Amber Archive Aug 2018 by author
321 messages
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Starting
Wed Aug 01 2018 - 03:00:03 PDT,
Ending
Fri Aug 31 2018 - 17:00:02 PDT
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accuratefreeenergy.gmail.com
Re: [AMBER] Amber18 error: an illegal memory access was encountered launching kernel kNLSkinTest
(Sat Aug 25 2018 - 06:30:40 PDT)
Adam Jo Elatico
[AMBER] Free energy landscape on principal components
(Thu Aug 02 2018 - 08:34:04 PDT)
[AMBER] Calculate protein energy from simulation trajectory
(Thu Aug 02 2018 - 01:10:28 PDT)
Re: [AMBER] Eigenvalues from PCA in cpptraj
(Wed Aug 01 2018 - 09:49:36 PDT)
[AMBER] Eigenvalues from PCA in cpptraj
(Wed Aug 01 2018 - 04:39:50 PDT)
Alechania Misturini
Re: [AMBER] Best Methods
(Mon Aug 27 2018 - 09:28:00 PDT)
Re: [AMBER] Are there any forcefield present of bio-organic polyphosphate in AMBER ??
(Mon Aug 27 2018 - 08:52:21 PDT)
Re: [AMBER] Multiple PDB files to a MDCRD file
(Thu Aug 02 2018 - 08:05:58 PDT)
Re: [AMBER] Multiple PDB files to a MDCRD file
(Thu Aug 02 2018 - 08:00:37 PDT)
Re: [AMBER] Multiple PDB files to a MDCRD file
(Wed Aug 01 2018 - 10:10:41 PDT)
[AMBER] Multiple PDB files to a MDCRD file
(Wed Aug 01 2018 - 06:58:26 PDT)
Alexandra Carvalho
[AMBER] GPUs
(Wed Aug 01 2018 - 14:11:49 PDT)
Anaid Flores
Re: [AMBER] SCF convergence problems and write density matrix
(Sun Aug 19 2018 - 20:57:22 PDT)
[AMBER] SCF convergence problems and write density matrix
(Fri Aug 17 2018 - 15:08:39 PDT)
Anthony Bogetti
[AMBER] R.E.D. Server is down
(Tue Aug 28 2018 - 10:13:00 PDT)
Antonio Amber Carlesso
Re: [AMBER] Protein_ligand_preparation_general_rule
(Wed Aug 29 2018 - 02:56:00 PDT)
[AMBER] Protein_ligand_preparation_general_rule
(Tue Aug 28 2018 - 05:59:28 PDT)
Re: [AMBER] implement_revised_RNA_force_field_general rule?
(Sun Aug 19 2018 - 04:41:52 PDT)
Re: [AMBER] implement_revised_RNA_force_field_general rule?
(Sat Aug 18 2018 - 09:59:45 PDT)
[AMBER] implement_revised_RNA_force_field_general rule?
(Thu Aug 16 2018 - 01:57:47 PDT)
Re: [AMBER] tleap_protein_preparation_general_rule
(Tue Aug 14 2018 - 14:41:27 PDT)
Re: [AMBER] tleap_protein_preparation_general_rule
(Tue Aug 14 2018 - 11:20:17 PDT)
[AMBER] tleap_protein_preparation_general_rule
(Tue Aug 14 2018 - 01:06:07 PDT)
Re: [AMBER] .frcmod_file_generation
(Tue Aug 07 2018 - 22:59:40 PDT)
Re: [AMBER] counterions_automatic
(Tue Aug 07 2018 - 07:59:26 PDT)
[AMBER] .frcmod_file_generation
(Tue Aug 07 2018 - 07:57:39 PDT)
[AMBER] counterions_automatic
(Sun Aug 05 2018 - 08:56:50 PDT)
Anuja Ware
[AMBER] Parameters for non-standard residues
(Mon Aug 06 2018 - 02:49:13 PDT)
Aravind Ravichandran
[AMBER] MG Coordination System: Nonbonded Cationic Dummy Model
(Sun Aug 26 2018 - 22:57:15 PDT)
[AMBER] Amber Installation: MPI Error
(Fri Aug 10 2018 - 00:07:24 PDT)
Atila Petrosian
[AMBER] miRNA-mRNA structure / NAB
(Thu Aug 09 2018 - 08:59:49 PDT)
Re: [AMBER] RES: error_antechamber (QMMM: ERROR!)
(Fri Aug 03 2018 - 12:28:07 PDT)
[AMBER] error_antechamber (QMMM: ERROR!)
(Fri Aug 03 2018 - 08:52:17 PDT)
[AMBER] error_antechamber (QMMM: ERROR!)
(Fri Aug 03 2018 - 07:11:30 PDT)
ATUL KUMAR
Re: [AMBER] Solute-solvent hydrogen bond lifetime
(Tue Aug 07 2018 - 00:03:29 PDT)
[AMBER] Solute-solvent hydrogen bond lifetime
(Fri Aug 03 2018 - 06:01:36 PDT)
Bellesis, Andrew G
[AMBER] The R.E.D. server is down
(Wed Aug 29 2018 - 09:36:01 PDT)
Bharat Manna
[AMBER] Need help regarding calculation of Coordination number from RDF Profile
(Fri Aug 24 2018 - 03:21:02 PDT)
[AMBER] Need help regarding Lifetime Curve of Hydrogen bond analysis
(Wed Aug 22 2018 - 22:32:25 PDT)
Bill Ross
Re: [AMBER] Amber16 installation error
(Mon Aug 27 2018 - 17:07:35 PDT)
Re: [AMBER] Problems with constant pH production step
(Thu Aug 23 2018 - 01:25:46 PDT)
Re: [AMBER] Umbrella sampling run error
(Mon Aug 20 2018 - 22:44:46 PDT)
BLEY Michael
[AMBER] Velocity Format in AMBER
(Thu Aug 02 2018 - 06:58:24 PDT)
Carlos Simmerling
Re: [AMBER] A part of protein molecule moving out of the box
(Mon Aug 27 2018 - 05:49:48 PDT)
Re: [AMBER] Fwd: Issue with imploding structure during heating and equilibration
(Thu Aug 02 2018 - 05:18:22 PDT)
Charles-Alexandre Mattelaer
Re: [AMBER] Multiple PDB files to a MDCRD file
(Wed Aug 01 2018 - 09:22:17 PDT)
Charo del Genio
Re: [AMBER] cpptraj segmentation fault when using avgout in cluster
(Tue Aug 21 2018 - 10:21:36 PDT)
[AMBER] cpptraj segmentation fault when using avgout in cluster
(Thu Aug 16 2018 - 03:55:11 PDT)
Chetna Tyagi
[AMBER] number of interconversions from free energy landscape (FEL) plot
(Wed Aug 08 2018 - 05:54:17 PDT)
Chris Neale
Re: [AMBER] Change in boxlength during memebrane simulation
(Fri Aug 03 2018 - 15:50:40 PDT)
Corinn Durham
[AMBER] RED SERVER DOWN
(Wed Aug 29 2018 - 09:44:23 PDT)
Cruzeiro,Vinicius Wilian D
Re: [AMBER] Problems with constant pH production step
(Fri Aug 24 2018 - 03:11:30 PDT)
Re: [AMBER] Problems with constant pH production step
(Fri Aug 24 2018 - 01:52:42 PDT)
Daniel Roe
Re: [AMBER] How to use cpptraj to wrap protein
(Fri Aug 31 2018 - 16:31:57 PDT)
Re: [AMBER] CPPTRAJ issues parsing NETCDF RST file
(Thu Aug 30 2018 - 08:43:43 PDT)
Re: [AMBER] H-bond between the substrate molecule and protein in the MD traj
(Thu Aug 30 2018 - 06:34:51 PDT)
Re: [AMBER] Need help regarding Lifetime Curve of Hydrogen bond analysis
(Thu Aug 30 2018 - 06:15:52 PDT)
Re: [AMBER] How to use cpptraj to wrap protein
(Thu Aug 30 2018 - 05:59:36 PDT)
Re: [AMBER] CPPTRAJ issues parsing NETCDF RST file
(Thu Aug 30 2018 - 05:46:59 PDT)
Re: [AMBER] GIST calculation
(Tue Aug 28 2018 - 09:30:00 PDT)
Re: [AMBER] Amber 18 targeted MD errorin input::atommask.f::pop_evalstack stack underflow
(Mon Aug 27 2018 - 09:38:45 PDT)
Re: [AMBER] Need help regarding calculation of Coordination number from RDF Profile
(Fri Aug 24 2018 - 10:02:34 PDT)
Re: [AMBER] # of Coordinates Mismatch in PCA
(Tue Aug 21 2018 - 09:29:22 PDT)
Re: [AMBER] cpptraj segmentation fault when using avgout in cluster
(Tue Aug 21 2018 - 08:27:08 PDT)
Re: [AMBER] # of Coordinates Mismatch in PCA
(Tue Aug 21 2018 - 06:39:30 PDT)
Re: [AMBER] Warning: DISABLING BOX in topology '<name>.pdb'!
(Mon Aug 20 2018 - 11:12:05 PDT)
Re: [AMBER] Multiple trajectory analysis with CPPTRAJ and getting output for each of them separately
(Mon Aug 20 2018 - 11:07:24 PDT)
Re: [AMBER] cpptraj / ambpdb only selected atoms / residues
(Thu Aug 09 2018 - 11:19:35 PDT)
Re: [AMBER] Cpptraj not working
(Thu Aug 09 2018 - 09:37:09 PDT)
Re: [AMBER] cpptraj / ambpdb only selected atoms / residues
(Thu Aug 09 2018 - 09:23:54 PDT)
Re: [AMBER] how to install PTRAJ and CPPTRAJ
(Thu Aug 09 2018 - 06:30:08 PDT)
Re: [AMBER] Solute-solvent hydrogen bond lifetime
(Mon Aug 06 2018 - 06:18:27 PDT)
Re: [AMBER] Eigenvalues from PCA in cpptraj
(Wed Aug 01 2018 - 09:59:16 PDT)
Re: [AMBER] Multiple PDB files to a MDCRD file
(Wed Aug 01 2018 - 09:44:30 PDT)
Re: [AMBER] Multiple PDB files to a MDCRD file
(Wed Aug 01 2018 - 09:15:12 PDT)
Re: [AMBER] Eigenvalues from PCA in cpptraj
(Wed Aug 01 2018 - 09:12:48 PDT)
David A Case
Re: [AMBER] Heating error in complex
(Fri Aug 31 2018 - 06:47:36 PDT)
Re: [AMBER] Heating error in complex
(Thu Aug 30 2018 - 05:55:57 PDT)
Re: [AMBER] Protein_ligand_preparation_general_rule
(Tue Aug 28 2018 - 14:35:25 PDT)
Re: [AMBER] Amber16 installation error
(Mon Aug 27 2018 - 18:04:03 PDT)
Re: [AMBER] Error: System density has likely changed
(Mon Aug 27 2018 - 05:08:53 PDT)
Re: [AMBER] Amber18 error: an illegal memory access was encountered launching kernel kNLSkinTest
(Sun Aug 26 2018 - 06:10:01 PDT)
Re: [AMBER] restraintmask input setup
(Thu Aug 23 2018 - 05:10:58 PDT)
Re: [AMBER] Umbrella sampling rst file error
(Thu Aug 23 2018 - 05:04:02 PDT)
Re: [AMBER] Scripting Bash to tleap
(Mon Aug 20 2018 - 04:39:57 PDT)
Re: [AMBER] implement_revised_RNA_force_field_general rule?
(Sat Aug 18 2018 - 17:01:22 PDT)
[AMBER] update to Amber18's pmemd.cuda code
(Sat Aug 18 2018 - 06:08:35 PDT)
Re: [AMBER] Error in Running heating in GPU enabled AMBER
(Fri Aug 17 2018 - 18:28:41 PDT)
Re: [AMBER] Where is the source code adjusting the size of the periodic boundary condition box in NPT ensemble ?
(Fri Aug 17 2018 - 06:34:22 PDT)
Re: [AMBER] TLEAP script
(Fri Aug 17 2018 - 06:29:37 PDT)
Re: [AMBER] Mutation Free Energy
(Fri Aug 17 2018 - 06:21:48 PDT)
Re: [AMBER] About calculating entropy in MM_PB/GBSA using mm_pbsa.pl
(Fri Aug 17 2018 - 06:12:45 PDT)
Re: [AMBER] implement_revised_RNA_force_field_general rule?
(Thu Aug 16 2018 - 08:57:49 PDT)
Re: [AMBER] AM1BCC challenge with atomic types recognition and convertion of .ac to .mol2
(Thu Aug 16 2018 - 08:46:20 PDT)
Re: [AMBER] HOW to type a free CYS molecule
(Wed Aug 15 2018 - 09:48:56 PDT)
Re: [AMBER] RDCs in pmemd?
(Tue Aug 14 2018 - 08:03:03 PDT)
Re: [AMBER] QM/MM Thermodynamic Integration
(Tue Aug 14 2018 - 07:37:09 PDT)
Re: [AMBER] tleap_protein_preparation_general_rule
(Tue Aug 14 2018 - 07:33:22 PDT)
Re: [AMBER] command not found
(Fri Aug 10 2018 - 05:14:22 PDT)
Re: [AMBER] Amber Installation: MPI Error
(Fri Aug 10 2018 - 05:10:56 PDT)
Re: [AMBER] miRNA-mRNA structure / NAB
(Thu Aug 09 2018 - 11:18:25 PDT)
Re: [AMBER] Speeding up sqm, PM6 vs AM1 for am1-bcc
(Wed Aug 08 2018 - 11:59:07 PDT)
Re: [AMBER] checkmolecule.c
(Wed Aug 08 2018 - 11:56:04 PDT)
Re: [AMBER] checkmolecule.c
(Wed Aug 08 2018 - 11:35:50 PDT)
Re: [AMBER] problem with amber 16
(Wed Aug 08 2018 - 06:41:51 PDT)
Re: [AMBER] max# cpu's for sander, specify which gpu runs a job
(Tue Aug 07 2018 - 13:19:26 PDT)
Re: [AMBER] .frcmod_file_generation
(Tue Aug 07 2018 - 13:07:52 PDT)
Re: [AMBER] Parameters for non-standard residues
(Mon Aug 06 2018 - 05:04:12 PDT)
Re: [AMBER] Adding box dimension
(Mon Aug 06 2018 - 05:00:41 PDT)
Re: [AMBER] Error for Amber16 and Amber tools 17 installation
(Sat Aug 04 2018 - 06:41:34 PDT)
Re: [AMBER] Velocity Format in AMBER
(Thu Aug 02 2018 - 09:21:56 PDT)
Re: [AMBER] Multiple PDB files to a MDCRD file
(Wed Aug 01 2018 - 17:09:28 PDT)
David Cerutti
Re: [AMBER] Error: System density has likely changed
(Mon Aug 27 2018 - 10:51:49 PDT)
Re: [AMBER] Error: System density has likely changed
(Mon Aug 27 2018 - 10:49:14 PDT)
Re: [AMBER] amber18 and amazon aws
(Mon Aug 13 2018 - 08:57:32 PDT)
Re: [AMBER] Amber18 on NVIDIA Quadro Cards
(Wed Aug 08 2018 - 10:48:01 PDT)
Re: [AMBER] Adding box dimension
(Mon Aug 06 2018 - 11:50:14 PDT)
Re: [AMBER] Change in boxlength during memebrane simulation
(Fri Aug 03 2018 - 17:07:33 PDT)
Re: [AMBER] Change in boxlength during memebrane simulation
(Fri Aug 03 2018 - 15:22:06 PDT)
Re: [AMBER] Change in boxlength during memebrane simulation
(Fri Aug 03 2018 - 08:19:00 PDT)
Re: [AMBER] GPUs
(Wed Aug 01 2018 - 16:13:10 PDT)
David Christopher Schröder
Re: [AMBER] max# cpu's for sander, specify which gpu runs a job
(Tue Aug 14 2018 - 00:28:32 PDT)
[AMBER] max# cpu's for sander, specify which gpu runs a job
(Tue Aug 07 2018 - 09:40:56 PDT)
David Stevens
[AMBER] Fwd: Issue with imploding structure during heating and equilibration
(Wed Aug 01 2018 - 10:45:46 PDT)
David Sáez
[AMBER] Distance HH TIP3P
(Fri Aug 31 2018 - 12:55:49 PDT)
Debarati DasGupta
[AMBER] Restraints on a system
(Tue Aug 07 2018 - 14:15:06 PDT)
Re: [AMBER] Running a small minimization with amber 16 package
(Mon Aug 06 2018 - 14:38:36 PDT)
Dickson, Callum
Re: [AMBER] alkyl chain unsaturated bond
(Thu Aug 16 2018 - 07:16:44 PDT)
Re: [AMBER] alkyl chain unsaturated bond
(Mon Aug 13 2018 - 07:03:18 PDT)
Re: [AMBER] Erreneous PMF
(Fri Aug 10 2018 - 10:53:16 PDT)
Re: [AMBER] Erreneous PMF
(Thu Aug 09 2018 - 06:21:22 PDT)
Dmitry Suplatov
[AMBER] Warning: DISABLING BOX in topology '<name>.pdb'!
(Sun Aug 12 2018 - 04:04:19 PDT)
elias_christoforides
Re: [AMBER] Thank you
(Mon Aug 27 2018 - 06:57:28 PDT)
emanuele
[AMBER] QM/MM Thermodynamic Integration
(Tue Aug 14 2018 - 03:44:46 PDT)
emanuele falbo
Re: [AMBER] QM/MM link atoms
(Thu Aug 02 2018 - 07:59:08 PDT)
Eric Lang
Re: [AMBER] Constant pH simulation in explicit solvent
(Wed Aug 01 2018 - 03:19:53 PDT)
Feng Pan
Re: [AMBER] Steered molecular dynamics..... pulling force is not decreasing
(Fri Aug 31 2018 - 15:14:33 PDT)
Re: [AMBER] NCSU_SMD for protein-ligand complex pulling
(Sat Aug 25 2018 - 09:11:21 PDT)
Re: [AMBER] ASMD for decrease in distance between ligand and catalytic site
(Tue Aug 21 2018 - 20:35:23 PDT)
Re: [AMBER] COM pulling in direction
(Tue Aug 07 2018 - 05:54:52 PDT)
Gerald Monard
Re: [AMBER] SCF convergence problems and write density matrix
(Sat Aug 18 2018 - 00:55:01 PDT)
giovanna rogati
Re: [AMBER] problem with amber 16
(Wed Aug 15 2018 - 23:04:20 PDT)
[AMBER] problem with amber 16
(Wed Aug 08 2018 - 01:29:38 PDT)
Goetz, Andreas
Re: [AMBER] Problem with QMMM with Amber/Gaussian interface.
(Tue Aug 14 2018 - 22:33:57 PDT)
Re: [AMBER] error_antechamber (QMMM: ERROR!)
(Fri Aug 03 2018 - 10:57:31 PDT)
Re: [AMBER] QM/MM link atoms
(Thu Aug 02 2018 - 15:46:30 PDT)
Re: [AMBER] QM/MM link atoms
(Thu Aug 02 2018 - 12:14:19 PDT)
Gustaf Olsson
Re: [AMBER] CPPTRAJ issues parsing NETCDF RST file
(Thu Aug 30 2018 - 23:20:07 PDT)
Re: [AMBER] CPPTRAJ issues parsing NETCDF RST file
(Thu Aug 30 2018 - 07:35:15 PDT)
[AMBER] CPPTRAJ issues parsing NETCDF RST file
(Thu Aug 30 2018 - 05:20:09 PDT)
Gustavo Seabra
Re: [AMBER] error_antechamber (QMMM: ERROR!)
(Fri Aug 03 2018 - 08:23:28 PDT)
Re: [AMBER] QM/MM link atoms
(Thu Aug 02 2018 - 08:25:00 PDT)
gustavo.seabra.gmail.com
[AMBER] RES: error_antechamber (QMMM: ERROR!)
(Fri Aug 03 2018 - 11:56:45 PDT)
Hai Nguyen
Re: [AMBER] cpptraj and ptraj not installed
(Sun Aug 19 2018 - 08:04:40 PDT)
Helena Damtoft Tjørnelund
Re: [AMBER] Problems with constant pH production step
(Fri Aug 24 2018 - 02:47:18 PDT)
Re: [AMBER] Problems with constant pH production step
(Thu Aug 23 2018 - 23:41:15 PDT)
[AMBER] Problems with constant pH production step
(Thu Aug 23 2018 - 01:18:27 PDT)
hosein geraili
[AMBER] Mutation Free Energy
(Fri Aug 17 2018 - 03:28:22 PDT)
I Lőrincz
Re: [AMBER] Reading grid data from standard datafile
(Fri Aug 03 2018 - 10:35:38 PDT)
James Kress
Re: [AMBER] QM/MM Thermodynamic Integration
(Tue Aug 14 2018 - 08:16:45 PDT)
Re: [AMBER] Amber18 on NVIDIA Quadro Cards
(Wed Aug 08 2018 - 12:13:27 PDT)
Re: [AMBER] Amber18 on NVIDIA Quadro Cards
(Wed Aug 08 2018 - 10:22:54 PDT)
Re: [AMBER] QM/MM link atoms
(Thu Aug 02 2018 - 14:12:53 PDT)
Jason Swails
Re: [AMBER] Problems with constant pH production step
(Fri Aug 24 2018 - 07:25:12 PDT)
Re: [AMBER] Problems with constant pH production step
(Thu Aug 23 2018 - 07:48:45 PDT)
Re: [AMBER] # of Coordinates Mismatch in PCA
(Tue Aug 21 2018 - 15:15:07 PDT)
Re: [AMBER] # of Coordinates Mismatch in PCA
(Mon Aug 20 2018 - 19:54:01 PDT)
Re: [AMBER] PrmtopError: Inconsistent charge definition for atom
(Tue Aug 14 2018 - 19:27:45 PDT)
Re: [AMBER] MMPBSA.PY
(Tue Aug 14 2018 - 19:20:33 PDT)
Re: [AMBER] # of Coordinates Mismatch in PCA
(Tue Aug 14 2018 - 16:55:05 PDT)
Re: [AMBER] very slow implicit simulation on GPU!!!
(Wed Aug 01 2018 - 14:22:54 PDT)
Re: [AMBER] Possible bug on addLJType command of Parmed
(Wed Aug 01 2018 - 14:20:07 PDT)
Jinfeng Chen
[AMBER] MCPB.py with G09 rev. B.01
(Thu Aug 02 2018 - 18:26:49 PDT)
jinfeng liu
Re: [AMBER] Where is the source code adjusting the size of the periodic boundary condition box in NPT ensemble ?
(Fri Aug 17 2018 - 07:04:58 PDT)
[AMBER] Where is the source code adjusting the size of the periodic boundary condition box in NPT ensemble ?
(Fri Aug 17 2018 - 01:15:40 PDT)
Johannes Kalliauer
[AMBER] mistake in source-code in egb.F90
(Thu Aug 09 2018 - 04:15:45 PDT)
John Kulp
Re: [AMBER] checkmolecule.c
(Thu Aug 16 2018 - 05:35:27 PDT)
John L. Kulp, Jr.
[AMBER] Speeding up sqm, PM6 vs AM1 for am1-bcc
(Wed Aug 08 2018 - 06:13:14 PDT)
[AMBER] checkmolecule.c
(Wed Aug 08 2018 - 06:10:13 PDT)
Josh Berryman
Re: [AMBER] Error for Amber16 and Amber tools 17 installation
(Fri Aug 03 2018 - 12:34:42 PDT)
João Ribeiro
[AMBER] Research Programmers Positions Available
(Fri Aug 10 2018 - 11:35:23 PDT)
Junmei Wang
Re: [AMBER] Parameters for non-standard residues
(Mon Aug 06 2018 - 05:57:13 PDT)
Kasprzak, Wojciech (NIH/NCI) [C]
[AMBER] How to calculate SASA for an arbitrary solvent
(Mon Aug 20 2018 - 13:37:19 PDT)
Keiran Corbett
Re: [AMBER] Protein_ligand_preparation_general_rule
(Tue Aug 28 2018 - 06:41:51 PDT)
[AMBER] Scripting Bash to tleap
(Mon Aug 20 2018 - 02:39:32 PDT)
Re: [AMBER] TLEAP script
(Mon Aug 20 2018 - 02:20:34 PDT)
[AMBER] TLEAP script
(Fri Aug 17 2018 - 03:58:59 PDT)
Kenneth Huang
Re: [AMBER] # of Coordinates Mismatch in PCA
(Tue Aug 14 2018 - 13:20:34 PDT)
Re: [AMBER] # of Coordinates Mismatch in PCA
(Sun Aug 12 2018 - 20:21:38 PDT)
Kevin Keane (USD)
Re: [AMBER] Error for Amber16 and Amber tools 17 installation
(Sun Aug 05 2018 - 00:03:41 PDT)
kuldeep singh
[AMBER] Error in Running heating in GPU enabled AMBER
(Fri Aug 17 2018 - 10:50:02 PDT)
Leena Aggarwal
[AMBER] sander.MPI running on only one node
(Sat Aug 11 2018 - 03:01:15 PDT)
Leon Hardy
[AMBER] Best Methods
(Mon Aug 27 2018 - 06:01:58 PDT)
Lod King
[AMBER] restraintmask input setup
(Wed Aug 22 2018 - 18:26:43 PDT)
Luca Codutti
Re: [AMBER] amber18 and amazon aws
(Wed Aug 22 2018 - 03:45:47 PDT)
[AMBER] amber18 and amazon aws
(Mon Aug 13 2018 - 08:37:44 PDT)
Luka Bilić
[AMBER] Multiple trajectory analysis with CPPTRAJ and getting output for each of them separately
(Thu Aug 16 2018 - 00:06:23 PDT)
M RCC
[AMBER] Steered molecular dynamics..... pulling force is not decreasing
(Thu Aug 30 2018 - 03:01:51 PDT)
[AMBER] How to define the speed of pulling ligand in SMD?
(Wed Aug 29 2018 - 06:39:41 PDT)
[AMBER] Error: System density has likely changed
(Mon Aug 27 2018 - 02:40:07 PDT)
[AMBER] GIST calculation
(Sun Aug 26 2018 - 23:32:07 PDT)
[AMBER] NCSU_SMD for protein-ligand complex pulling
(Sat Aug 25 2018 - 08:15:08 PDT)
[AMBER] Umbrella sampling rst file error
(Wed Aug 22 2018 - 12:02:38 PDT)
malkeet singh Bahia
Re: [AMBER] Amber18 on NVIDIA Quadro Cards
(Thu Aug 09 2018 - 02:09:27 PDT)
Marcelo Andrade Chagas
Re: [AMBER] Cpptraj not working
(Thu Aug 09 2018 - 04:52:16 PDT)
Marek Maly
[AMBER] X-mer analysis or statistics ?
(Thu Aug 09 2018 - 16:49:29 PDT)
Marko Tomin
[AMBER] Normal mode calculation on a truncated system
(Thu Aug 30 2018 - 08:13:33 PDT)
Markowska
[AMBER] How to use filter command to find the structures of high density during PCA analysis?
(Fri Aug 10 2018 - 05:08:41 PDT)
maryam azimzadehirani
[AMBER] Can I calculate the domain-domain interaction energy using the MMPBSA.py tool?
(Mon Aug 13 2018 - 03:35:43 PDT)
Re: [AMBER] Error for Amber16 and Amber tools 17 installation
(Tue Aug 07 2018 - 05:56:28 PDT)
Re: [AMBER] Error for Amber16 and Amber tools 17 installation
(Sat Aug 04 2018 - 03:19:12 PDT)
[AMBER] Error for Amber16 and Amber tools 17 installation
(Fri Aug 03 2018 - 05:16:11 PDT)
Matias Machado
Re: [AMBER] implement_revised_RNA_force_field_general rule?
(Thu Aug 16 2018 - 08:09:58 PDT)
Re: [AMBER] HOW to type a free CYS molecule
(Wed Aug 15 2018 - 14:59:18 PDT)
Re: [AMBER] tleap_protein_preparation_general_rule
(Tue Aug 14 2018 - 13:48:08 PDT)
Re: [AMBER] Restraints on a system
(Sat Aug 11 2018 - 13:11:48 PDT)
Re: [AMBER] Restraints on a system
(Sat Aug 11 2018 - 13:06:43 PDT)
Re: [AMBER] sander.MPI running on only one node
(Sat Aug 11 2018 - 08:20:20 PDT)
Re: [AMBER] counterions_automatic
(Sun Aug 05 2018 - 13:31:24 PDT)
Re: [AMBER] Amber16 Installation error
(Fri Aug 03 2018 - 05:08:17 PDT)
Re: [AMBER] Amber16 Installation error
(Fri Aug 03 2018 - 05:04:44 PDT)
Re: [AMBER] Amber16 Installation error
(Fri Aug 03 2018 - 04:38:15 PDT)
Re: [AMBER] Possible bug on addLJType command of Parmed
(Thu Aug 02 2018 - 12:52:06 PDT)
Meng Wu
[AMBER] H-bond between the substrate molecule and protein in the MD traj
(Wed Aug 22 2018 - 01:18:13 PDT)
Re: [AMBER] COM pulling in direction
(Tue Aug 07 2018 - 18:59:31 PDT)
[AMBER] COM pulling in direction
(Mon Aug 06 2018 - 18:51:28 PDT)
Re: [AMBER] COM pulling in direction
(Sat Aug 04 2018 - 02:08:56 PDT)
[AMBER] COM pulling in direction
(Fri Aug 03 2018 - 02:52:24 PDT)
MinYuan
[AMBER] How to convert QM parameters to AMBER force field parameters
(Sat Aug 18 2018 - 06:40:40 PDT)
Re: [AMBER] HOW to type a free CYS molecule
(Wed Aug 15 2018 - 19:38:04 PDT)
Re: [AMBER] HOW to type a free CYS molecule
(Wed Aug 15 2018 - 19:26:00 PDT)
[AMBER] HOW to type a free CYS molecule
(Wed Aug 15 2018 - 06:57:13 PDT)
mish
Re: [AMBER] Amber18 on NVIDIA Quadro Cards
(Fri Aug 10 2018 - 04:01:41 PDT)
Re: [AMBER] Amber18 on NVIDIA Quadro Cards
(Thu Aug 09 2018 - 02:10:14 PDT)
Re: [AMBER] Amber18 on NVIDIA Quadro Cards
(Thu Aug 09 2018 - 01:54:41 PDT)
[AMBER] Amber18 on NVIDIA Quadro Cards
(Wed Aug 08 2018 - 08:51:02 PDT)
Nikolay N. Kuzmich
[AMBER] System density decrease during accelerated MD: why?
(Thu Aug 02 2018 - 07:13:59 PDT)
Re: [AMBER] Constant pH simulation in explicit solvent
(Thu Aug 02 2018 - 03:32:35 PDT)
[AMBER] Constant pH simulation in explicit solvent
(Wed Aug 01 2018 - 02:32:06 PDT)
Nisha Amarnath Jonniya
Re: [AMBER] A question about tleap
(Tue Aug 14 2018 - 01:50:04 PDT)
Pengfei Li
Re: [AMBER] MCPB.py with G09 rev. B.01
(Tue Aug 07 2018 - 12:16:31 PDT)
Qinghua Liao
Re: [AMBER] MG Coordination System: Nonbonded Cationic Dummy Model
(Mon Aug 27 2018 - 02:29:26 PDT)
Rakesh Srivastava
Re: [AMBER] Umbrella sampling run error
(Mon Aug 20 2018 - 23:23:28 PDT)
[AMBER] Umbrella sampling run error
(Mon Aug 20 2018 - 21:43:37 PDT)
Renato Araujo
Re: [AMBER] Amber16 installation error
(Mon Aug 27 2018 - 17:35:08 PDT)
Re: [AMBER] Amber16 installation error
(Mon Aug 27 2018 - 17:13:47 PDT)
[AMBER] Amber16 installation error
(Mon Aug 27 2018 - 16:50:44 PDT)
Robert Molt
Re: [AMBER] # of Coordinates Mismatch in PCA
(Tue Aug 21 2018 - 09:57:35 PDT)
Re: [AMBER] # of Coordinates Mismatch in PCA
(Tue Aug 21 2018 - 09:09:43 PDT)
Re: [AMBER] # of Coordinates Mismatch in PCA
(Mon Aug 20 2018 - 13:50:18 PDT)
Re: [AMBER] # of Coordinates Mismatch in PCA
(Tue Aug 14 2018 - 18:21:41 PDT)
Re: [AMBER] # of Coordinates Mismatch in PCA
(Mon Aug 13 2018 - 18:07:24 PDT)
[AMBER] # of Coordinates Mismatch in PCA
(Sat Aug 11 2018 - 22:04:35 PDT)
Rodrigo Galindo-Murillo
Re: [AMBER] how to install PTRAJ and CPPTRAJ
(Thu Aug 09 2018 - 00:27:39 PDT)
Ross Walker
Re: [AMBER] Amber18 on NVIDIA Quadro Cards
(Thu Aug 09 2018 - 06:56:20 PDT)
Re: [AMBER] Amber18 on NVIDIA Quadro Cards
(Thu Aug 09 2018 - 06:40:16 PDT)
Re: [AMBER] Amber18 on NVIDIA Quadro Cards
(Wed Aug 08 2018 - 11:53:49 PDT)
Re: [AMBER] Amber18 on NVIDIA Quadro Cards
(Wed Aug 08 2018 - 11:52:50 PDT)
Re: [AMBER] Amber18 on NVIDIA Quadro Cards
(Wed Aug 08 2018 - 09:55:17 PDT)
Sadra Aghajani
Re: [AMBER] SCF convergence problems and write density matrix
(Sat Aug 18 2018 - 09:34:38 PDT)
[AMBER] Problem with QMMM with Amber/Gaussian interface.
(Tue Aug 14 2018 - 20:53:47 PDT)
Saikat Pal
[AMBER] I want to calculate electrostatic and van der Waals energy
(Wed Aug 29 2018 - 03:44:03 PDT)
[AMBER] Are there any forcefield present of bio-organic polyphosphate in AMBER ??
(Mon Aug 27 2018 - 08:10:06 PDT)
Sally Pias
Re: [AMBER] Change in boxlength during memebrane simulation
(Fri Aug 10 2018 - 15:13:08 PDT)
Re: [AMBER] Change in boxlength during memebrane simulation
(Fri Aug 03 2018 - 14:55:35 PDT)
sandeep singh
Re: [AMBER] Heating error in complex
(Thu Aug 30 2018 - 13:37:23 PDT)
[AMBER] Heating error in complex
(Wed Aug 29 2018 - 12:52:45 PDT)
sangita kachhap
Re: [AMBER] ASMD for decrease in distance between ligand and catalytic site
(Wed Aug 22 2018 - 03:59:22 PDT)
[AMBER] ASMD for decrease in distance between ligand and catalytic site
(Tue Aug 21 2018 - 03:42:04 PDT)
Sanjib Paul
[AMBER] A part of protein molecule moving out of the box
(Sun Aug 26 2018 - 23:16:36 PDT)
Santanu Santra
[AMBER] PrmtopError: Inconsistent charge definition for atom
(Thu Aug 09 2018 - 06:40:08 PDT)
Scott Brozell
Re: [AMBER] checkmolecule.c
(Wed Aug 15 2018 - 10:48:41 PDT)
Re: [AMBER] Running a small minimization with amber 16 package
(Mon Aug 06 2018 - 16:42:16 PDT)
Seibold, Steve Allan
[AMBER] metalParm2.xml or metalParm.xml
(Mon Aug 20 2018 - 08:47:27 PDT)
Re: [AMBER] MCBP force constants
(Wed Aug 01 2018 - 08:18:14 PDT)
Sergey Samsonov
Re: [AMBER] AM1BCC challenge with atomic types recognition and convertion of .ac to .mol2
(Fri Aug 17 2018 - 00:03:21 PDT)
[AMBER] AM1BCC challenge with atomic types recognition and convertion of .ac to .mol2
(Thu Aug 16 2018 - 08:05:29 PDT)
Setyanto Md
[AMBER] asking about PBRadii in MMPBSA an other else
(Wed Aug 01 2018 - 04:49:16 PDT)
Simon Kit Sang Chu
Re: [AMBER] cpptraj / ambpdb only selected atoms / residues
(Thu Aug 09 2018 - 10:30:54 PDT)
[AMBER] cpptraj / ambpdb only selected atoms / residues
(Thu Aug 09 2018 - 09:04:36 PDT)
Re: [AMBER] Adding box dimension
(Mon Aug 06 2018 - 05:04:14 PDT)
[AMBER] Adding box dimension
(Sun Aug 05 2018 - 09:31:19 PDT)
somdev pahari
Re: [AMBER] Change in boxlength during memebrane simulation
(Fri Aug 03 2018 - 10:05:05 PDT)
[AMBER] Change in boxlength during memebrane simulation
(Fri Aug 03 2018 - 07:59:19 PDT)
Stefan Ivanov
Re: [AMBER] Erreneous PMF
(Fri Aug 10 2018 - 16:57:20 PDT)
Re: [AMBER] Erreneous PMF
(Thu Aug 09 2018 - 18:31:15 PDT)
[AMBER] Erreneous PMF
(Wed Aug 08 2018 - 23:21:14 PDT)
Steven Ramsey
Re: [AMBER] GIST calculation
(Tue Aug 28 2018 - 08:31:02 PDT)
Subrata Paul
[AMBER] cpptraj and ptraj not installed
(Sun Aug 19 2018 - 04:49:54 PDT)
Re: [AMBER] Cpptraj not working
(Thu Aug 09 2018 - 09:33:42 PDT)
[AMBER] Cpptraj not working
(Thu Aug 09 2018 - 03:38:53 PDT)
Re: [AMBER] how to install PTRAJ and CPPTRAJ
(Thu Aug 09 2018 - 00:36:39 PDT)
[AMBER] how to install PTRAJ and CPPTRAJ
(Thu Aug 09 2018 - 00:17:30 PDT)
Supriyo Bhattacharya
[AMBER] Reproduce part of AMBER trajectory
(Wed Aug 01 2018 - 16:36:03 PDT)
Sushi Shilpa
[AMBER] command not found
(Fri Aug 10 2018 - 04:47:41 PDT)
Re: [AMBER] Amber16 Installation error
(Fri Aug 03 2018 - 23:43:37 PDT)
Re: [AMBER] Amber16 Installation error
(Fri Aug 03 2018 - 05:15:08 PDT)
Re: [AMBER] Amber16 Installation error
(Fri Aug 03 2018 - 05:14:15 PDT)
Re: [AMBER] Amber16 Installation error
(Fri Aug 03 2018 - 04:44:20 PDT)
[AMBER] Amber16 Installation error
(Fri Aug 03 2018 - 03:46:33 PDT)
Szymon Żaczek
Re: [AMBER] minimization restrain in Qm-mm/MD
(Thu Aug 30 2018 - 13:29:30 PDT)
Tai Tze Hong
[AMBER] Thank you
(Fri Aug 24 2018 - 19:10:56 PDT)
Thakur, Abhishek
[AMBER] minimization restrain in Qm-mm/MD
(Thu Aug 30 2018 - 12:05:50 PDT)
Thomas Exner
Re: [AMBER] eCheminfo Oxford 3-7 Sep., Training and Innovation Course in Drug Design, bursary and early-bird deadline approaching quickly
(Fri Aug 03 2018 - 04:07:56 PDT)
Thomas Pochapsky
[AMBER] RDCs in pmemd?
(Mon Aug 06 2018 - 09:02:32 PDT)
Tyler Luchko (Lists)
Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM
(Wed Aug 01 2018 - 15:55:25 PDT)
Vijay Achari
Re: [AMBER] alkyl chain unsaturated bond
(Thu Aug 16 2018 - 05:26:46 PDT)
[AMBER] alkyl chain unsaturated bond
(Sun Aug 12 2018 - 14:58:42 PDT)
[AMBER] Atom Types for carbons with unsaturated bond
(Mon Aug 06 2018 - 01:37:22 PDT)
Wesley Michael Botello-Smith
Re: [AMBER] Scripting Bash to tleap
(Mon Aug 20 2018 - 05:48:50 PDT)
Re: [AMBER] Scripting Bash to tleap
(Mon Aug 20 2018 - 05:45:04 PDT)
Yang, Tianyi
Re: [AMBER] How to use cpptraj to wrap protein
(Fri Aug 31 2018 - 13:04:10 PDT)
[AMBER] How to use cpptraj to wrap protein
(Wed Aug 29 2018 - 17:12:19 PDT)
Zhonghua Xia
Re: [AMBER] The instructions of the .out file
(Fri Aug 17 2018 - 06:19:34 PDT)
Re: [AMBER] Parameters for non-standard residues
(Mon Aug 06 2018 - 04:47:52 PDT)
李耀
[AMBER] Amber 18 targeted MD errorin input::atommask.f::pop_evalstack stack underflow
(Mon Aug 27 2018 - 00:24:27 PDT)
[AMBER] Amber18 error: an illegal memory access was encountered launching kernel kNLSkinTest
(Sat Aug 25 2018 - 06:22:32 PDT)
龚乾坤
[AMBER] MMPBSA.PY
(Fri Aug 17 2018 - 00:21:07 PDT)
[AMBER] About calculating entropy in MM_PB/GBSA using mm_pbsa.pl
(Fri Aug 17 2018 - 00:17:32 PDT)
[AMBER] A question about tleap
(Tue Aug 14 2018 - 01:01:56 PDT)
[AMBER] MMPBSA.PY
(Sun Aug 12 2018 - 19:37:37 PDT)
Last message date
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Fri Aug 31 2018 - 17:00:02 PDT
Archived on
: Wed Dec 25 2024 - 05:55:43 PST
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