fri Feb 14 2020 - 08:43:58 PST)
[AMBER] Dihedral restraint problems in AMBER16/18
Rebecca Twidale
(Fri Feb 14 2020 - 04:33:56 PST)
Re: [AMBER] Dihedral restraint problems in AMBER16/18
Kellon Belfon
(Fri Feb 14 2020 - 19:12:52 PST)
[AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin.
Marcelo Andrade Chagas
(Fri Feb 14 2020 - 12:41:32 PST)
Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin.
Lachele Foley
(Fri Feb 14 2020 - 16:24:55 PST)
Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin.
Marcelo Andrade Chagas
(Sun Feb 16 2020 - 09:49:41 PST)
Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin.
Oliver Grant
(Mon Feb 17 2020 - 08:20:04 PST)
Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin.
Marcelo Andrade Chagas
(Mon Feb 17 2020 - 08:56:37 PST)
Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin.
Karl Kirschner
(Mon Feb 17 2020 - 11:33:30 PST)
Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin.
Lachele Foley
(Tue Feb 18 2020 - 08:20:41 PST)
Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin.
Lachele Foley
(Wed Feb 19 2020 - 19:27:03 PST)
[AMBER] tLEaP error of the N-terminal OXT atom
Wei-Tse Hsu
(Sat Feb 15 2020 - 11:55:04 PST)
Re: [AMBER] tLEaP error of the N-terminal OXT atom
Carlos Simmerling
(Sat Feb 15 2020 - 15:34:20 PST)
[AMBER] no bonds formed between AA and non-standard residue
Vaibhav Dixit
(Sun Feb 16 2020 - 03:30:32 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
Clorice Reinhardt
(Sun Feb 16 2020 - 07:24:57 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
Vaibhav Dixit
(Sun Feb 16 2020 - 08:14:51 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
Carlos Simmerling
(Sun Feb 16 2020 - 07:29:21 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
Vaibhav Dixit
(Sun Feb 16 2020 - 08:27:52 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
Busra Demir
(Sun Feb 16 2020 - 10:55:23 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
Vaibhav Dixit
(Sun Feb 16 2020 - 18:25:51 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
Busra Demir
(Mon Feb 17 2020 - 00:12:54 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
Vaibhav Dixit
(Mon Feb 17 2020 - 00:45:45 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
David A Case
(Mon Feb 17 2020 - 04:38:01 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
Vaibhav Dixit
(Mon Feb 17 2020 - 01:41:12 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
Vaibhav Dixit
(Mon Feb 17 2020 - 01:48:10 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
Vaibhav Dixit
(Mon Feb 17 2020 - 16:08:48 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
Vaibhav Dixit
(Tue Feb 18 2020 - 18:19:28 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
David A Case
(Wed Feb 19 2020 - 05:55:28 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
Vaibhav Dixit
(Wed Feb 19 2020 - 16:16:46 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
Vaibhav Dixit
(Thu Feb 20 2020 - 00:52:16 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
Vaibhav Dixit
(Thu Feb 20 2020 - 17:48:32 PST)
Re: [AMBER] no bonds formed between AA and non-standard residue
Vaibhav Dixit
(Thu Feb 20 2020 - 18:15:29 PST)
[AMBER] MMPBSA.py error
Sruthi Sudhakar
(Mon Feb 17 2020 - 02:57:54 PST)
Re: [AMBER] MMPBSA.py error
Pietro Aronica
(Mon Feb 17 2020 - 02:42:44 PST)
[AMBER] install amber
Nicolas Feldman
(Mon Feb 17 2020 - 08:07:51 PST)
Re: [AMBER] install amber
Elvis Martis
(Mon Feb 17 2020 - 08:13:56 PST)
Re: [AMBER] install amber
Nicolas Feldman
(Mon Feb 17 2020 - 08:19:47 PST)
[AMBER] installing
Nicolas Feldman
(Mon Feb 17 2020 - 12:35:38 PST)
Re: [AMBER] installing
Gerardo Zerbetto De Palma
(Mon Feb 17 2020 - 12:38:31 PST)
Re: [AMBER] installing
Nicolas Feldman
(Mon Feb 17 2020 - 12:41:02 PST)
Re: [AMBER] installing
Gerardo Zerbetto De Palma
(Mon Feb 17 2020 - 12:48:29 PST)
Re: [AMBER] installing
Gerardo Zerbetto De Palma
(Mon Feb 17 2020 - 12:49:28 PST)
Re: [AMBER] installing
Nicolas Feldman
(Mon Feb 17 2020 - 12:56:45 PST)
Re: [AMBER] installing
Gerardo Zerbetto De Palma
(Mon Feb 17 2020 - 13:07:11 PST)
Re: [AMBER] installing
Nicolas Feldman
(Mon Feb 17 2020 - 13:10:08 PST)
Re: [AMBER] installing
Nicolas Feldman
(Mon Feb 17 2020 - 13:11:07 PST)
Re: [AMBER] installing
Gerardo Zerbetto De Palma
(Mon Feb 17 2020 - 13:32:30 PST)
Re: [AMBER] installing
Gustaf Olsson
(Mon Feb 17 2020 - 14:47:26 PST)
Re: [AMBER] installing
Nicolas Feldman
(Mon Feb 17 2020 - 14:53:36 PST)
Re: [AMBER] installing
Gustaf Olsson
(Mon Feb 17 2020 - 14:56:12 PST)
Re: [AMBER] installing
Gerardo Zerbetto De Palma
(Mon Feb 17 2020 - 15:20:54 PST)
Re: [AMBER] installing
Nicolas Feldman
(Mon Feb 17 2020 - 15:28:13 PST)
Re: [AMBER] installing
Gerardo Zerbetto De Palma
(Mon Feb 17 2020 - 16:10:45 PST)
Re: [AMBER] installing
Nicolas Feldman
(Mon Feb 17 2020 - 16:14:09 PST)
Re: [AMBER] installing
Gerardo Zerbetto De Palma
(Mon Feb 17 2020 - 16:17:17 PST)
Re: [AMBER] installing
Nicolas Feldman
(Mon Feb 17 2020 - 16:20:38 PST)
Re: [AMBER] installing
Daniel Roe
(Tue Feb 18 2020 - 06:02:37 PST)
Re: [AMBER] installing
Nicolas Feldman
(Tue Feb 18 2020 - 06:33:55 PST)
Re: [AMBER] installing
Gerardo Zerbetto De Palma
(Tue Feb 18 2020 - 03:44:33 PST)
Re: [AMBER] installing
Nicolas Feldman
(Tue Feb 18 2020 - 06:55:15 PST)
Re: [AMBER] installing
Gerardo Zerbetto De Palma
(Tue Feb 18 2020 - 04:04:43 PST)
Re: [AMBER] installing
Nicolas Feldman
(Tue Feb 18 2020 - 07:07:31 PST)
Re: [AMBER] installing
Gerardo Zerbetto De Palma
(Tue Feb 18 2020 - 04:08:44 PST)
[AMBER] suggest an article for MD for covalent inhibitors
ALAMGIR KHAN
(Mon Feb 17 2020 - 21:44:04 PST)
[AMBER] Force field for terminal phosphorylated residues
Ming Tang
(Mon Feb 17 2020 - 23:11:57 PST)
Re: [AMBER] Force field for terminal phosphorylated residues
David A Case
(Tue Feb 18 2020 - 05:35:16 PST)
Re: [AMBER] Force field for terminal phosphorylated residues
Ming Tang
(Tue Feb 18 2020 - 14:50:33 PST)
Re: [AMBER] Force field for terminal phosphorylated residues
Ming Tang
(Tue Feb 18 2020 - 21:37:23 PST)
[AMBER] What Can I do for Mixture of Solutions simulation and what should I assign epsilon value for this?
Erdem Yeler
(Tue Feb 18 2020 - 02:19:47 PST)
Re: [AMBER] What Can I do for Mixture of Solutions simulation and what should I assign epsilon value for this?
David A Case
(Tue Feb 18 2020 - 08:17:33 PST)
[AMBER] mmpbsa.py
Sruthi Sudhakar
(Tue Feb 18 2020 - 05:34:27 PST)
Re: [AMBER] mmpbsa.py
David A Case
(Tue Feb 18 2020 - 05:39:31 PST)
Re: [AMBER] mmpbsa.py
Sruthi Sudhakar
(Tue Feb 18 2020 - 07:07:14 PST)
Re: [AMBER] mmpbsa.py
Ray Luo
(Tue Feb 18 2020 - 07:03:05 PST)
Re: [AMBER] mmpbsa.py
Sruthi Sudhakar
(Tue Feb 18 2020 - 07:05:35 PST)
[AMBER] Shearing useful tips for adding ions to biomolecular simulations
Matias Machado
(Tue Feb 18 2020 - 10:13:54 PST)
[AMBER] kindly guide me
ALAMGIR KHAN
(Wed Feb 19 2020 - 03:33:59 PST)
Re: [AMBER] kindly guide me
Pietro Aronica
(Wed Feb 19 2020 - 03:43:27 PST)
Re: [AMBER] kindly guide me
David A Case
(Wed Feb 19 2020 - 05:56:47 PST)
[AMBER] Running Amber in a GPU cluster
Aravind R
(Wed Feb 19 2020 - 04:23:35 PST)
Re: [AMBER] Running Amber in a GPU cluster
Carlos Simmerling
(Wed Feb 19 2020 - 04:26:49 PST)
[AMBER] facing problem in installation of Amber18 with CUDA support
SATYAJIT KHATUA
(Wed Feb 19 2020 - 06:12:21 PST)
[AMBER] Doubt in running mmpbsa
Sruthi Sudhakar
(Wed Feb 19 2020 - 07:32:11 PST)
Re: [AMBER] Doubt in running mmpbsa
Elvis Martis
(Wed Feb 19 2020 - 07:27:28 PST)
Re: [AMBER] Doubt in running mmpbsa
Sruthi Sudhakar
(Wed Feb 19 2020 - 08:23:03 PST)
Re: [AMBER] Doubt in running mmpbsa
Elvis Martis
(Wed Feb 19 2020 - 08:25:43 PST)
Re: [AMBER] Doubt in running mmpbsa
Sruthi Sudhakar
(Wed Feb 19 2020 - 08:30:35 PST)
[AMBER] amber18 tests failures
Antonio Bauzá Riera
(Wed Feb 19 2020 - 07:46:51 PST)
Re: [AMBER] amber18 tests failures
David Cerutti
(Wed Feb 19 2020 - 08:02:41 PST)
[AMBER] Versions of AMBER
Frederico Henrique
(Wed Feb 19 2020 - 11:17:57 PST)
Re: [AMBER] Versions of AMBER
David A Case
(Wed Feb 19 2020 - 12:14:23 PST)
[AMBER] Unexpected reaction occurred in QM/MM umbrella sampling
Qing Lv
(Wed Feb 19 2020 - 17:56:18 PST)
Re: [AMBER] Unexpected reaction occurred in QM/MM umbrella sampling
Goetz, Andreas
(Wed Feb 19 2020 - 18:41:06 PST)
Re: [AMBER] Unexpected reaction occurred in QM/MM umbrella sampling
Qing Lv
(Thu Feb 20 2020 - 02:59:38 PST)
[AMBER] facing problem in installation of Amber18 with CUDA support
SATYAJIT KHATUA
(Wed Feb 19 2020 - 22:56:48 PST)
Re: [AMBER] facing problem in installation of Amber18 with CUDA support
David Cerutti
(Wed Feb 19 2020 - 22:58:28 PST)
[AMBER] amber18 tests failure
Antonio Bauzá
(Thu Feb 20 2020 - 01:37:39 PST)
[AMBER] facing problem in installation of Amber18 with CUDA
SATYAJIT KHATUA
(Thu Feb 20 2020 - 22:56:34 PST)
[AMBER] Using cutoffs smaller than 8 A
Abdullah Bin Faheem
(Thu Feb 20 2020 - 23:51:23 PST)
[AMBER] Amber 16 or 20
Fabian Glaser
(Sat Feb 22 2020 - 00:32:22 PST)
Re: [AMBER] Amber 16 or 20
David A Case
(Sat Feb 22 2020 - 05:17:57 PST)
Re: [AMBER] Amber 16 or 20
Vaibhav Dixit
(Sat Feb 22 2020 - 19:17:27 PST)
[AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available?
Pietro Amodeo
(Sat Feb 22 2020 - 05:05:32 PST)
Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available?
Abhilash J
(Thu Feb 27 2020 - 08:06:27 PST)
Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available?
Ross Walker
(Thu Feb 27 2020 - 09:13:47 PST)
Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available?
Ross Walker
(Thu Feb 27 2020 - 09:42:18 PST)
Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available?
Abhilash J
(Thu Feb 27 2020 - 09:42:40 PST)
Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available?
Ross Walker
(Thu Feb 27 2020 - 09:45:36 PST)
Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available?
Abhilash J
(Thu Feb 27 2020 - 09:48:41 PST)
Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available?
Pietro Amodeo
(Sat Feb 29 2020 - 12:26:38 PST)
[AMBER] Regarding compatibility of PLUMED with the MPI and CUDA versions of pmemd
SATYAJIT KHATUA
(Sat Feb 22 2020 - 21:58:43 PST)
[AMBER] vmd progress time
Fabian Glaser
(Sun Feb 23 2020 - 07:11:53 PST)
Re: [AMBER] vmd progress time
James Kress
(Sun Feb 23 2020 - 10:19:33 PST)
Re: [AMBER] vmd progress time
Fabian Glaser
(Tue Feb 25 2020 - 23:50:03 PST)
Re: [AMBER] vmd progress time
Gustaf Olsson
(Wed Feb 26 2020 - 00:59:45 PST)
Re: [AMBER] vmd progress time
Fabian Glaser
(Wed Feb 26 2020 - 01:44:05 PST)
Re: [AMBER] vmd progress time
Gustaf Olsson
(Wed Feb 26 2020 - 02:58:04 PST)
Re: [AMBER] vmd progress time
Arun Srikanth
(Wed Feb 26 2020 - 03:04:10 PST)
Re: [AMBER] vmd progress time
Fabian Glaser
(Wed Feb 26 2020 - 05:52:39 PST)
[AMBER] inquiry regarding minimum-image convention in cpptraj
Akshay Prabhakant
(Sun Feb 23 2020 - 11:13:03 PST)
Re: [AMBER] inquiry regarding minimum-image convention in cpptraj
Daniel Roe
(Mon Feb 24 2020 - 06:39:51 PST)
[AMBER] frcmod.urea Parameters for urea (or urea-water mixtures).
Fabian Glaser
(Mon Feb 24 2020 - 07:25:41 PST)
[AMBER] Clustering logistics
Debarati DasGupta
(Mon Feb 24 2020 - 09:27:01 PST)
Re: [AMBER] Clustering logistics
Daniel Roe
(Mon Feb 24 2020 - 09:59:02 PST)
[AMBER] make test MPI don't continue
Nicolas Feldman
(Tue Feb 25 2020 - 05:51:17 PST)
Re: [AMBER] make test MPI don't continue
Gustaf Olsson
(Thu Feb 27 2020 - 04:48:26 PST)
Re: [AMBER] make test MPI don't continue
Gustaf Olsson
(Thu Feb 27 2020 - 05:15:40 PST)
[AMBER] Single ion solvation free energy calculations.
Akhilesh Paspureddi
(Wed Feb 26 2020 - 13:33:30 PST)
Re: [AMBER] Single ion solvation free energy calculations.
Tyler Luchko (Lists)
(Thu Feb 27 2020 - 10:07:01 PST)
[AMBER] Weird error with antechamber for metal ion / MCPB tutorial
Gustavo Seabra
(Wed Feb 26 2020 - 14:01:03 PST)
Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial
David A Case
(Wed Feb 26 2020 - 18:17:50 PST)
Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial
David A Case
(Wed Feb 26 2020 - 18:18:50 PST)
Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial
Marcelo Andrade Chagas
(Thu Feb 27 2020 - 00:49:37 PST)
Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial
Gustavo Seabra
(Thu Feb 27 2020 - 06:10:03 PST)
[AMBER] lack scripts for Continuous constant pH molecular dynamics
Yingang Feng
(Thu Feb 27 2020 - 01:23:04 PST)
[AMBER] MCPB.py with mixed valence di-iron system?
Gustavo Seabra
(Thu Feb 27 2020 - 14:11:06 PST)
Re: [AMBER] MCPB.py with mixed valence di-iron system?
Marcelo Andrade Chagas
(Thu Feb 27 2020 - 17:47:58 PST)
[AMBER] generate ligand frcmod and lib files
Madhur Aggarwal
(Fri Feb 28 2020 - 03:44:33 PST)
Re: [AMBER] generate ligand frcmod and lib files
Elvis Martis
(Fri Feb 28 2020 - 04:07:42 PST)
[AMBER] replica exchange with GPU
bbalta.itu.edu.tr
(Fri Feb 28 2020 - 04:14:59 PST)
Re: [AMBER] replica exchange with GPU
Carlos Simmerling
(Fri Feb 28 2020 - 04:22:05 PST)
[AMBER] Tutorial A08
Nicolas Feldman
(Fri Feb 28 2020 - 08:23:16 PST)
[AMBER] TI calculations in AMBER18
Debarati DasGupta
(Fri Feb 28 2020 - 11:23:45 PST)
[AMBER] G quadruplex simulation
Sruthi Sudhakar
(Fri Feb 28 2020 - 22:13:16 PST)
Re: [AMBER] G quadruplex simulation
Sruthi Sudhakar
(Sat Feb 29 2020 - 02:02:22 PST)
[AMBER] Amber and Domains Conformational Dynamics
mario
(Sat Feb 29 2020 - 11:00:01 PST)
Last message date
:
Sat Feb 29 2020 - 12:30:02 PST
Archived on
: Wed Nov 20 2024 - 05:55:45 PST
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