Amber Archive Nov 2018 by author
308 messages
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Starting
Wed Oct 31 2018 - 21:30:03 PDT,
Ending
Fri Nov 30 2018 - 10:00:01 PST
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201612095.mail.sdu.edu.cn
[AMBER] 回复： non-bonded params
(Fri Nov 02 2018 - 16:06:10 PDT)
Aashish Bhatt
[AMBER] Velocity autocorrelation function(VACF)
(Tue Nov 27 2018 - 04:24:28 PST)
[AMBER] RESP charge calculation
(Mon Nov 26 2018 - 04:43:09 PST)
Abdullah Bin Faheem
[AMBER] IR Spectra
(Sun Nov 04 2018 - 22:07:16 PST)
ABEL Stephane
Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
(Mon Nov 12 2018 - 05:23:17 PST)
accuratefreeenergy.gmail.com
Re: [AMBER] Accelerated MD stopped with Cuda GPU error.
(Wed Nov 07 2018 - 20:31:34 PST)
Adrian Roitberg
Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18
(Thu Nov 29 2018 - 11:31:18 PST)
Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18
(Thu Nov 29 2018 - 10:46:48 PST)
Alain Chaumont
[AMBER] RTX 2080 slower then 1080 Ti with pmemd 18 ?
(Wed Nov 21 2018 - 11:24:29 PST)
Alechania Misturini
Re: [AMBER] Running tleap for topology generation of a list of pdb files.
(Fri Nov 23 2018 - 03:39:57 PST)
Re: [AMBER] Running tleap for topology generation of a list of pdb files.
(Fri Nov 23 2018 - 03:33:56 PST)
Ali Khodayari
Re: [AMBER] Building crystal structures
(Thu Nov 15 2018 - 13:16:12 PST)
[AMBER] Building crystal structures
(Thu Nov 15 2018 - 11:28:52 PST)
Amy Rice
Re: [AMBER] CpH simulation- error reading charges in long cpin file
(Thu Nov 01 2018 - 12:49:47 PDT)
[AMBER] CpH simulation- error reading charges in long cpin file
(Thu Nov 01 2018 - 09:28:54 PDT)
andreas.tosstorff.cup.uni-muenchen.de
Re: [AMBER] Latest force field
(Sun Nov 25 2018 - 09:28:27 PST)
Re: [AMBER] polymer state
(Thu Nov 22 2018 - 10:00:46 PST)
Antonio Amber Carlesso
[AMBER] Post_analysis_Amber_tools_suggestion
(Sun Nov 18 2018 - 06:09:51 PST)
Re: [AMBER] MD_Box_size_and_counterions_counting_general_rule
(Thu Nov 08 2018 - 01:43:16 PST)
Arkajyoti Sengupta
[AMBER] equilibration of Packmol generated boxes
(Wed Nov 28 2018 - 15:30:31 PST)
Beale, John
[AMBER] Amber 18 memory
(Thu Nov 15 2018 - 01:05:19 PST)
Bharat Manna
[AMBER] Problem in designing MD simulation based on Experimental data
(Fri Nov 16 2018 - 07:53:12 PST)
Bill Ross
Re: [AMBER] Head-to-tail cyclized Peptides
(Thu Nov 29 2018 - 21:11:57 PST)
Re: [AMBER] regarding ambpdb
(Sun Nov 18 2018 - 05:12:43 PST)
Re: [AMBER] Amber 18 memory
(Thu Nov 15 2018 - 13:40:15 PST)
Re: [AMBER] regarding tutorials
(Mon Nov 12 2018 - 22:26:12 PST)
Re: [AMBER] Accelerated MD stopped with Cuda GPU error.
(Wed Nov 07 2018 - 20:23:34 PST)
Re: [AMBER] Accelerated MD stopped with Cuda GPU error.
(Wed Nov 07 2018 - 01:53:54 PST)
Re: [AMBER] Help regarding AMBER16 CUDA installation
(Wed Nov 07 2018 - 00:55:35 PST)
Re: [AMBER] Accelerated MD stopped with Cuda GPU error.
(Mon Nov 05 2018 - 00:25:41 PST)
Re: [AMBER] Accelerated MD stopped with Cuda GPU error.
(Mon Nov 05 2018 - 00:08:43 PST)
Braden Kelly
Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18
(Thu Nov 29 2018 - 10:35:40 PST)
Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18
(Wed Nov 28 2018 - 13:15:14 PST)
[AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18
(Tue Nov 27 2018 - 00:10:01 PST)
Brian Radak
Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18
(Thu Nov 29 2018 - 13:56:36 PST)
Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18
(Thu Nov 29 2018 - 07:18:06 PST)
Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18
(Tue Nov 27 2018 - 08:51:35 PST)
Bruno Falcone
Re: [AMBER] Hamiltonian Replica Exchange with Amber 18
(Mon Nov 26 2018 - 13:22:48 PST)
[AMBER] Hamiltonian Replica Exchange with Amber 18
(Fri Nov 23 2018 - 07:28:29 PST)
Carlos Simmerling
Re: [AMBER] Regarding the Targeted MD
(Fri Nov 30 2018 - 04:29:03 PST)
Re: [AMBER] Regarding the Targeted MD
(Thu Nov 29 2018 - 14:38:11 PST)
Re: [AMBER] Regarding the Targeted MD
(Mon Nov 26 2018 - 12:53:42 PST)
Re: [AMBER] Regarding the Targeted MD
(Mon Nov 26 2018 - 12:52:42 PST)
Re: [AMBER] Regarding output file processing of temperature replica exchange
(Mon Nov 26 2018 - 09:10:21 PST)
Re: [AMBER] cpptraj error
(Mon Nov 19 2018 - 09:31:27 PST)
Re: [AMBER] REMD: What can I do with much larger replicas than the number of processors
(Wed Nov 07 2018 - 11:37:29 PST)
Re: [AMBER] Implicit solvent simulation effects for the folding
(Tue Nov 06 2018 - 03:32:54 PST)
Casalini Tommaso
Re: [AMBER] About dpeaks implementation in cpptraj
(Mon Nov 19 2018 - 07:47:10 PST)
[AMBER] About dpeaks implementation in cpptraj
(Mon Nov 19 2018 - 05:49:19 PST)
Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
(Mon Nov 12 2018 - 23:39:40 PST)
Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
(Mon Nov 12 2018 - 05:36:45 PST)
Charo del Genio
[AMBER] Geometric hard constraints
(Wed Nov 07 2018 - 02:44:16 PST)
Charu Sharma (JRF)
[AMBER] RMSD
(Sun Nov 25 2018 - 22:01:47 PST)
Re: [AMBER] RMSF
(Sun Nov 25 2018 - 20:34:12 PST)
[AMBER] RMSF
(Sat Nov 24 2018 - 03:25:44 PST)
[AMBER] REGARDING TUTORIAL
(Tue Nov 20 2018 - 15:39:07 PST)
Re: [AMBER] cpptraj error
(Mon Nov 19 2018 - 09:22:15 PST)
Re: [AMBER] regarding ambpdb
(Sun Nov 18 2018 - 03:45:51 PST)
[AMBER] regarding ambpdb
(Sun Nov 18 2018 - 01:22:59 PST)
[AMBER] graph
(Fri Nov 16 2018 - 22:01:24 PST)
[AMBER] xmgrace
(Fri Nov 16 2018 - 21:23:11 PST)
[AMBER] md production
(Fri Nov 16 2018 - 21:07:57 PST)
Re: [AMBER] regarding creation of production MD output
(Fri Nov 16 2018 - 08:48:52 PST)
[AMBER] regarding creation of production MD output
(Fri Nov 16 2018 - 08:33:23 PST)
[AMBER] regarding MD simulation
(Wed Nov 14 2018 - 02:57:36 PST)
[AMBER] query
(Mon Nov 12 2018 - 22:27:35 PST)
[AMBER] regarding tutorials
(Mon Nov 12 2018 - 21:41:28 PST)
[AMBER] regarding ter
(Sat Nov 03 2018 - 22:39:15 PDT)
Chetna Tyagi
Re: [AMBER] regarding creation of production MD output
(Fri Nov 16 2018 - 08:27:29 PST)
Re: [AMBER] very high values of "wrapping mol" when potential boost applied to chloroform solvent system
(Fri Nov 16 2018 - 02:58:58 PST)
Re: [AMBER] very high values of "wrapping mol" when potential boost applied to chloroform solvent system
(Fri Nov 16 2018 - 02:40:39 PST)
[AMBER] very high values of "wrapping mol" when potential boost applied to chloroform solvent system
(Thu Nov 15 2018 - 05:24:53 PST)
Chhaya Singh
Re: [AMBER] reminder
(Thu Nov 29 2018 - 09:13:50 PST)
Chris Moth
Re: [AMBER] Problem in designing MD simulation based on Experimental data
(Fri Nov 16 2018 - 06:16:40 PST)
Cruzeiro,Vinicius Wilian D
Re: [AMBER] REMD: What can I do with much larger replicas than the number of processors
(Wed Nov 07 2018 - 07:50:20 PST)
Re: [AMBER] CpH simulation- error reading charges in long cpin file
(Thu Nov 01 2018 - 12:57:38 PDT)
Re: [AMBER] CpH simulation- error reading charges in long cpin file
(Thu Nov 01 2018 - 12:33:52 PDT)
Daniel Roe
Re: [AMBER] Correction needed for output of energy action command in cpptraj
(Wed Nov 28 2018 - 07:49:25 PST)
Re: [AMBER] new amber mailing list for beginner questions/mailing list for advanced users&bug reports
(Tue Nov 27 2018 - 06:34:31 PST)
Re: [AMBER] Velocity autocorrelation function(VACF)
(Tue Nov 27 2018 - 05:58:36 PST)
Re: [AMBER] CPPTRAJ/PnetCDF error
(Mon Nov 26 2018 - 06:39:23 PST)
Re: [AMBER] Correction needed for output of energy action command in cpptraj
(Mon Nov 19 2018 - 10:14:58 PST)
Re: [AMBER] cpptraj error
(Mon Nov 19 2018 - 10:04:59 PST)
Re: [AMBER] Regarding output file processing of temperature replica exchange
(Mon Nov 19 2018 - 06:34:30 PST)
Re: [AMBER] xmgrace
(Mon Nov 19 2018 - 06:27:10 PST)
Re: [AMBER] About dpeaks implementation in cpptraj
(Mon Nov 19 2018 - 06:23:26 PST)
Re: [AMBER] cpptraj error
(Mon Nov 19 2018 - 06:00:25 PST)
Re: [AMBER] reconstruction of pH-based trajectory files
(Fri Nov 16 2018 - 07:11:03 PST)
Re: [AMBER] Regarding output file processing of temperature replica exchange
(Fri Nov 16 2018 - 06:59:13 PST)
Re: [AMBER] reconstruction of pH-based trajectory files
(Thu Nov 15 2018 - 05:15:21 PST)
Re: [AMBER] RMSD mask selection and closestwater clarification
(Thu Nov 15 2018 - 05:12:01 PST)
Re: [AMBER] Radial Distribution Function of Waters with respect to a particular Atom
(Wed Nov 14 2018 - 15:57:35 PST)
Re: [AMBER] different residue numbering
(Wed Nov 14 2018 - 15:33:38 PST)
Re: [AMBER] Regarding output file processing of temperature replica exchange
(Wed Nov 14 2018 - 06:10:06 PST)
Re: [AMBER-Developers] [AMBER] CPPTRAJ "usefrcascoords"
(Fri Nov 09 2018 - 12:22:56 PST)
Re: [AMBER] CPPTRAJ "usefrcascoords"
(Fri Nov 09 2018 - 12:17:20 PST)
Re: [AMBER] CPPTRAJ "usefrcascoords"
(Thu Nov 08 2018 - 12:56:10 PST)
Re: [AMBER] CPPTRAJ "usefrcascoords"
(Thu Nov 08 2018 - 12:46:45 PST)
Re: [AMBER] 02_03.rms problem
(Thu Nov 08 2018 - 05:08:49 PST)
Re: [AMBER] Interplane angles using vector and vectormath in cpptraj
(Wed Nov 07 2018 - 05:54:30 PST)
Re: [AMBER] different residue numbering
(Tue Nov 06 2018 - 12:59:28 PST)
Re: [AMBER] Problem regarding radial command
(Mon Nov 05 2018 - 07:12:29 PST)
Re: [AMBER] 02_03.rms problem
(Mon Nov 05 2018 - 06:39:48 PST)
Re: [AMBER] 02_03.rms problem
(Sat Nov 03 2018 - 06:41:53 PDT)
David A Case
Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18
(Fri Nov 30 2018 - 05:15:20 PST)
Re: [AMBER] Head-to-tail cyclized Peptides
(Fri Nov 30 2018 - 05:06:06 PST)
Re: [AMBER] Failed to merge the protein-ligand amoeba parameters
(Wed Nov 28 2018 - 04:43:48 PST)
Re: [AMBER] Why does makeCHIR_RST create restraints for side chains?
(Tue Nov 27 2018 - 10:08:38 PST)
Re: [AMBER] REGARDING TUTORIAL
(Wed Nov 21 2018 - 06:46:10 PST)
Re: [AMBER] Antechamber for PCBM
(Mon Nov 19 2018 - 05:28:36 PST)
Re: [AMBER] antechamber
(Mon Nov 19 2018 - 05:27:18 PST)
Re: [AMBER] Errors regarding generation of parameter file
(Mon Nov 19 2018 - 05:20:23 PST)
Re: [AMBER] Energies
(Mon Nov 12 2018 - 10:03:25 PST)
Re: [AMBER] Preparation of force field of zwitterion glycine molecule
(Mon Nov 12 2018 - 05:36:44 PST)
Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
(Mon Nov 12 2018 - 05:26:58 PST)
Re: [AMBER] tLeap sequence overlap with new residues
(Mon Nov 12 2018 - 05:18:50 PST)
Re: [AMBER] post-simulation thermodynamic integration calculations
(Fri Nov 09 2018 - 05:26:04 PST)
Re: [AMBER] phosphorylated peptide with implicit solvent
(Fri Nov 09 2018 - 05:17:44 PST)
Re: [AMBER] problem of GPU with ibelly
(Wed Nov 07 2018 - 11:50:30 PST)
Re: [AMBER] amber 18 compilation issue
(Wed Nov 07 2018 - 05:05:23 PST)
Re: [AMBER] Generation of velocities depends on conformation?
(Wed Nov 07 2018 - 04:52:24 PST)
Re: [AMBER] Help regarding AMBER16 CUDA installation
(Wed Nov 07 2018 - 04:43:28 PST)
Re: [AMBER] Non-convergence when calculating partial charges for aromatic-adjacent nitriles
(Mon Nov 05 2018 - 11:11:22 PST)
David Case
Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18
(Tue Nov 27 2018 - 18:51:46 PST)
Re: [AMBER] Ante-MMPBSA.py error
(Sun Nov 25 2018 - 12:06:45 PST)
Re: [AMBER] RMSF
(Sat Nov 24 2018 - 06:41:26 PST)
Re: [AMBER] Getting error for MMPB/GBSA calculaton
(Fri Nov 23 2018 - 06:47:34 PST)
Re: [AMBER] Antechamber for PCBM
(Mon Nov 19 2018 - 14:27:18 PST)
Re: [AMBER] Antechamber for PCBM
(Mon Nov 19 2018 - 14:22:58 PST)
Re: [AMBER-Developers] [AMBER] regarding ambpdb
(Sun Nov 18 2018 - 05:23:12 PST)
Re: [AMBER] very high values of "wrapping mol" when potential boost applied to chloroform solvent system
(Thu Nov 15 2018 - 13:30:24 PST)
Re: [AMBER] Antechamber with protonated arginine
(Thu Nov 15 2018 - 05:41:30 PST)
Re: [AMBER] How long should a NPT equilibrium take in QM/MM MD?
(Mon Nov 12 2018 - 17:22:17 PST)
Re: [AMBER] Files work with sander and not pmemd
(Mon Nov 12 2018 - 14:20:22 PST)
Re: [AMBER] How long should a NPT equilibrium take in QM/MM MD?
(Mon Nov 12 2018 - 14:16:48 PST)
Re: [AMBER] Error while using antechamber (AMBER 18)
(Thu Nov 08 2018 - 05:52:54 PST)
Re: [AMBER] Accelerated MD stopped with Cuda GPU error.
(Thu Nov 08 2018 - 05:49:37 PST)
Re: [AMBER] problem of GPU with ibelly
(Thu Nov 08 2018 - 05:41:39 PST)
Re: [AMBER] Help regarding AMBER16 CUDA installation
(Tue Nov 06 2018 - 16:54:16 PST)
Re: [AMBER] IR Spectra
(Mon Nov 05 2018 - 17:40:00 PST)
David Cerutti
Re: [AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar
(Thu Nov 29 2018 - 08:59:30 PST)
Re: [AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar
(Wed Nov 28 2018 - 10:53:58 PST)
Re: [AMBER] Building crystal structures
(Thu Nov 15 2018 - 13:25:26 PST)
Re: [AMBER] Building crystal structures
(Thu Nov 15 2018 - 11:41:54 PST)
Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
(Mon Nov 12 2018 - 23:49:45 PST)
Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
(Mon Nov 12 2018 - 23:24:20 PST)
Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
(Sun Nov 11 2018 - 23:03:04 PST)
David Minh
[AMBER] Postdoctoral position in the area of FFT-based binding free energy calculations
(Fri Nov 02 2018 - 10:59:01 PDT)
David Poole
[AMBER] tLeap sequence overlap with new residues
(Sat Nov 10 2018 - 06:45:13 PST)
diego.soler.uam.es
[AMBER] Radial Distribution Function of Waters with respect to a particular Atom
(Wed Nov 14 2018 - 02:11:06 PST)
Dow Hurst
Re: [AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory
(Wed Oct 31 2018 - 22:42:14 PDT)
Re: [AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory
(Wed Oct 31 2018 - 21:23:59 PDT)
Dr. Anselm Horn
Re: [AMBER] Head-to-tail cyclized Peptides
(Fri Nov 30 2018 - 07:16:27 PST)
Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
(Tue Nov 13 2018 - 04:50:58 PST)
E. Kuechler
Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18
(Thu Nov 29 2018 - 17:13:32 PST)
Elvira Tarasova
Re: [AMBER] reconstruction of pH-based trajectory files
(Sat Nov 17 2018 - 05:09:41 PST)
Re: [AMBER] reconstruction of pH-based trajectory files
(Thu Nov 15 2018 - 20:21:36 PST)
[AMBER] reconstruction of pH-based trajectory files
(Wed Nov 14 2018 - 20:25:15 PST)
Elvis Martis
Re: [AMBER] regarding ambpdb
(Sun Nov 18 2018 - 03:13:42 PST)
euq1702
Re: [AMBER] Preparation of force field of zwitterion glycine molecule
(Mon Nov 12 2018 - 06:20:44 PST)
[AMBER] Preparation of force field of zwitterion glycine molecule
(Sun Nov 11 2018 - 08:14:49 PST)
Fabian Glaser
Re: [AMBER] GPU card for AMBER
(Sun Nov 18 2018 - 08:20:36 PST)
[AMBER] GPU card for AMBER
(Thu Nov 15 2018 - 03:16:43 PST)
giulia palermo
[AMBER] Post-doctoral position in MD at UC Riverside
(Fri Nov 09 2018 - 23:57:30 PST)
Goetz, Andreas
Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18
(Thu Nov 29 2018 - 11:23:14 PST)
Hadi Rahmaninejad
Re: [AMBER] problem of GPU with ibelly
(Wed Nov 07 2018 - 15:59:19 PST)
[AMBER] problem of GPU with ibelly
(Wed Nov 07 2018 - 08:05:44 PST)
Hai Nguyen
Re: [AMBER] Help regarding AMBER16 CUDA installation
(Tue Nov 06 2018 - 20:46:13 PST)
Re: [AMBER] Implicit solvent simulation effects for the folding
(Mon Nov 05 2018 - 20:16:50 PST)
hosein geraili
[AMBER] thermostat on solvent
(Tue Nov 27 2018 - 23:47:19 PST)
Re: [AMBER] polymer state
(Thu Nov 22 2018 - 12:26:26 PST)
[AMBER] polymer state
(Thu Nov 22 2018 - 07:35:38 PST)
Re: [AMBER] non-bonded params
(Wed Nov 07 2018 - 00:31:31 PST)
[AMBER] ligand force field
(Fri Nov 02 2018 - 11:22:13 PDT)
Re: [AMBER] non-bonded params
(Fri Nov 02 2018 - 09:50:47 PDT)
Ibrahim M. Moustafa
[AMBER] Installation & testing of AMBER18 parallel GPU problem
(Fri Nov 30 2018 - 09:38:11 PST)
jacky zhao
[AMBER] Ante-MMPBSA.py error
(Sat Nov 24 2018 - 19:05:54 PST)
Jaime Rubio Martinez
Re: [AMBER] Antechamber with protonated arginine
(Tue Nov 20 2018 - 08:47:34 PST)
James Kress
Re: [AMBER] Non-convergence when calculating partial charges for aromatic-adjacent nitriles
(Fri Nov 02 2018 - 12:02:27 PDT)
Jason Swails
Re: [AMBER] new amber mailing list for beginner questions/mailing list for advanced users&bug reports
(Mon Nov 26 2018 - 08:44:44 PST)
Re: [AMBER] Hamiltonian Replica Exchange with Amber 18
(Mon Nov 26 2018 - 08:20:36 PST)
Jeffrey Wagner
Re: [AMBER] Non-convergence when calculating partial charges for aromatic-adjacent nitriles
(Tue Nov 06 2018 - 08:06:02 PST)
[AMBER] Non-convergence when calculating partial charges for aromatic-adjacent nitriles
(Fri Nov 02 2018 - 10:50:49 PDT)
Joan Torras
Re: [AMBER] how long should a NPT equilibrium take in QM/MM MD?
(Mon Nov 12 2018 - 18:05:11 PST)
Jose Manuel Granadino Roldán
[AMBER] Antechamber with protonated arginine
(Wed Nov 14 2018 - 23:05:12 PST)
José Daniel Martinez
Re: [AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar
(Thu Nov 29 2018 - 00:52:44 PST)
Re: [AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar
(Thu Nov 29 2018 - 00:52:14 PST)
[AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar
(Wed Nov 28 2018 - 08:50:38 PST)
Julio Dominguez
Re: [AMBER] CUDA problems in Amber18
(Wed Nov 21 2018 - 14:09:06 PST)
[AMBER] CUDA problems in Amber18
(Sun Nov 18 2018 - 19:33:30 PST)
Junmei Wang
Re: [AMBER] Antechamber with protonated arginine
(Tue Nov 20 2018 - 12:50:52 PST)
Keiran Corbett
Re: [AMBER] query
(Tue Nov 13 2018 - 00:40:59 PST)
Korey M Reid
Re: [AMBER] RMSD mask selection and closestwater clarification
(Thu Nov 15 2018 - 14:18:28 PST)
Re: [AMBER] RMSD mask selection and closestwater clarification
(Tue Nov 13 2018 - 14:40:05 PST)
[AMBER] RMSD mask selection and closestwater clarification
(Tue Nov 13 2018 - 14:17:06 PST)
Lachele Foley
Re: [AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar
(Wed Nov 28 2018 - 11:19:14 PST)
Re: [AMBER] new amber mailing list for beginner questions/mailing list for advanced users&bug reports
(Tue Nov 27 2018 - 12:49:29 PST)
Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
(Tue Nov 13 2018 - 05:57:59 PST)
Leena Aggarwal
Re: [AMBER] Running tleap for topology generation of a list of pdb files.
(Fri Nov 23 2018 - 21:42:01 PST)
[AMBER] Running tleap for topology generation of a list of pdb files.
(Fri Nov 23 2018 - 02:44:39 PST)
Luca Codutti
Re: [AMBER] new amber mailing list for beginner questions
(Thu Nov 15 2018 - 04:05:02 PST)
M RCC
Re: [AMBER] Accelerated MD stopped with Cuda GPU error.
(Wed Nov 07 2018 - 19:21:54 PST)
Re: [AMBER] Accelerated MD stopped with Cuda GPU error.
(Wed Nov 07 2018 - 01:32:57 PST)
[AMBER] Accelerated MD stopped with Cuda GPU error.
(Sun Nov 04 2018 - 23:10:11 PST)
M. Reza Ganjalikhany
Re: [AMBER] Regarding the Targeted MD
(Fri Nov 30 2018 - 05:25:08 PST)
Re: [AMBER] Regarding the Targeted MD
(Fri Nov 30 2018 - 01:22:00 PST)
Re: [AMBER] Regarding the Targeted MD
(Thu Nov 29 2018 - 05:31:29 PST)
Re: [AMBER] Regarding the Targeted MD
(Mon Nov 26 2018 - 12:25:11 PST)
[AMBER] Regarding the Targeted MD
(Mon Nov 26 2018 - 12:21:59 PST)
Markowska
Re: [AMBER] Problem with obtaining iodine parameters via R.E.D. Server
(Sun Nov 18 2018 - 23:32:33 PST)
Re: [AMBER] graph
(Fri Nov 16 2018 - 22:43:50 PST)
[AMBER] Problem with obtaining iodine parameters via R.E.D. Server
(Thu Nov 08 2018 - 04:29:21 PST)
maryam azimzadehirani
Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
(Tue Nov 13 2018 - 23:10:11 PST)
Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
(Tue Nov 13 2018 - 06:06:15 PST)
Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
(Mon Nov 12 2018 - 23:41:42 PST)
Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
(Mon Nov 12 2018 - 06:10:17 PST)
Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
(Mon Nov 12 2018 - 04:05:02 PST)
[AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning?
(Sun Nov 11 2018 - 04:40:39 PST)
Matias Machado
Re: [AMBER] ligand force field
(Fri Nov 09 2018 - 07:41:26 PST)
Re: [AMBER] non-bonded params
(Fri Nov 09 2018 - 07:32:01 PST)
Re: [AMBER] non-bonded params
(Fri Nov 02 2018 - 12:11:26 PDT)
Maura Malinska
Re: [AMBER] Antechamber for PCBM
(Fri Nov 23 2018 - 09:01:20 PST)
Meng Wu
[AMBER] The interaction energy between substrate molecule and protein
(Thu Nov 22 2018 - 02:44:55 PST)
[AMBER] How long should a NPT equilibrium take in QM/MM MD?
(Mon Nov 12 2018 - 02:28:14 PST)
Mijiddorj B
Re: [AMBER] Implicit solvent simulation effects for the folding
(Mon Nov 05 2018 - 20:50:14 PST)
[AMBER] Implicit solvent simulation effects for the folding
(Mon Nov 05 2018 - 19:17:47 PST)
Mohamad Reza G.
[AMBER] Parametrs for Targeted MD
(Sat Nov 24 2018 - 03:52:26 PST)
neelam wafa
[AMBER] Generating topologies with antechamber and acpype
(Wed Nov 07 2018 - 01:37:16 PST)
[AMBER] Acpype error. No such file or directory
(Mon Nov 05 2018 - 07:18:51 PST)
Nicolas Cheron
Re: [AMBER] Files work with sander and not pmemd
(Tue Nov 13 2018 - 02:03:57 PST)
Re: [AMBER] Generation of velocities depends on conformation?
(Thu Nov 08 2018 - 00:54:59 PST)
[AMBER] Files work with sander and not pmemd
(Wed Nov 07 2018 - 03:12:38 PST)
[AMBER] Generation of velocities depends on conformation?
(Wed Nov 07 2018 - 02:44:11 PST)
Nikolay N. Kuzmich
[AMBER] CPPTRAJ/PnetCDF error
(Wed Nov 21 2018 - 01:34:37 PST)
Re: [AMBER] CUDA 10.0 vs CUDA 9.2 for Amber18&1080Ti GTX - any gain in performance?
(Fri Nov 02 2018 - 02:12:44 PDT)
Paul Westphälinger
Re: [AMBER] new amber mailing list for beginner questions/mailing list for advanced users&bug reports
(Tue Nov 27 2018 - 03:18:07 PST)
[AMBER] new amber mailing list for beginner questions/mailing list for advanced users&bug reports
(Mon Nov 26 2018 - 01:15:01 PST)
[AMBER] new amber mailing list for beginner questions
(Thu Nov 15 2018 - 03:19:28 PST)
Pengfei Li
Re: [AMBER] MCPB.py
(Sat Nov 10 2018 - 15:18:59 PST)
Pietro Aronica
Re: [AMBER] Head-to-tail cyclized Peptides
(Thu Nov 29 2018 - 21:37:21 PST)
[AMBER] Head-to-tail cyclized Peptides
(Thu Nov 29 2018 - 20:46:30 PST)
[AMBER] Linear Interaction Energy
(Thu Nov 29 2018 - 01:43:51 PST)
Premila Samuel Mohan Dass
Re: [AMBER] xmgrace
(Fri Nov 16 2018 - 21:35:20 PST)
Qinghua Liao
Re: [AMBER] REMD: What can I do with much larger replicas than the number of processors
(Wed Nov 07 2018 - 11:43:00 PST)
Rajarshi Roy
Re: [AMBER] Regarding output file processing of temperature replica exchange
(Mon Nov 26 2018 - 08:37:42 PST)
Re: [AMBER] Regarding output file processing of temperature replica exchange
(Sat Nov 24 2018 - 09:45:51 PST)
Re: [AMBER] Regarding output file processing of temperature replica exchange
(Fri Nov 16 2018 - 09:46:50 PST)
Re: [AMBER] Regarding output file processing of temperature replica exchange
(Fri Nov 16 2018 - 00:13:36 PST)
[AMBER] Regarding output file processing of temperature replica exchange
(Wed Nov 14 2018 - 04:01:50 PST)
Rajbinder Kaur Virk
[AMBER] Choosing a temperature schedule for Simulated annealing
(Wed Nov 28 2018 - 23:19:39 PST)
[AMBER] cpptraj error
(Mon Nov 19 2018 - 04:59:02 PST)
[AMBER] cpptraj eroor
(Sun Nov 18 2018 - 05:33:03 PST)
Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error
(Sat Nov 03 2018 - 01:01:01 PDT)
RITUPARNA ROY
[AMBER] Error while using antechamber (AMBER 18)
(Wed Nov 07 2018 - 23:08:13 PST)
Rosellen, Martin
[AMBER] different residue numbering
(Tue Nov 06 2018 - 07:27:37 PST)
Ross Walker
Re: [AMBER] RTX 2080 slower then 1080 Ti with pmemd 18 ?
(Wed Nov 21 2018 - 12:43:35 PST)
Re: [AMBER] RTX 2080 slower then 1080 Ti with pmemd 18 ?
(Wed Nov 21 2018 - 12:37:27 PST)
Re: [AMBER] CUDA problems in Amber18
(Mon Nov 19 2018 - 18:14:40 PST)
Re: [AMBER] GPU card for AMBER
(Sat Nov 17 2018 - 02:15:02 PST)
Saikat Dutta chowdhury
Re: [AMBER] Help regarding AMBER16 CUDA installation
(Wed Nov 07 2018 - 00:29:44 PST)
Re: [AMBER] Help regarding AMBER16 CUDA installation
(Tue Nov 06 2018 - 20:04:48 PST)
[AMBER] Help regarding AMBER16 CUDA installation
(Tue Nov 06 2018 - 05:13:29 PST)
Saikat Pal
[AMBER] Getting error for MMPB/GBSA calculaton
(Thu Nov 22 2018 - 07:44:49 PST)
Sally Pias
Re: [AMBER] Minimisation and periodic boundaries.
(Wed Nov 28 2018 - 10:53:55 PST)
SARAH JEANNE LEFAVE
Re: [AMBER] CPPTRAJ "usefrcascoords"
(Mon Nov 26 2018 - 09:31:26 PST)
Re: [AMBER] Energies
(Mon Nov 12 2018 - 08:14:56 PST)
Re: [AMBER] CPPTRAJ "usefrcascoords"
(Fri Nov 09 2018 - 12:35:37 PST)
Re: [AMBER] CPPTRAJ "usefrcascoords"
(Thu Nov 08 2018 - 13:31:37 PST)
Re: [AMBER] CPPTRAJ "usefrcascoords"
(Thu Nov 08 2018 - 12:50:44 PST)
[AMBER] CPPTRAJ "usefrcascoords"
(Thu Nov 08 2018 - 12:33:36 PST)
Scott Brozell
[AMBER] Announcement: Release of DOCK 6.9
(Tue Nov 27 2018 - 17:29:21 PST)
shivangi agarwal
[AMBER] Latest force field
(Sat Nov 24 2018 - 09:15:50 PST)
Re: [AMBER] Errors regarding generation of parameter file
(Mon Nov 19 2018 - 06:54:54 PST)
[AMBER] Errors regarding generation of parameter file
(Sun Nov 18 2018 - 19:15:50 PST)
simon chapman
Re: [AMBER] 02_03.rms problem
(Wed Nov 07 2018 - 13:16:08 PST)
Re: [AMBER] 02_03.rms problem
(Mon Nov 05 2018 - 14:09:42 PST)
Re: [AMBER] 02_03.rms problem
(Sat Nov 03 2018 - 07:49:19 PDT)
[AMBER] 02_03.rms problem
(Sat Nov 03 2018 - 02:08:29 PDT)
soukaina louerdi
Re: [AMBER] Antechamber for PCBM
(Fri Nov 23 2018 - 14:12:04 PST)
Re: [AMBER] Antechamber for PCBM
(Fri Nov 23 2018 - 07:37:24 PST)
Re: [AMBER] Antechamber for PCBM
(Mon Nov 19 2018 - 11:17:19 PST)
[AMBER] antechamber
(Mon Nov 19 2018 - 03:29:51 PST)
[AMBER] Antechamber for PCBM
(Thu Nov 15 2018 - 05:07:50 PST)
Re: [AMBER] the unperturbed charge of the unit is not zero
(Thu Nov 01 2018 - 12:15:15 PDT)
Stefan Ivanov
Re: [AMBER] Why does makeCHIR_RST create restraints for side chains?
(Tue Nov 27 2018 - 10:35:46 PST)
[AMBER] Why does makeCHIR_RST create restraints for side chains?
(Tue Nov 27 2018 - 01:11:39 PST)
[AMBER] Obtaining contact maps with cpptraj
(Thu Nov 22 2018 - 20:47:59 PST)
Stejskal, Lenka
Re: [AMBER] Minimisation and periodic boundaries.
(Wed Nov 28 2018 - 12:17:14 PST)
[AMBER] Minimisation and periodic boundaries.
(Wed Nov 28 2018 - 09:56:30 PST)
Stephan Schott
Re: [AMBER] amber 18 compilation issue
(Wed Nov 07 2018 - 08:57:07 PST)
Re: [AMBER] amber 18 compilation issue
(Wed Nov 07 2018 - 07:21:54 PST)
Sukanya Sasmal
[AMBER] free energy calculation for restraining ligand
(Thu Nov 29 2018 - 18:27:53 PST)
Thomas Cheatham
Re: [AMBER] Regarding output file processing of temperature replica exchange
(Sat Nov 24 2018 - 18:53:20 PST)
Re: [AMBER] Generation of velocities depends on conformation?
(Wed Nov 07 2018 - 04:15:05 PST)
Vaibhav Dixit
Re: [AMBER] regarding ter
(Sat Nov 03 2018 - 22:49:47 PDT)
Veenis, Andrew Jay
[AMBER] Correction needed for output of energy action command in cpptraj
(Mon Nov 19 2018 - 10:02:18 PST)
Re: [AMBER] post-simulation thermodynamic integration calculations
(Fri Nov 09 2018 - 09:57:29 PST)
[AMBER] post-simulation thermodynamic integration calculations
(Thu Nov 08 2018 - 12:17:03 PST)
Viviani, Lucas
[AMBER] MCPB.py
(Wed Nov 07 2018 - 02:49:48 PST)
Vlad Cojocaru
Re: [AMBER] amber 18 compilation issue
(Wed Nov 07 2018 - 07:54:51 PST)
[AMBER] amber 18 compilation issue
(Tue Nov 06 2018 - 06:29:54 PST)
Wesley Michael Botello-Smith
Re: [AMBER] REMD: What can I do with much larger replicas than the number of processors
(Wed Nov 07 2018 - 14:40:14 PST)
Zhonghua Xia
Re: [AMBER] REMD: What can I do with much larger replicas than the number of processors
(Fri Nov 09 2018 - 05:27:07 PST)
[AMBER] REMD: What can I do with much larger replicas than the number of processors
(Wed Nov 07 2018 - 07:22:51 PST)
王茜茜
Re: [AMBER] Failed to merge the protein-ligand amoeba parameters
(Wed Nov 28 2018 - 05:38:18 PST)
[AMBER] Failed to merge the protein-ligand amoeba parameters
(Tue Nov 27 2018 - 00:46:01 PST)
郭昱
[AMBER] how long should a NPT equilibrium take in QM/MM MD?
(Mon Nov 12 2018 - 17:17:56 PST)
鲍劲霄
[AMBER] Protein residues CA atoms treated as sidechain in binding energy decomposition?
(Fri Nov 02 2018 - 07:58:31 PDT)
Last message date
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Fri Nov 30 2018 - 10:00:01 PST
Archived on
: Wed Dec 25 2024 - 05:55:45 PST
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