Amber Archive Jul 2020 by author
361 messages
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Starting
Tue Jun 30 2020 - 22:00:03 PDT,
Ending
Fri Jul 31 2020 - 14:30:04 PDT
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Aashish Bhatt
Re: [AMBER] How to set salt concentration
(Wed Jul 01 2020 - 21:15:29 PDT)
Adrian Roitberg
Re: [AMBER] ASMD equil4 not producing output files
(Tue Jul 28 2020 - 09:56:35 PDT)
Adriano José Ferruzzi
Re: [AMBER] Amber 20 - Support Multi GPU
(Thu Jul 23 2020 - 07:11:26 PDT)
[AMBER] Amber 20 - Support Multi GPU
(Wed Jul 22 2020 - 12:31:29 PDT)
Akshay Prabhakant
[AMBER] REPEATED LINMIN FAILURE
(Fri Jul 10 2020 - 04:20:12 PDT)
Alejandro Cagnoni
[AMBER] Issue while installing Amber20
(Fri Jul 24 2020 - 13:44:29 PDT)
Amanda Buyan
Re: [AMBER] Amber20 Compiling problem with b2 and Boost.Regex
(Wed Jul 29 2020 - 16:40:29 PDT)
Re: [AMBER] Amber20 Compiling problem with b2 and Boost.Regex
(Mon Jul 27 2020 - 15:50:37 PDT)
[AMBER] Amber20 Compiling problem with b2 and Boost.Regex
(Sun Jul 26 2020 - 18:35:07 PDT)
[AMBER] Problem compiling Amber20 - undefined reference to 'plumedmain_create'
(Wed Jul 22 2020 - 23:07:39 PDT)
[AMBER] Using multiple distance restraints or creating exclusion sphere
(Sun Jul 12 2020 - 18:20:16 PDT)
An Ta
Re: [AMBER] Accounting for PBC in Density Plots
(Mon Jul 06 2020 - 10:46:41 PDT)
[AMBER] Accounting for PBC in Density Plots
(Mon Jul 06 2020 - 10:44:06 PDT)
Andrea Cavalli
Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol
(Sat Jul 25 2020 - 07:26:42 PDT)
ANDREA PASQUADIBISCEGLIE
Re: [AMBER] Barostat and thermostat for membrane protein-ligand simulation
(Sat Jul 11 2020 - 00:11:29 PDT)
Re: [AMBER] Barostat and thermostat for membrane protein-ligand simulation
(Thu Jul 09 2020 - 02:32:05 PDT)
[AMBER] Barostat and thermostat for membrane protein-ligand simulation
(Mon Jul 06 2020 - 08:49:36 PDT)
angad sharma
[AMBER] fatal error in 3D RISM calculation
(Tue Jul 21 2020 - 01:57:07 PDT)
[AMBER] error in 3d rism calculation
(Mon Jul 20 2020 - 10:27:05 PDT)
[AMBER] matching paramters of methane
(Thu Jul 16 2020 - 08:27:44 PDT)
[AMBER] generating parameters of methane for RISM
(Sun Jul 05 2020 - 04:25:07 PDT)
[AMBER] generating methane parameters for rism
(Sat Jul 04 2020 - 05:22:17 PDT)
[AMBER] calculating methane parameters using RISM
(Thu Jul 02 2020 - 01:31:03 PDT)
ankita mehta
Re: [AMBER] Amber installation error
(Wed Jul 01 2020 - 11:10:40 PDT)
Arthur Glasfeld
[AMBER] gamess/MCPB.py tutorial
(Sat Jul 04 2020 - 11:03:32 PDT)
Athena N
[AMBER] amber trajectory nc file to pdb ensemble
(Fri Jul 31 2020 - 09:28:26 PDT)
Bill Ross
Re: [AMBER] Adding ions to implicit solvent models
(Thu Jul 30 2020 - 02:00:18 PDT)
Camila Clemente
Re: [AMBER] SPLIT method doubt
(Wed Jul 15 2020 - 08:45:52 PDT)
[AMBER] SPLIT method doubt
(Tue Jul 14 2020 - 15:01:49 PDT)
[AMBER] Error pmemd.cuda amber 20 GPU
(Thu Jul 09 2020 - 07:11:29 PDT)
Camila Mara Clemente
Re: [AMBER] SPLIT method doubt
(Wed Jul 15 2020 - 12:24:44 PDT)
Carlos
Re: [AMBER] amber14 gpu installation failed
(Mon Jul 13 2020 - 12:08:47 PDT)
[AMBER] amber14 gpu installation failed
(Tue Jul 07 2020 - 20:42:57 PDT)
Carlos Simmerling
Re: [AMBER] Issue heating system in equilibration step
(Fri Jul 31 2020 - 12:19:23 PDT)
Re: [AMBER] Issue heating system in equilibration step
(Fri Jul 31 2020 - 12:10:07 PDT)
Re: [AMBER] FW: restraint 10 kcal/mol
(Mon Jul 20 2020 - 07:23:54 PDT)
Re: [AMBER] Default temperature regulation during production run: Missed to declare ntt option
(Tue Jul 14 2020 - 09:41:37 PDT)
Re: [AMBER] Question about SMD using polymer
(Mon Jul 13 2020 - 07:14:24 PDT)
Re: [AMBER] attach pull release method exploration for free energy calculations
(Thu Jul 09 2020 - 13:24:12 PDT)
Re: [AMBER] FW: restraint 10 kcal/mol
(Mon Jul 06 2020 - 08:32:00 PDT)
Re: [AMBER] Question about SMD using polymer
(Mon Jul 06 2020 - 08:05:08 PDT)
Re: [AMBER] how to create nice animated videos to show simulations
(Wed Jul 01 2020 - 03:40:47 PDT)
Casalini Tommaso
[AMBER] Refitting charges with MCPB destabilizes the active site
(Wed Jul 29 2020 - 04:23:44 PDT)
[AMBER] Download link for AmberTools17
(Thu Jul 23 2020 - 01:44:20 PDT)
Chetna Tyagi
Re: [AMBER] how to create nice animated videos to show simulations
(Wed Jul 01 2020 - 04:54:35 PDT)
[AMBER] how to create nice animated videos to show simulations
(Wed Jul 01 2020 - 03:31:34 PDT)
Christina Bergonzo
Re: [AMBER] About time-dependent positional restraints
(Mon Jul 13 2020 - 05:42:04 PDT)
Clorice Reinhardt
Re: [AMBER] How to set salt concentration
(Fri Jul 03 2020 - 12:10:18 PDT)
Conrad F Li
[AMBER] Adding ions to implicit solvent models
(Wed Jul 29 2020 - 18:17:34 PDT)
Cruzeiro,Vinicius Wilian D
Re: [AMBER] Fortran error in constant pH MD
(Fri Jul 03 2020 - 08:23:37 PDT)
Daniel Roe
Re: [AMBER] Amber nc trajectory file analysis by x3dna
(Fri Jul 31 2020 - 08:28:19 PDT)
Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..."
(Fri Jul 31 2020 - 05:52:47 PDT)
Re: [AMBER] fatal error in 3D RISM calculation
(Tue Jul 21 2020 - 10:34:04 PDT)
Re: [AMBER] CPPTRAJ: Time Correlation Function (TCF)
(Mon Jul 20 2020 - 07:54:56 PDT)
Re: [AMBER] Reonstructing frames from PCA projection
(Mon Jul 20 2020 - 07:43:58 PDT)
Re: [AMBER] libnetcdf.so.7 needed by /usr/local/src/amber18/lib/libcpptraj.so, not found when upgrading AT18 to AT19
(Mon Jul 20 2020 - 06:59:36 PDT)
Re: [AMBER] Mask behavior vs distance measurement?
(Thu Jul 09 2020 - 19:06:18 PDT)
Re: [AMBER] Strip water job is killed after 10-40% completion
(Tue Jul 07 2020 - 07:11:16 PDT)
Re: [AMBER] Amber20 installation
(Tue Jul 07 2020 - 05:48:48 PDT)
David A Case
Re: [AMBER] Erro Amber18 GPU
(Thu Jul 30 2020 - 17:29:39 PDT)
Re: [AMBER] Error building Amber
(Thu Jul 30 2020 - 04:54:10 PDT)
Re: [AMBER] Error building Amber
(Wed Jul 29 2020 - 18:21:11 PDT)
[AMBER] running QM/MM calculations
(Wed Jul 29 2020 - 04:40:51 PDT)
Re: [AMBER] Error building Amber
(Tue Jul 28 2020 - 20:17:05 PDT)
Re: [AMBER] Error building Amber
(Tue Jul 28 2020 - 18:57:44 PDT)
Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..."
(Tue Jul 28 2020 - 06:59:16 PDT)
Re: [AMBER] Error building Amber
(Tue Jul 28 2020 - 06:43:52 PDT)
Re: [AMBER] Error building Amber
(Mon Jul 27 2020 - 10:48:48 PDT)
Re: [AMBER] Error building Amber
(Mon Jul 27 2020 - 10:15:14 PDT)
Re: [AMBER] Amber20 Compiling problem with b2 and Boost.Regex
(Mon Jul 27 2020 - 06:10:37 PDT)
Re: [AMBER] Maximum system size
(Sun Jul 26 2020 - 17:57:50 PDT)
Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..."
(Sun Jul 26 2020 - 17:44:15 PDT)
Re: [AMBER] How to install Amber20 with pmemd.amoeba?
(Sat Jul 25 2020 - 17:36:21 PDT)
Re: [AMBER] Issue while installing Amber20
(Sat Jul 25 2020 - 05:37:24 PDT)
Re: [AMBER] smooth soft core potentials
(Thu Jul 23 2020 - 17:49:30 PDT)
Re: [AMBER] Download link for AmberTools17
(Thu Jul 23 2020 - 05:08:06 PDT)
Re: [AMBER] Problem compiling Amber20 - undefined reference to 'plumedmain_create'
(Thu Jul 23 2020 - 05:05:39 PDT)
Re: [AMBER] Amber 20 - Support Multi GPU
(Wed Jul 22 2020 - 17:36:38 PDT)
Re: [AMBER] tinker_to_amber force fields
(Wed Jul 22 2020 - 17:28:48 PDT)
Re: [AMBER] tinker_to_amber force fields
(Wed Jul 22 2020 - 12:24:37 PDT)
Re: [AMBER] Size of Solvent Box
(Wed Jul 22 2020 - 12:16:56 PDT)
[AMBER] problem with pdb4amber
(Wed Jul 22 2020 - 07:59:02 PDT)
Re: [AMBER] AMBER20 Error: No package metadata was found for pdb4amber
(Wed Jul 22 2020 - 04:55:10 PDT)
Re: [AMBER] amber website down?
(Mon Jul 20 2020 - 18:26:01 PDT)
Re: [AMBER] libnetcdf.so.7 needed by /usr/local/src/amber18/lib/libcpptraj.so, not found when upgrading AT18 to AT19
(Mon Jul 20 2020 - 10:05:00 PDT)
Re: [AMBER] Units from quasiharmonic analysis of Principal Components
(Sun Jul 19 2020 - 17:57:58 PDT)
Re: [AMBER] Modified cysteine parameters
(Sun Jul 19 2020 - 04:43:13 PDT)
Re: [AMBER] Tinker_to_amber problem
(Fri Jul 17 2020 - 17:54:54 PDT)
Re: [AMBER] Several tutorial not found
(Fri Jul 17 2020 - 09:53:41 PDT)
Re: [AMBER] matching paramters of methane
(Thu Jul 16 2020 - 09:36:28 PDT)
Re: [AMBER] Questions on random seed
(Thu Jul 16 2020 - 05:25:17 PDT)
Re: [AMBER] Default temperature regulation during production run: Missed to declare ntt option
(Wed Jul 15 2020 - 05:08:42 PDT)
Re: [AMBER] Clarification of Amber Post on Heating Protocol
(Tue Jul 14 2020 - 19:11:44 PDT)
Re: [AMBER] Default temperature regulation during production run: Missed to declare ntt option
(Tue Jul 14 2020 - 09:38:56 PDT)
Re: [AMBER] Amber vs Namd energy values are different.
(Sun Jul 12 2020 - 18:23:52 PDT)
Re: [AMBER] GPU compatible with AMBER
(Fri Jul 10 2020 - 05:04:24 PDT)
Re: [AMBER] Problem with running Python script in AMBER environment.
(Thu Jul 09 2020 - 17:32:24 PDT)
Re: [AMBER] Forcefield for 5' phosphate in RNA
(Thu Jul 09 2020 - 05:42:51 PDT)
Re: [AMBER] Amber prmtop and inpcrd of complex file with a water molecular cutoff
(Thu Jul 09 2020 - 05:36:15 PDT)
Re: [AMBER] Error in SMD running
(Thu Jul 09 2020 - 05:32:53 PDT)
Re: [AMBER] LJ potential for OPC water model
(Wed Jul 08 2020 - 09:30:42 PDT)
Re: [AMBER] MBAR with Amber 18
(Wed Jul 08 2020 - 05:19:59 PDT)
Re: [AMBER] amber14 gpu installation failed
(Wed Jul 08 2020 - 05:16:50 PDT)
Re: [AMBER] Asking for help: cross linking polymer
(Tue Jul 07 2020 - 18:42:53 PDT)
Re: [AMBER] Atomic Polarizability
(Tue Jul 07 2020 - 10:58:39 PDT)
Re: [AMBER] Amber prmtop and inpcrd of complex file with a water molecular cutoff
(Tue Jul 07 2020 - 10:56:07 PDT)
Re: [AMBER] Error in Installing Amber 20 on GPU
(Sat Jul 04 2020 - 05:01:40 PDT)
Re: [AMBER] The most update force fields for DNA and RNA
(Fri Jul 03 2020 - 17:52:45 PDT)
Re: [AMBER] Error while running Antechamber
(Fri Jul 03 2020 - 14:12:24 PDT)
Re: [AMBER] How to set salt concentration
(Fri Jul 03 2020 - 06:44:48 PDT)
Re: [AMBER] Defining new atoms in AMBER
(Fri Jul 03 2020 - 06:41:54 PDT)
Re: [AMBER] Error in Installing Amber 20 on GPU
(Fri Jul 03 2020 - 06:37:24 PDT)
Re: [AMBER] Defining new atoms in AMBER
(Thu Jul 02 2020 - 10:20:11 PDT)
Re: [AMBER] Error in Installing Amber 20 on GPU
(Thu Jul 02 2020 - 10:11:24 PDT)
Re: [AMBER] how to use triclinic box shape
(Thu Jul 02 2020 - 05:35:14 PDT)
Re: [AMBER] calculating methane parameters using RISM
(Thu Jul 02 2020 - 05:14:52 PDT)
Re: [AMBER] Error in Installing Amber 20 on GPU
(Thu Jul 02 2020 - 05:07:02 PDT)
[AMBER] ntx and irest
(Thu Jul 02 2020 - 04:55:35 PDT)
Re: [AMBER] Error in Installing Amber 20 on GPU
(Wed Jul 01 2020 - 08:45:01 PDT)
Re: [AMBER] "Does not have a type" error in tleap
(Wed Jul 01 2020 - 08:43:20 PDT)
David Cerutti
Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol
(Sat Jul 25 2020 - 05:40:36 PDT)
Re: [AMBER] Using Orca to develop RESP Charges
(Fri Jul 24 2020 - 11:08:22 PDT)
Re: [AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming
(Tue Jul 21 2020 - 09:06:31 PDT)
Re: [AMBER] Several tutorial not found
(Fri Jul 17 2020 - 08:59:27 PDT)
Re: [AMBER] Error pmemd.cuda amber 20 GPU
(Thu Jul 09 2020 - 09:44:51 PDT)
Re: [AMBER] Error pmemd.cuda amber 20 GPU
(Thu Jul 09 2020 - 09:30:28 PDT)
Re: [AMBER] how to use triclinic box shape
(Thu Jul 02 2020 - 05:48:10 PDT)
David Sáez
Re: [AMBER] About time-dependent positional restraints
(Mon Jul 13 2020 - 08:34:33 PDT)
Re: [AMBER] About time-dependent positional restraints
(Fri Jul 10 2020 - 18:40:27 PDT)
[AMBER] About time-dependent positional restraints
(Fri Jul 10 2020 - 18:37:45 PDT)
Debarati DasGupta
[AMBER] smooth soft core potentials
(Thu Jul 23 2020 - 13:26:32 PDT)
Re: [AMBER] FW: restraint 10 kcal/mol
(Wed Jul 15 2020 - 14:50:24 PDT)
[AMBER] attach pull release method exploration for free energy calculations
(Thu Jul 09 2020 - 12:40:32 PDT)
Re: [AMBER] FW: restraint 10 kcal/mol
(Mon Jul 06 2020 - 15:57:38 PDT)
[AMBER] FW: restraint 10 kcal/mol
(Mon Jul 06 2020 - 08:16:07 PDT)
DHEERAJ CHITARA
[AMBER] Size of Solvent Box
(Wed Jul 22 2020 - 11:14:20 PDT)
[AMBER] Reg. MMGBSA Calculations
(Sat Jul 11 2020 - 11:26:52 PDT)
Diego Morone
Re: [AMBER] ABMD with RMSD and RoG: ** NFE-Error ** : Cannot read &colvar namelist!
(Thu Jul 23 2020 - 08:22:09 PDT)
[AMBER] ABMD with RMSD and RoG: ** NFE-Error ** : Cannot read &colvar namelist!
(Mon Jul 20 2020 - 06:37:31 PDT)
dnlfr1994.gmail.com
[AMBER] Forcefield for 5' phosphate in RNA
(Thu Jul 09 2020 - 05:01:36 PDT)
Dr. Anselm Horn
Re: [AMBER] carboxylated Lys
(Fri Jul 24 2020 - 07:46:10 PDT)
Re: [AMBER] Modified cysteine parameters
(Mon Jul 20 2020 - 01:46:00 PDT)
Re: [AMBER] Command for making atoms rigid
(Wed Jul 15 2020 - 08:38:56 PDT)
Re: [AMBER] SPLIT method doubt
(Wed Jul 15 2020 - 08:30:37 PDT)
Re: [AMBER] Asking for help: cross linking polymer
(Wed Jul 08 2020 - 00:56:29 PDT)
Re: [AMBER] Atomic Polarizability
(Tue Jul 07 2020 - 14:24:55 PDT)
Re: [AMBER] Strip water job is killed after 10-40% completion
(Tue Jul 07 2020 - 07:08:38 PDT)
Re: [AMBER] How to set salt concentration
(Fri Jul 03 2020 - 08:59:08 PDT)
Elvis Martis
Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..."
(Sun Jul 26 2020 - 05:43:46 PDT)
Re: [AMBER] XMGRACE giving error
(Mon Jul 13 2020 - 22:53:37 PDT)
Re: [AMBER] XMGRACE giving error
(Mon Jul 13 2020 - 04:07:40 PDT)
Re: [AMBER] XMGRACE giving error
(Mon Jul 13 2020 - 03:19:43 PDT)
Re: [AMBER] REPEATED LINMIN FAILURE
(Fri Jul 10 2020 - 04:27:55 PDT)
Re: [AMBER] Error in partial MINIMIZATION STEP
(Sat Jul 04 2020 - 09:53:33 PDT)
Re: [AMBER] how to create nice animated videos to show simulations
(Wed Jul 01 2020 - 03:39:08 PDT)
Re: [AMBER] Caping error
(Tue Jun 30 2020 - 21:48:01 PDT)
emanuele falbo
Re: [AMBER] CPPTRAJ: Time Correlation Function (TCF)
(Thu Jul 16 2020 - 01:55:57 PDT)
Re: [AMBER] CPPTRAJ: Time Correlation Function (TCF)
(Wed Jul 15 2020 - 07:29:40 PDT)
Feng Pan
Re: [AMBER] ABMD with RMSD and RoG: ** NFE-Error ** : Cannot read &colvar namelist!
(Wed Jul 22 2020 - 18:21:51 PDT)
Re: [AMBER] nmropt vs infe
(Thu Jul 09 2020 - 22:01:21 PDT)
Francesca Lønstad Bleken
[AMBER] How to make pass extra argument "--bind-to none" to mpirun for ORCA when running QMMM from sander?
(Fri Jul 31 2020 - 02:42:32 PDT)
gagandeep singh
[AMBER] Error in Gausian file preparation using MCPB.py
(Fri Jul 24 2020 - 14:55:47 PDT)
Gerardo Zerbetto De Palma
Re: [AMBER] How to set salt concentration
(Wed Jul 01 2020 - 20:57:37 PDT)
German P. Barletta
Re: [AMBER] Units from quasiharmonic analysis of Principal Components
(Mon Jul 20 2020 - 12:25:23 PDT)
[AMBER] Units from quasiharmonic analysis of Principal Components
(Sun Jul 19 2020 - 09:48:38 PDT)
Gilberto Pereira
[AMBER] Usage of the Density Peaks Algorithm.
(Thu Jul 02 2020 - 08:34:50 PDT)
Goetz, Andreas
Re: [AMBER] How to make pass extra argument "--bind-to none" to mpirun for ORCA when running QMMM from sander?
(Fri Jul 31 2020 - 03:12:22 PDT)
Gustaf Olsson
Re: [AMBER] Error building Amber
(Thu Jul 30 2020 - 09:56:12 PDT)
Re: [AMBER] Error building Amber
(Wed Jul 29 2020 - 12:50:32 PDT)
Re: [AMBER] Error building Amber
(Wed Jul 29 2020 - 04:58:32 PDT)
Re: [AMBER] Error building Amber
(Tue Jul 28 2020 - 14:35:15 PDT)
Re: [AMBER] Error building Amber
(Tue Jul 28 2020 - 02:14:47 PDT)
Re: [AMBER] amber website down?
(Mon Jul 20 2020 - 14:18:29 PDT)
Re: [AMBER] Amber20: Error in the linking of the pysander
(Sat Jul 18 2020 - 12:39:37 PDT)
Re: [AMBER] Install broke and compilation fails
(Tue Jul 07 2020 - 14:12:51 PDT)
[AMBER] Install broke and compilation fails
(Tue Jul 07 2020 - 06:58:10 PDT)
Re: [AMBER] Error in Installing Amber 20 on GPU
(Thu Jul 02 2020 - 05:58:40 PDT)
Re: [AMBER] Error in Installing Amber 20 on GPU
(Thu Jul 02 2020 - 05:56:29 PDT)
Re: [AMBER] Error in Installing Amber 20 on GPU
(Wed Jul 01 2020 - 23:44:09 PDT)
Re: [AMBER] Amber20 installation
(Wed Jul 01 2020 - 23:06:29 PDT)
Re: [AMBER] Error in Installing Amber 20 on GPU
(Wed Jul 01 2020 - 22:55:21 PDT)
Re: [AMBER] Amber installation error
(Wed Jul 01 2020 - 22:46:33 PDT)
Hai Nguyen
Re: [AMBER] problem with pdb4amber
(Wed Jul 22 2020 - 09:13:40 PDT)
Re: [AMBER] Problem with running Python script in AMBER environment.
(Thu Jul 09 2020 - 14:36:02 PDT)
Hantz, Eric R.
Re: [AMBER] ASMD equil4 not producing output files
(Wed Jul 29 2020 - 13:11:18 PDT)
[AMBER] ASMD equil4 not producing output files
(Tue Jul 28 2020 - 06:51:23 PDT)
Huang Tao
Re: [AMBER] AMBER20 Error: No package metadata was found for pdb4amber
(Wed Jul 22 2020 - 05:14:41 PDT)
[AMBER] AMBER20 Error: No package metadata was found for pdb4amber
(Tue Jul 21 2020 - 19:39:21 PDT)
Isabelle Navizet
[AMBER] GPU compatible with AMBER
(Thu Jul 09 2020 - 05:34:06 PDT)
Jack Shepherd
[AMBER] Maximum system size
(Sat Jul 25 2020 - 17:57:01 PDT)
Jacob Remington
[AMBER] Seg fault with pmemd.cuda.MPI using plumed
(Sat Jul 11 2020 - 12:16:54 PDT)
Jakub Jalowiec
[AMBER] Problem installing AmberMD with MPI support on Cray XC40
(Mon Jul 27 2020 - 15:27:13 PDT)
James Kress
Re: [AMBER] Cores, CPU RAM, GPU RAM
(Wed Jul 22 2020 - 15:19:25 PDT)
Re: [AMBER] Cores, CPU RAM, GPU RAM
(Fri Jul 17 2020 - 15:28:37 PDT)
Re: [AMBER] REPEATED LINMIN FAILURE
(Fri Jul 10 2020 - 15:05:27 PDT)
Jan Mičan
[AMBER] What would you like to see in visualization of chemical data?
(Mon Jul 20 2020 - 03:48:06 PDT)
Jatin Kashyap
Re: [AMBER] "Does not have a type" error in tleap
(Wed Jul 01 2020 - 10:00:14 PDT)
Jenny 148
[AMBER] Amber nc trajectory file analysis by x3dna
(Fri Jul 31 2020 - 08:05:56 PDT)
Jisha B
[AMBER] AMBER trajectory analysis in MINT package
(Thu Jul 23 2020 - 05:40:18 PDT)
Re: [AMBER] Hoogsteen H-bond
(Wed Jul 01 2020 - 08:18:10 PDT)
JoAnne Babula
Re: [AMBER] tleap does not recognize nonstandard residue from lib file
(Wed Jul 22 2020 - 13:49:49 PDT)
[AMBER] tleap does not recognize nonstandard residue from lib file
(Wed Jul 22 2020 - 12:43:59 PDT)
Jonathon Ferrell
[AMBER] Force Trajectory Output ABMD
(Mon Jul 06 2020 - 09:56:24 PDT)
Jorden Cabal
Re: [AMBER] Default temperature regulation during production run: Missed to declare ntt option
(Tue Jul 14 2020 - 20:29:20 PDT)
Re: [AMBER] Default temperature regulation during production run: Missed to declare ntt option
(Tue Jul 14 2020 - 20:22:14 PDT)
[AMBER] Default temperature regulation during production run: Missed to declare ntt option
(Tue Jul 14 2020 - 04:26:02 PDT)
Kenneth Huang
[AMBER] Tracking lifetime distance by closest of specific water IDs?
(Tue Jul 28 2020 - 07:28:51 PDT)
[AMBER] Charges for modified DNA base at the termini?
(Sun Jul 26 2020 - 23:50:39 PDT)
Re: [AMBER] Mask behavior vs distance measurement?
(Fri Jul 10 2020 - 10:31:28 PDT)
[AMBER] Mask behavior vs distance measurement?
(Thu Jul 09 2020 - 17:04:10 PDT)
Kliuchnikov, Evgenii
Re: [AMBER] How to install Amber20 with pmemd.amoeba?
(Sat Jul 25 2020 - 21:46:59 PDT)
[AMBER] How to install Amber20 with pmemd.amoeba?
(Sat Jul 25 2020 - 12:29:56 PDT)
Re: [AMBER] tinker_to_amber force fields
(Wed Jul 22 2020 - 12:10:14 PDT)
[AMBER] tinker_to_amber force fields
(Wed Jul 22 2020 - 11:37:33 PDT)
Re: [AMBER] Tinker_to_amber problem
(Fri Jul 17 2020 - 17:59:00 PDT)
[AMBER] Tinker_to_amber problem
(Fri Jul 17 2020 - 12:50:01 PDT)
[AMBER] Amber20 installation
(Wed Jul 01 2020 - 11:16:21 PDT)
Kolattukudy P. Santo
Re: [AMBER] Defining new atoms in AMBER
(Thu Jul 02 2020 - 13:18:28 PDT)
[AMBER] Defining new atoms in AMBER
(Thu Jul 02 2020 - 08:47:00 PDT)
krishnendu sinha
[AMBER] Modified cysteine parameters
(Sun Jul 19 2020 - 00:49:40 PDT)
Kshatresh Dutta Dubey
Re: [AMBER] mmpbsa error
(Sat Jul 18 2020 - 03:19:02 PDT)
Lachele Foley
Re: [AMBER] Interaction of cellulose-hemicellulose
(Wed Jul 29 2020 - 00:17:07 PDT)
[AMBER] OT: Job Posting
(Thu Jul 16 2020 - 16:40:13 PDT)
Re: [AMBER] bulding a monosaccharide with N-acetylation
(Wed Jul 01 2020 - 04:55:06 PDT)
Leena Aggarwal
Re: [AMBER] fatal error in 3D RISM calculation
(Tue Jul 21 2020 - 04:39:21 PDT)
Re: [AMBER] generating methane parameters for rism
(Sun Jul 05 2020 - 11:05:20 PDT)
Re: [AMBER] Problem of Steered MD Simulation for unfolding of RNA
(Thu Jul 02 2020 - 07:43:04 PDT)
Lod King
[AMBER] AMD parameter: protein residue should count ligand or not
(Tue Jul 28 2020 - 10:55:43 PDT)
Loki
Re: [AMBER] LJ potential for OPC water model
(Fri Jul 03 2020 - 09:28:55 PDT)
Re: [AMBER] LJ potential for OPC water model
(Fri Jul 03 2020 - 09:01:58 PDT)
[AMBER] LJ potential for OPC water model
(Fri Jul 03 2020 - 05:07:04 PDT)
Lucas Bandeira
[AMBER] Problems deriving charges with RESP
(Mon Jul 27 2020 - 17:23:52 PDT)
[AMBER] Problems generating charges with RESP
(Mon Jul 27 2020 - 13:39:01 PDT)
[AMBER] Using Orca to develop RESP Charges
(Thu Jul 23 2020 - 13:37:56 PDT)
Maria Nagan
Re: [AMBER] Amber nc trajectory file analysis by x3dna
(Fri Jul 31 2020 - 08:22:17 PDT)
Markowska
Re: [AMBER] libnetcdf.so.7 needed by /usr/local/src/amber18/lib/libcpptraj.so, not found when upgrading AT18 to AT19
(Mon Jul 20 2020 - 12:59:05 PDT)
Re: [AMBER] libnetcdf.so.7 needed by /usr/local/src/amber18/lib/libcpptraj.so, not found when upgrading AT18 to AT19
(Mon Jul 20 2020 - 07:44:13 PDT)
[AMBER] libnetcdf.so.7 needed by /usr/local/src/amber18/lib/libcpptraj.so, not found when upgrading AT18 to AT19
(Mon Jul 20 2020 - 06:56:26 PDT)
Matias Machado
Re: [AMBER] SPLIT method doubt
(Wed Jul 15 2020 - 10:22:14 PDT)
Re: [AMBER] How to set salt concentration
(Sat Jul 04 2020 - 11:17:07 PDT)
Re: [AMBER] LJ potential for OPC water model
(Fri Jul 03 2020 - 09:35:32 PDT)
Re: [AMBER] How to set salt concentration
(Thu Jul 02 2020 - 06:17:27 PDT)
Michael F. Bruist
Re: [AMBER] Several tutorial not found
(Mon Jul 20 2020 - 09:22:13 PDT)
[AMBER] Reonstructing frames from PCA projection
(Fri Jul 17 2020 - 08:24:03 PDT)
[AMBER] Several tutorial not found
(Fri Jul 17 2020 - 08:19:56 PDT)
Mikhael, Simoun
[AMBER] Structure Artifact After Autoimage
(Fri Jul 31 2020 - 14:01:52 PDT)
mirzo
Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol
(Sat Jul 25 2020 - 06:36:52 PDT)
mohamed marzouk
[AMBER] Caping error
(Tue Jun 30 2020 - 21:38:15 PDT)
MYRIAN TORRES RICO
Re: [AMBER] mmpbsa error
(Mon Jul 20 2020 - 00:45:27 PDT)
[AMBER] mmpbsa error
(Fri Jul 17 2020 - 04:31:13 PDT)
Nada Afiva
Re: [AMBER] Questions on random seed
(Thu Jul 16 2020 - 16:20:23 PDT)
[AMBER] Questions on random seed
(Wed Jul 15 2020 - 20:35:37 PDT)
Re: [AMBER] MMGBSA and MMPBSA error (CalcError: failed with prmtop file complex.prmtop!)
(Mon Jul 06 2020 - 14:18:44 PDT)
Re: [AMBER] MMGBSA and MMPBSA error (CalcError: failed with prmtop file complex.prmtop!)
(Sat Jul 04 2020 - 20:17:36 PDT)
[AMBER] MMGBSA and MMPBSA error (CalcError: failed with prmtop file complex.prmtop!)
(Sat Jul 04 2020 - 14:58:44 PDT)
Re: [AMBER] How to set salt concentration
(Sat Jul 04 2020 - 11:42:11 PDT)
Re: [AMBER] The most update force fields for DNA and RNA
(Fri Jul 03 2020 - 18:10:18 PDT)
[AMBER] The most update force fields for DNA and RNA
(Fri Jul 03 2020 - 14:30:27 PDT)
Re: [AMBER] How to set salt concentration
(Fri Jul 03 2020 - 12:58:26 PDT)
Re: [AMBER] How to set salt concentration
(Fri Jul 03 2020 - 12:00:43 PDT)
Re: [AMBER] How to set salt concentration
(Fri Jul 03 2020 - 02:49:24 PDT)
Re: [AMBER] how to use triclinic box shape
(Thu Jul 02 2020 - 17:38:11 PDT)
[AMBER] how to use triclinic box shape
(Thu Jul 02 2020 - 01:47:46 PDT)
Re: [AMBER] How to set salt concentration
(Thu Jul 02 2020 - 01:34:28 PDT)
[AMBER] How to set salt concentration
(Wed Jul 01 2020 - 20:54:44 PDT)
Niel Henriksen
Re: [AMBER] attach pull release method exploration for free energy calculations
(Thu Jul 09 2020 - 16:34:55 PDT)
Paul Meister
[AMBER] Fortran error in constant pH MD
(Thu Jul 02 2020 - 09:28:56 PDT)
Pengfei Li
Re: [AMBER] Missing bond parameters after MCPB.py
(Mon Jul 20 2020 - 12:17:50 PDT)
Re: [AMBER] gamess/MCPB.py tutorial
(Mon Jul 20 2020 - 11:14:55 PDT)
Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450)
(Mon Jul 20 2020 - 10:53:34 PDT)
Pinky Mazumder
Re: [AMBER] Interaction of cellulose-hemicellulose
(Tue Jul 28 2020 - 08:48:49 PDT)
Re: [AMBER] Steered molecular dynamics Simulation
(Sat Jul 25 2020 - 21:16:28 PDT)
[AMBER] How to calculate velocity in steered simulation
(Fri Jul 24 2020 - 20:58:05 PDT)
Re: [AMBER] steered MD with restraints on a selection
(Fri Jul 24 2020 - 19:51:46 PDT)
[AMBER] Steered molecular dynamics Simulation
(Fri Jul 24 2020 - 19:47:39 PDT)
[AMBER] Error in incprd file while performing steered molecular dynamics simulation
(Sat Jul 18 2020 - 00:09:30 PDT)
[AMBER] Command for making atoms rigid
(Tue Jul 14 2020 - 15:55:40 PDT)
Re: [AMBER] Question about SMD using polymer
(Fri Jul 10 2020 - 13:24:35 PDT)
[AMBER] Question about SMD using polymer
(Mon Jul 06 2020 - 08:01:38 PDT)
Preeti Pandey
Re: [AMBER] Error in Gausian file preparation using MCPB.py
(Fri Jul 31 2020 - 14:20:16 PDT)
PRITI ROY
[AMBER] Error in SMD running
(Wed Jul 08 2020 - 19:05:50 PDT)
Raman Preet Singh
Re: [AMBER] how to create nice animated videos to show simulations
(Wed Jul 01 2020 - 04:56:06 PDT)
Ray Luo
Re: [AMBER] MMGBSA and MMPBSA error (CalcError: failed with prmtop file complex.prmtop!)
(Sun Jul 05 2020 - 11:31:34 PDT)
Razil Tahir
Re: [AMBER] Undefined angle parameter and torsion terms in Amber18
(Wed Jul 22 2020 - 08:13:08 PDT)
[AMBER] Undefined angle parameter and torsion terms in Antechamber
(Tue Jul 21 2020 - 21:03:20 PDT)
Renato Araujo
Re: [AMBER] Erro Amber18 GPU
(Thu Jul 30 2020 - 18:07:17 PDT)
[AMBER] Erro Amber18 GPU
(Thu Jul 30 2020 - 12:55:42 PDT)
Robert Molt
Re: [AMBER] What would you like to see in visualization of chemical data?
(Mon Jul 20 2020 - 04:31:50 PDT)
[AMBER] Clarification of Amber Post on Heating Protocol
(Tue Jul 14 2020 - 14:46:25 PDT)
Rodrigo Galindo-Murillo
Re: [AMBER] amber trajectory nc file to pdb ensemble
(Fri Jul 31 2020 - 10:54:29 PDT)
Re: [AMBER] amber trajectory nc file to pdb ensemble
(Fri Jul 31 2020 - 10:53:30 PDT)
Re: [AMBER] amber trajectory nc file to pdb ensemble
(Fri Jul 31 2020 - 10:04:00 PDT)
Re: [AMBER] how to create nice animated videos to show simulations
(Wed Jul 01 2020 - 06:57:01 PDT)
Rosellen, Martin
[AMBER] EAMD_BOOST and reweighting of AMD runs
(Tue Jul 14 2020 - 08:00:51 PDT)
[AMBER] Accelerated Molecular Dynamics and convergence
(Wed Jul 08 2020 - 06:58:20 PDT)
SAKO MIRZAIE
Re: [AMBER] Asking for help: cross linking polymer
(Tue Jul 07 2020 - 20:31:21 PDT)
[AMBER] Asking for help: cross linking polymer
(Tue Jul 07 2020 - 17:28:10 PDT)
Sally Pias
Re: [AMBER] Barostat and thermostat for membrane protein-ligand simulation
(Thu Jul 09 2020 - 18:27:40 PDT)
Re: [AMBER] Barostat and thermostat for membrane protein-ligand simulation
(Tue Jul 07 2020 - 20:16:56 PDT)
Samuel A. Ratliff
Re: [AMBER] Issue heating system in equilibration step
(Fri Jul 31 2020 - 13:14:09 PDT)
Re: [AMBER] Issue heating system in equilibration step
(Fri Jul 31 2020 - 12:16:01 PDT)
Re: [AMBER] Issue heating system in equilibration step
(Fri Jul 31 2020 - 09:58:44 PDT)
[AMBER] Issue heating system in equilibration step
(Tue Jul 28 2020 - 10:05:00 PDT)
Schröder, David Christopher
Re: [AMBER] Installing Amber20 with cuda9
(Thu Jul 02 2020 - 10:22:44 PDT)
Re: [AMBER] Installing Amber20 with cuda9
(Thu Jul 02 2020 - 08:11:36 PDT)
[AMBER] Installing Amber20 with cuda9
(Thu Jul 02 2020 - 06:58:38 PDT)
Sharif Nada
Re: [AMBER] REPEATED LINMIN FAILURE
(Fri Jul 10 2020 - 14:39:32 PDT)
[AMBER] Using ntt=10 in PMEMD
(Mon Jul 06 2020 - 03:29:40 PDT)
Shilpa Gupta
[AMBER] Solvent excluded volume
(Sat Jul 04 2020 - 03:21:31 PDT)
Shreeramesh
[AMBER] Strip water job is killed after 10-40% completion
(Mon Jul 06 2020 - 09:23:26 PDT)
[AMBER] Error in partial MINIMIZATION STEP
(Sat Jul 04 2020 - 09:39:01 PDT)
[AMBER] Error while running Antechamber
(Fri Jul 03 2020 - 11:02:15 PDT)
Souvik
Re: [AMBER] CPPTRAJ: Time Correlation Function (TCF)
(Wed Jul 15 2020 - 09:06:15 PDT)
Re: [AMBER] Problem of Steered MD Simulation for unfolding of RNA
(Thu Jul 02 2020 - 09:34:22 PDT)
Suchetana Gupta
Re: [AMBER] Error in Installing Amber 20 on GPU
(Sat Jul 04 2020 - 02:43:47 PDT)
Re: [AMBER] Error in Installing Amber 20 on GPU
(Thu Jul 02 2020 - 21:51:54 PDT)
Re: [AMBER] Error in Installing Amber 20 on GPU
(Thu Jul 02 2020 - 05:22:52 PDT)
Re: [AMBER] Error in Installing Amber 20 on GPU
(Wed Jul 01 2020 - 22:57:41 PDT)
[AMBER] Amber 20 on Google Colab
(Wed Jul 01 2020 - 22:54:07 PDT)
Re: [AMBER] How to set salt concentration
(Wed Jul 01 2020 - 20:59:37 PDT)
Re: [AMBER] Error in Installing Amber 20 on GPU
(Wed Jul 01 2020 - 11:13:29 PDT)
Re: [AMBER] Error in Installing Amber 20 on GPU
(Wed Jul 01 2020 - 10:39:51 PDT)
Re: [AMBER] how to create nice animated videos to show simulations
(Wed Jul 01 2020 - 03:34:48 PDT)
Re: [AMBER] Error in Installing Amber 20 on GPU
(Tue Jun 30 2020 - 22:28:23 PDT)
Sumra Abbasi
Re: [AMBER] XMGRACE giving error
(Mon Jul 13 2020 - 22:33:20 PDT)
Re: [AMBER] XMGRACE giving error
(Mon Jul 13 2020 - 03:37:50 PDT)
[AMBER] XMGRACE giving error
(Mon Jul 13 2020 - 03:07:36 PDT)
Thakur, Abhishek
[AMBER] fixatomorder
(Tue Jul 07 2020 - 10:38:56 PDT)
[AMBER] Atomic Polarizability
(Tue Jul 07 2020 - 09:58:48 PDT)
Thirakorn Mokkawes
[AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450)
(Thu Jul 09 2020 - 03:59:16 PDT)
Thomas Cheatham
Re: [AMBER] amber trajectory nc file to pdb ensemble
(Fri Jul 31 2020 - 09:45:45 PDT)
Tim Travers
Re: [AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming
(Tue Jul 21 2020 - 09:40:40 PDT)
Re: [AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming
(Tue Jul 21 2020 - 08:17:07 PDT)
Tru Huynh
Re: [AMBER] XMGRACE giving error
(Mon Jul 13 2020 - 04:27:48 PDT)
Tyler Luchko
Re: [AMBER] fatal error in 3D RISM calculation
(Wed Jul 22 2020 - 09:32:05 PDT)
Tyler Luchko (Lists)
Re: [AMBER] error in 3d rism calculation
(Mon Jul 20 2020 - 13:25:09 PDT)
Re: [AMBER] generating methane parameters for rism
(Sun Jul 05 2020 - 15:02:14 PDT)
Ulf Ryde
[AMBER] MBAR with Amber 18
(Wed Jul 01 2020 - 03:25:00 PDT)
venkat
[AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol
(Sat Jul 25 2020 - 05:02:26 PDT)
Vishal Reddy
[AMBER] Amber vs Namd energy values are different.
(Sun Jul 12 2020 - 14:24:50 PDT)
Vishal Singh
Re: [AMBER] Steered molecular dynamics Simulation
(Fri Jul 24 2020 - 21:39:40 PDT)
[AMBER] Problem with running Python script in AMBER environment.
(Wed Jul 08 2020 - 23:51:52 PDT)
[AMBER] Problem of Steered MD Simulation for unfolding of RNA
(Thu Jul 02 2020 - 04:46:22 PDT)
Walton Smith
Re: [AMBER] Error building Amber
(Wed Jul 29 2020 - 17:57:21 PDT)
Re: [AMBER] Error building Amber
(Wed Jul 29 2020 - 17:09:55 PDT)
Re: [AMBER] Error building Amber
(Wed Jul 29 2020 - 07:26:19 PDT)
Re: [AMBER] Error building Amber
(Wed Jul 29 2020 - 06:31:31 PDT)
Re: [AMBER] Error building Amber
(Tue Jul 28 2020 - 07:03:42 PDT)
Re: [AMBER] Error building Amber
(Mon Jul 27 2020 - 12:50:54 PDT)
[AMBER] Error building Amber
(Mon Jul 27 2020 - 07:04:33 PDT)
Wim R. Cardoen
[AMBER] amber website down?
(Mon Jul 20 2020 - 14:07:08 PDT)
[AMBER] Amber20: Error in the linking of the pysander
(Fri Jul 17 2020 - 13:54:04 PDT)
Yessica
[AMBER] Problems with MC barostat
(Sun Jul 12 2020 - 16:53:08 PDT)
Állan Ferrari
[AMBER] carboxylated Lys
(Thu Jul 23 2020 - 14:30:32 PDT)
辛志宏
Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..."
(Thu Jul 30 2020 - 20:46:21 PDT)
[AMBER] 6. Re: Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." (???)
(Wed Jul 29 2020 - 02:10:13 PDT)
Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..."
(Mon Jul 27 2020 - 18:48:41 PDT)
[AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..."
(Sun Jul 26 2020 - 04:59:21 PDT)
[AMBER] Amber prmtop and inpcrd of complex file with a water molecular cutoff
(Wed Jul 08 2020 - 21:11:32 PDT)
[AMBER] Amber prmtop and inpcrd of complex file with a water molecular cutoff
(Tue Jul 07 2020 - 07:54:04 PDT)
변진영
[AMBER] Amber SHAKE error when running REMD
(Sun Jul 19 2020 - 23:56:58 PDT)
Last message date
:
Fri Jul 31 2020 - 14:30:04 PDT
Archived on
: Fri Dec 20 2024 - 05:56:01 PST
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