Amber Archive Jul 2016 by author
558 messages
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Starting
Thu Jun 30 2016 - 18:30:02 PDT,
Ending
Sun Jul 31 2016 - 07:00:03 PDT
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ABHIJEET CHOWDHURY
Re: [AMBER] NAB
(Sat Jul 23 2016 - 06:23:04 PDT)
[AMBER] NAB
(Sat Jul 23 2016 - 05:02:06 PDT)
Adrian Roitberg
Re: [AMBER] ntr vs ibelly.
(Tue Jul 26 2016 - 03:28:16 PDT)
Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
(Mon Jul 25 2016 - 10:23:20 PDT)
Re: [AMBER] charmmlipid2amber not found
(Mon Jul 25 2016 - 09:14:31 PDT)
Re: [AMBER] Steered Molecular Dynamics
(Mon Jul 25 2016 - 00:06:11 PDT)
Re: [AMBER] SMD simulation protocols
(Sun Jul 24 2016 - 10:35:50 PDT)
Re: [AMBER] HMR 4fs failure?
(Fri Jul 15 2016 - 14:18:14 PDT)
Re: [AMBER] QM/MM problems with Amber/Gaussian
(Tue Jul 12 2016 - 08:17:23 PDT)
Re: [AMBER] Potential on each atom
(Tue Jul 05 2016 - 11:21:39 PDT)
Re: [AMBER] Potential on each atom
(Mon Jul 04 2016 - 09:23:33 PDT)
Albert
Re: [AMBER] where is amber.jupyter?
(Sat Jul 30 2016 - 01:59:30 PDT)
Re: [AMBER] where is amber.jupyter?
(Sat Jul 30 2016 - 01:35:19 PDT)
Re: [AMBER] where is amber.jupyter?
(Sat Jul 30 2016 - 01:32:47 PDT)
Re: [AMBER] where is amber.jupyter?
(Sat Jul 30 2016 - 00:59:24 PDT)
[AMBER] where is amber.jupyter?
(Sat Jul 30 2016 - 00:17:08 PDT)
[AMBER] figure legend problem in the tutorial?
(Fri Jul 29 2016 - 12:50:53 PDT)
Aleksandra Skoric
Re: [AMBER] Regarding Parameter file not saved
(Mon Jul 18 2016 - 06:21:31 PDT)
Alessandra Lacetera
Re: [AMBER] WHAM-2D analysis
(Thu Jul 14 2016 - 02:31:55 PDT)
[AMBER] WHAM-2D analysis
(Wed Jul 13 2016 - 09:55:20 PDT)
Alessandro Contini
Re: [AMBER] ff99SB*-ildn again
(Thu Jul 14 2016 - 02:57:24 PDT)
Allen Zou
[AMBER] QM/MM problems with Amber/Gaussian
(Tue Jul 12 2016 - 08:11:25 PDT)
Amy Rice
Re: [AMBER] Calculating lipid diffusion using stfcdiffusion
(Mon Jul 25 2016 - 09:24:04 PDT)
Re: [AMBER] Calculating lipid diffusion using stfcdiffusion
(Wed Jul 20 2016 - 11:57:32 PDT)
Re: [AMBER] Calculating lipid diffusion using stfcdiffusion
(Wed Jul 20 2016 - 11:34:14 PDT)
Re: [AMBER] Calculating lipid diffusion using stfcdiffusion
(Thu Jul 14 2016 - 09:13:57 PDT)
Re: [AMBER] WHAM-2D analysis
(Wed Jul 13 2016 - 10:02:03 PDT)
[AMBER] Calculating lipid diffusion using stfcdiffusion
(Thu Jul 07 2016 - 10:49:07 PDT)
Re: [AMBER] re-imaging bilayer
(Thu Jul 07 2016 - 09:12:48 PDT)
Andreas Goetz
Re: [AMBER] QM/MM simulations with Amber/deMon2k
(Thu Jul 07 2016 - 21:04:52 PDT)
ankita mehta
[AMBER] Hii
(Sun Jul 31 2016 - 06:22:34 PDT)
Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
(Mon Jul 25 2016 - 00:34:56 PDT)
Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
(Mon Jul 25 2016 - 00:32:58 PDT)
Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
(Sat Jul 23 2016 - 10:39:23 PDT)
Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
(Sat Jul 23 2016 - 01:09:16 PDT)
Anna Cebrian Prats
[AMBER] Question about QM/MM
(Fri Jul 29 2016 - 06:45:19 PDT)
[AMBER] Error cuda
(Tue Jul 26 2016 - 07:33:39 PDT)
[AMBER] CPPTRAJ
(Thu Jul 21 2016 - 03:30:20 PDT)
Re: [AMBER] MCPB.py - coordinate sphere FE
(Wed Jul 20 2016 - 07:35:15 PDT)
[AMBER] MCPB.py
(Wed Jul 20 2016 - 06:44:08 PDT)
[AMBER] MCPB.py - coordinate sphere FE
(Wed Jul 20 2016 - 05:44:01 PDT)
Re: [AMBER] NEW parameters with AMBER
(Thu Jul 14 2016 - 06:52:43 PDT)
[AMBER] NEW parameters with AMBER
(Thu Jul 14 2016 - 02:55:16 PDT)
Annie Ancy
[AMBER] REMD Reg
(Fri Jul 15 2016 - 04:23:18 PDT)
anu chandra
[AMBER] Exposed hydrophobic surface area
(Fri Jul 29 2016 - 16:50:43 PDT)
[AMBER] Binding deltaG in ligand pose selction
(Wed Jul 20 2016 - 09:14:03 PDT)
Re: [AMBER] Ligand RMSD
(Tue Jul 19 2016 - 07:59:01 PDT)
[AMBER] Ligand RMSD
(Mon Jul 18 2016 - 10:27:26 PDT)
Anwesha Sarkar
[AMBER] Creating topology file in MMPBSA
(Mon Jul 25 2016 - 05:51:35 PDT)
Atila Petrosian
[AMBER] Decomposition in minimization step
(Tue Jul 12 2016 - 23:14:57 PDT)
ATUL KUMAR
[AMBER] Gunning GIST in parallel
(Thu Jul 07 2016 - 03:05:07 PDT)
Re: [AMBER] Problem to extending Simulation
(Wed Jul 06 2016 - 23:23:27 PDT)
Re: [AMBER] Problem to extending Simulation
(Wed Jul 06 2016 - 06:43:27 PDT)
[AMBER] Problem to extending Simulation
(Wed Jul 06 2016 - 04:38:16 PDT)
[AMBER] Regarding GIST calculation
(Thu Jun 30 2016 - 22:51:58 PDT)
Bahaa Mostafa
Re: [AMBER] a question about resp restraints strength
(Sat Jul 16 2016 - 09:43:55 PDT)
Re: [AMBER] a question about resp restraints strength
(Thu Jul 14 2016 - 05:56:24 PDT)
[AMBER] a question about resp restraints strength
(Thu Jul 14 2016 - 04:10:27 PDT)
[AMBER] a question about resp restraints strength
(Thu Jul 14 2016 - 04:04:13 PDT)
[AMBER] a question about resp restraints strength
(Wed Jul 13 2016 - 05:40:44 PDT)
Barbault Florent
Re: [AMBER] ntr vs ibelly.
(Tue Jul 26 2016 - 03:56:24 PDT)
Re: [AMBER] ntr vs ibelly.
(Tue Jul 26 2016 - 03:13:21 PDT)
Beale, John
Re: [AMBER] Amber 16 Installation
(Mon Jul 18 2016 - 00:44:27 PDT)
[AMBER] Amber 16 Installation
(Mon Jul 18 2016 - 00:17:35 PDT)
bharat gupta
Re: [AMBER] AMBER Digest, Vol 1646, Issue 1
(Mon Jul 25 2016 - 22:21:49 PDT)
Re: [AMBER] Steered Molecular Dynamics
(Mon Jul 25 2016 - 00:00:26 PDT)
Re: [AMBER] SMD and free energy value
(Thu Jul 21 2016 - 07:20:47 PDT)
Re: [AMBER] Help with SMD
(Tue Jul 12 2016 - 01:02:31 PDT)
Re: [AMBER] Patching Plumed 1.3 with Amber12
(Thu Jul 07 2016 - 18:04:39 PDT)
Re: [AMBER] Defining reaction coordinate for US
(Thu Jul 07 2016 - 01:38:33 PDT)
Re: [AMBER] Help with Umbrella Sampling
(Tue Jul 05 2016 - 22:31:57 PDT)
Re: [AMBER] Error during amber 12 installation
(Tue Jul 05 2016 - 06:07:37 PDT)
Re: [AMBER] Umbrella Sampling
(Sat Jul 02 2016 - 06:19:45 PDT)
Re: [AMBER] Slow performance of Amber12 on cluster
(Thu Jun 30 2016 - 22:03:14 PDT)
Re: [AMBER] Umbrella Sampling
(Thu Jun 30 2016 - 22:00:58 PDT)
Bilal Nizami
Re: [AMBER] Sander bomb: how to create a larger box
(Sat Jul 30 2016 - 13:58:29 PDT)
[AMBER] Gaussian error with MCPB ion modeling calculation
(Fri Jul 22 2016 - 01:19:36 PDT)
Re: [AMBER] Regarding Parameter file not saved
(Mon Jul 18 2016 - 04:58:42 PDT)
Re: [AMBER] Ambertool16 - MCPB.py angle cut off and Error with Pdbsearcher.py
(Wed Jul 06 2016 - 05:37:19 PDT)
[AMBER] Ambertool16 - MCPB.py angle cut off and Error with Pdbsearcher.py
(Mon Jul 04 2016 - 01:39:33 PDT)
Bill Ross
Re: [AMBER] Amber 16 Installation
(Mon Jul 18 2016 - 00:43:31 PDT)
Re: [AMBER] Problem to extending Simulation
(Thu Jul 07 2016 - 01:37:41 PDT)
Bin Sun
[AMBER] Multiple Replicas on a Single GPU
(Tue Jul 19 2016 - 18:12:32 PDT)
Bruno Falcone
[AMBER] MMPBSA.py for complex or receptor or ligand only
(Fri Jul 15 2016 - 07:10:17 PDT)
Re: [AMBER] bad atom type decomp
(Tue Jul 05 2016 - 07:04:21 PDT)
Re: [AMBER] bad atom type decomp
(Thu Jun 30 2016 - 20:45:48 PDT)
C.D. Okafor
[AMBER] Difference of two trajectories
(Wed Jul 20 2016 - 14:25:54 PDT)
Carlos Simmerling
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 08:47:23 PDT)
Re: [AMBER] modified potentials
(Fri Jul 29 2016 - 08:46:14 PDT)
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 08:30:34 PDT)
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 08:04:33 PDT)
Re: [AMBER] Implicit solvent with Glycam force field
(Mon Jul 25 2016 - 04:00:56 PDT)
Re: [AMBER] 回复： Re: MD simulation can not proceed normally
(Thu Jul 21 2016 - 07:45:51 PDT)
Re: [AMBER] Save individual PDBs from MD trajectory
(Thu Jul 21 2016 - 06:55:07 PDT)
Re: [AMBER] MD simulation can not proceed normally
(Thu Jul 21 2016 - 04:54:41 PDT)
Re: [AMBER] Proton wanders away from tryptophan and histadine sidechain carbon
(Tue Jul 19 2016 - 08:23:06 PDT)
Re: [AMBER] phosphorylated residues
(Tue Jul 19 2016 - 03:38:35 PDT)
Re: [AMBER] Discrepancy between mdcrd and output files for MD run
(Sun Jul 17 2016 - 14:08:21 PDT)
Re: [AMBER] strategies to speed up MM/GBSA screening
(Wed Jul 13 2016 - 18:23:54 PDT)
Re: [AMBER] carbon nanotube
(Wed Jul 13 2016 - 18:20:18 PDT)
Casalini Tommaso
[AMBER] Question about Charge derivation for GLYCAM force field
(Mon Jul 04 2016 - 07:03:00 PDT)
chemjxn
[AMBER] cpptraj.hbond: water in the complex
(Thu Jun 30 2016 - 18:10:42 PDT)
Christina Bergonzo
Re: [AMBER] WHAM-2D analysis
(Wed Jul 13 2016 - 10:03:21 PDT)
Corum, Katharine W
Re: [AMBER] Amber 16 Installation
(Mon Jul 18 2016 - 12:39:56 PDT)
Re: [AMBER] Amber16 tutorials
(Thu Jul 07 2016 - 08:26:02 PDT)
Re: [AMBER] Amber16 tutorials
(Thu Jul 07 2016 - 08:13:15 PDT)
Re: [AMBER] Amber16 tutorials
(Thu Jul 07 2016 - 07:54:12 PDT)
Re: [AMBER] Amber16 tutorials
(Thu Jul 07 2016 - 07:43:36 PDT)
Re: [AMBER] Amber16 tutorials
(Wed Jul 06 2016 - 14:16:06 PDT)
Re: [AMBER] Amber16 tutorials
(Wed Jul 06 2016 - 14:11:37 PDT)
[AMBER] Amber16 tutorials
(Wed Jul 06 2016 - 14:07:01 PDT)
Daniel Roe
Re: [AMBER] Hii
(Sun Jul 31 2016 - 06:58:12 PDT)
Re: [AMBER] dssp xlabel conversion.
(Sat Jul 30 2016 - 07:41:26 PDT)
Re: [AMBER] Exposed hydrophobic surface area
(Fri Jul 29 2016 - 19:15:05 PDT)
Re: [AMBER] MMPBSA (MD or aMD)
(Fri Jul 29 2016 - 19:13:46 PDT)
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 14:52:49 PDT)
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 14:27:59 PDT)
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 14:20:36 PDT)
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 13:45:57 PDT)
Re: [AMBER] Problem setting AMBERHOME as environment variable Ambertools 16 Linux
(Fri Jul 29 2016 - 09:24:25 PDT)
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 08:36:35 PDT)
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 08:34:25 PDT)
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 07:31:56 PDT)
Re: [AMBER] Cpptraj - Stat bug?
(Fri Jul 29 2016 - 07:17:48 PDT)
Re: [AMBER] Cpptraj - Stat bug?
(Thu Jul 28 2016 - 16:00:16 PDT)
Re: [AMBER] Cpptraj - Stat bug?
(Thu Jul 28 2016 - 15:03:33 PDT)
Re: [AMBER] Cpptraj - Stat bug?
(Thu Jul 28 2016 - 14:05:17 PDT)
Re: [AMBER] Calculating lipid diffusion using stfcdiffusion
(Thu Jul 28 2016 - 13:21:23 PDT)
Re: [AMBER] cpptraj grid command multiple trajectories
(Tue Jul 26 2016 - 13:31:34 PDT)
Re: [AMBER] Calculating lipid diffusion using stfcdiffusion
(Tue Jul 26 2016 - 12:53:14 PDT)
Re: [AMBER] cpptraj grid command multiple trajectories
(Tue Jul 26 2016 - 12:11:19 PDT)
Re: [AMBER] Calculating lipid diffusion using stfcdiffusion
(Tue Jul 19 2016 - 08:26:01 PDT)
Re: [AMBER] Decomposition in minimization step
(Wed Jul 13 2016 - 07:22:10 PDT)
Re: [AMBER] ligand bond distortion during MD run.
(Fri Jul 08 2016 - 13:12:26 PDT)
Re: [AMBER] MMPBSA
(Fri Jul 08 2016 - 13:09:46 PDT)
Re: [AMBER] rmsd plot error
(Fri Jul 08 2016 - 07:47:46 PDT)
Re: [AMBER] VMD
(Thu Jul 07 2016 - 09:48:08 PDT)
Re: [AMBER] Amber16 tutorials
(Thu Jul 07 2016 - 08:23:46 PDT)
Re: [AMBER] Gunning GIST in parallel
(Thu Jul 07 2016 - 08:04:56 PDT)
Re: [AMBER] Amber16 tutorials
(Thu Jul 07 2016 - 08:03:53 PDT)
Re: [AMBER] re-imaging bilayer
(Thu Jul 07 2016 - 07:37:57 PDT)
Re: [AMBER] Problem to extending Simulation
(Wed Jul 06 2016 - 08:32:18 PDT)
Re: [AMBER] Error during amber 12 installation
(Tue Jul 05 2016 - 06:38:04 PDT)
Re: [AMBER] iwrap=0
(Tue Jul 05 2016 - 04:56:49 PDT)
Re: [AMBER] ParmEd
(Mon Jul 04 2016 - 19:22:01 PDT)
Re: [AMBER] cpptraj.hbond: water in the complex
(Fri Jul 01 2016 - 10:37:12 PDT)
David A Case
Re: [AMBER] InVacuoWithDielc
(Sat Jul 30 2016 - 07:51:01 PDT)
Re: [AMBER] NMR restraint
(Fri Jul 29 2016 - 06:35:08 PDT)
Re: [AMBER] EEL become ****** in minimization
(Thu Jul 28 2016 - 15:46:38 PDT)
Re: [AMBER] How to modify forcefield to use TIP4P-D water model
(Wed Jul 27 2016 - 05:44:05 PDT)
Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
(Tue Jul 26 2016 - 13:40:52 PDT)
Re: [AMBER] ntr vs ibelly.
(Tue Jul 26 2016 - 07:40:17 PDT)
Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
(Mon Jul 25 2016 - 19:13:47 PDT)
Re: [AMBER] restraintmask: select residues around the coordinates of a point
(Mon Jul 25 2016 - 18:47:32 PDT)
Re: [AMBER] average pdb distorted
(Mon Jul 25 2016 - 18:43:48 PDT)
Re: [AMBER] restraintmask: select residues around the coordinates of a point
(Mon Jul 25 2016 - 14:03:06 PDT)
Re: [AMBER] Applying different restraints to different sets of atoms
(Mon Jul 25 2016 - 09:50:47 PDT)
Re: [AMBER] charmmlipid2amber not found
(Mon Jul 25 2016 - 07:16:43 PDT)
Re: [AMBER] Implicit solvent with Glycam force field
(Mon Jul 25 2016 - 07:08:52 PDT)
Re: [AMBER] restraintmask: select residues around the coordinates of a point
(Mon Jul 25 2016 - 07:05:18 PDT)
Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
(Sat Jul 23 2016 - 15:22:44 PDT)
Re: [AMBER] Create x.out and x.rst from x.mdcrd
(Sat Jul 23 2016 - 07:17:02 PDT)
Re: [AMBER] NMode binding entropy Error -- Line minimizer aborted
(Sat Jul 23 2016 - 07:14:18 PDT)
Re: [AMBER] MDCRD
(Sat Jul 23 2016 - 07:11:01 PDT)
Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
(Sat Jul 23 2016 - 07:05:33 PDT)
Re: [AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?)
(Fri Jul 22 2016 - 09:36:56 PDT)
Re: [AMBER] parmed chamber
(Fri Jul 22 2016 - 05:33:02 PDT)
Re: [AMBER] MDCRD
(Fri Jul 22 2016 - 05:29:04 PDT)
Re: [AMBER] Amber with Amoeba force field
(Fri Jul 22 2016 - 05:23:21 PDT)
Re: [AMBER] Minimization of a small molecule in gas phase
(Thu Jul 21 2016 - 18:23:46 PDT)
Re: [AMBER] Minimization of a small molecule in gas phase
(Thu Jul 21 2016 - 18:22:45 PDT)
Re: [AMBER] Binding deltaG in ligand pose selction
(Thu Jul 21 2016 - 08:30:05 PDT)
Re: [AMBER] Proton wanders away from tryptophan and histidine sidechain carbon
(Wed Jul 20 2016 - 14:40:58 PDT)
Re: [AMBER] NMR restraint
(Wed Jul 20 2016 - 14:31:39 PDT)
Re: [AMBER] Is the surf or the molsurf calculate the protein surface?
(Wed Jul 20 2016 - 06:46:27 PDT)
Re: [AMBER] Amber 16 Installation
(Mon Jul 18 2016 - 17:13:55 PDT)
Re: [AMBER] RDF
(Mon Jul 18 2016 - 12:56:03 PDT)
Re: [AMBER] Ligand RMSD
(Mon Jul 18 2016 - 12:49:48 PDT)
Re: [AMBER] Amber 16 Installation
(Mon Jul 18 2016 - 06:07:11 PDT)
Re: [AMBER] Is the surf or the molsurf calculate the protein surface?
(Sun Jul 17 2016 - 04:27:27 PDT)
Re: [AMBER] ff14SB compatible with Glycam_06j-1?
(Sat Jul 16 2016 - 05:42:27 PDT)
Re: [AMBER] Generating a HETATM database to use with reduce
(Fri Jul 15 2016 - 11:30:31 PDT)
Re: [AMBER] Generating a HETATM database to use with reduce
(Fri Jul 15 2016 - 05:12:18 PDT)
Re: [AMBER] Generating a HETATM database to use with reduce
(Thu Jul 14 2016 - 17:51:23 PDT)
Re: [AMBER] NEW parameters with AMBER
(Thu Jul 14 2016 - 04:59:06 PDT)
Re: [AMBER] ff99SB*-ildn again
(Thu Jul 14 2016 - 04:50:28 PDT)
Re: [AMBER] a question about resp restraints strength
(Thu Jul 14 2016 - 04:26:48 PDT)
Re: [AMBER] Born Mayer Potential
(Tue Jul 12 2016 - 18:37:30 PDT)
Re: [AMBER] predicting RDCs for un-restrained bonds
(Mon Jul 11 2016 - 18:36:38 PDT)
Re: [AMBER] adding non-standard residue to RNA strand
(Sat Jul 09 2016 - 15:29:41 PDT)
Re: [AMBER] Library errors while using NAB on Amber16
(Fri Jul 08 2016 - 13:22:49 PDT)
Re: [AMBER] convert amber topology and coordinates files into gromacs topology
(Thu Jul 07 2016 - 20:45:20 PDT)
Re: [AMBER] Problem to extending Simulation
(Thu Jul 07 2016 - 05:43:22 PDT)
Re: [AMBER] Stuck somewhere using antechamber
(Thu Jul 07 2016 - 05:40:13 PDT)
Re: [AMBER] addAtomType problem
(Sat Jul 02 2016 - 05:55:16 PDT)
Re: [AMBER] Regarding ho parameter in gaff
(Sat Jul 02 2016 - 05:51:11 PDT)
Re: [AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt
(Sat Jul 02 2016 - 04:58:41 PDT)
Re: [AMBER] MMPBSA -O: command not found
(Sat Jul 02 2016 - 04:50:23 PDT)
David Cerutti
Re: [AMBER] modified potentials
(Fri Jul 29 2016 - 09:33:22 PDT)
Re: [AMBER] modified potentials
(Fri Jul 29 2016 - 07:55:31 PDT)
Re: [AMBER] EEL become ****** in minimization
(Thu Jul 28 2016 - 07:44:08 PDT)
Re: [AMBER] paramfit
(Wed Jul 27 2016 - 10:02:02 PDT)
Re: [AMBER] MDGX tutorial?
(Mon Jul 25 2016 - 13:50:24 PDT)
Re: [AMBER] HMR 4fs failure?
(Fri Jul 15 2016 - 14:53:32 PDT)
Re: [AMBER] HMR 4fs failure?
(Fri Jul 15 2016 - 12:57:50 PDT)
Dd H
Re: [AMBER] Cpptraj
(Sun Jul 17 2016 - 18:13:15 PDT)
[AMBER] Cpptraj
(Sun Jul 17 2016 - 05:57:55 PDT)
Dickson, Callum J
Re: [AMBER] MDGX tutorial?
(Mon Jul 25 2016 - 15:40:42 PDT)
[AMBER] MDGX tutorial?
(Mon Jul 25 2016 - 13:20:01 PDT)
Re: [AMBER] Calculating lipid diffusion using stfcdiffusion
(Mon Jul 25 2016 - 13:14:42 PDT)
Re: [AMBER] Calculating lipid diffusion using stfcdiffusion
(Wed Jul 20 2016 - 14:25:40 PDT)
Re: [AMBER] Calculating lipid diffusion using stfcdiffusion
(Mon Jul 18 2016 - 13:25:17 PDT)
Re: [AMBER] re-imaging bilayer
(Thu Jul 07 2016 - 08:43:37 PDT)
Dmitry Suplatov
[AMBER] Applying different restraints to different sets of atoms
(Mon Jul 25 2016 - 05:38:52 PDT)
Dr. Andreas W. Goetz
Re: [AMBER] Question about QM/MM
(Fri Jul 29 2016 - 18:14:30 PDT)
Re: [AMBER] sander QM/MM MD
(Wed Jul 20 2016 - 11:23:30 PDT)
Re: [AMBER] QM/MM issue
(Thu Jul 07 2016 - 21:41:22 PDT)
Dr. M. K. Yadav
[AMBER] Help: make test fails during parallel amber installation
(Thu Jun 30 2016 - 20:52:03 PDT)
Dwight McGee
Re: [AMBER] SMD simulation protocols
(Sun Jul 24 2016 - 14:55:41 PDT)
Elisa Pieri
Re: [AMBER] Potential on each atom
(Wed Jul 06 2016 - 07:17:51 PDT)
Re: [AMBER] Potential on each atom
(Wed Jul 06 2016 - 02:11:55 PDT)
Re: [AMBER] Potential on each atom
(Tue Jul 05 2016 - 09:20:24 PDT)
[AMBER] Potential on each atom
(Mon Jul 04 2016 - 07:43:20 PDT)
Elissa Fink
[AMBER] Problem setting AMBERHOME as environment variable Ambertools 16 Linux
(Fri Jul 29 2016 - 09:15:59 PDT)
esther nehu
[AMBER] RMSD plot query
(Thu Jul 14 2016 - 07:29:41 PDT)
Fabrício Bracht
[AMBER] Remove rotation in postoprocess
(Wed Jul 20 2016 - 13:15:31 PDT)
Re: [AMBER] MCPB
(Thu Jul 07 2016 - 13:53:58 PDT)
[AMBER] GLYCAM naming
(Thu Jul 07 2016 - 11:56:05 PDT)
Re: [AMBER] MCPB
(Wed Jul 06 2016 - 12:51:37 PDT)
[AMBER] Multiplicity in antechamber
(Wed Jul 06 2016 - 11:22:44 PDT)
Re: [AMBER] MCPB
(Wed Jul 06 2016 - 10:51:27 PDT)
Re: [AMBER] MCPB
(Tue Jul 05 2016 - 10:27:37 PDT)
Re: [AMBER] MCPB
(Tue Jul 05 2016 - 10:16:39 PDT)
Re: [AMBER] MCPB
(Mon Jul 04 2016 - 11:49:16 PDT)
Re: [AMBER] MCPB
(Fri Jul 01 2016 - 16:29:58 PDT)
Fair, Ryan
[AMBER] Steered Molecular Dynamics
(Mon Jul 11 2016 - 09:05:38 PDT)
Feng Pan
Re: [AMBER] Help with SMD
(Tue Jul 12 2016 - 10:21:08 PDT)
Francesco Gentile
[AMBER] Compute SASA through molsurf
(Wed Jul 13 2016 - 15:02:21 PDT)
FyD
Re: [AMBER] a question about resp restraints strength
(Fri Jul 15 2016 - 10:22:13 PDT)
Re: [AMBER] carbon nanotube
(Fri Jul 15 2016 - 10:17:39 PDT)
Re: [AMBER] adding non-standard residue to RNA strand
(Tue Jul 12 2016 - 14:03:16 PDT)
Gerald Monard
Re: [AMBER] HMR 4fs failure?
(Fri Jul 15 2016 - 15:12:48 PDT)
Re: [AMBER] HMR 4fs failure?
(Fri Jul 15 2016 - 14:56:11 PDT)
Re: [AMBER] HMR 4fs failure?
(Fri Jul 15 2016 - 14:14:44 PDT)
[AMBER] HMR 4fs failure?
(Fri Jul 15 2016 - 12:54:29 PDT)
gsottile.unq.edu.ar
[AMBER] DPPC simulation temperature
(Wed Jul 06 2016 - 14:15:35 PDT)
Hai Nguyen
Re: [AMBER] where is amber.jupyter?
(Sat Jul 30 2016 - 01:47:09 PDT)
Re: [AMBER] where is amber.jupyter?
(Sat Jul 30 2016 - 01:11:21 PDT)
Re: [AMBER] where is amber.jupyter?
(Sat Jul 30 2016 - 00:26:42 PDT)
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 12:02:38 PDT)
Re: [AMBER] average pdb distorted
(Mon Jul 25 2016 - 12:28:34 PDT)
Re: [AMBER] REMD Reg
(Mon Jul 18 2016 - 20:33:22 PDT)
Re: [AMBER] Amber 16 Installation
(Mon Jul 18 2016 - 07:24:45 PDT)
Re: [AMBER] Cpptraj
(Sun Jul 17 2016 - 22:15:12 PDT)
Re: [AMBER] Regarding Parameter file not saved
(Sun Jul 17 2016 - 11:15:28 PDT)
Re: [AMBER] Cpptraj
(Sun Jul 17 2016 - 09:25:25 PDT)
Re: [AMBER] Cpptraj
(Sun Jul 17 2016 - 09:24:22 PDT)
Re: [AMBER] HMR 4fs failure?
(Fri Jul 15 2016 - 12:56:10 PDT)
Re: [AMBER] RMSD plot query
(Thu Jul 14 2016 - 07:57:10 PDT)
Re: [AMBER] Born Mayer Potential
(Tue Jul 12 2016 - 09:53:57 PDT)
Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein.
(Mon Jul 11 2016 - 21:56:28 PDT)
Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein.
(Mon Jul 11 2016 - 21:36:02 PDT)
Re: [AMBER] MMPBSA
(Mon Jul 11 2016 - 13:57:53 PDT)
Re: [AMBER] MMPBSA
(Mon Jul 11 2016 - 13:49:37 PDT)
Re: [AMBER] MMPBSA
(Mon Jul 11 2016 - 13:41:40 PDT)
Re: [AMBER] MMPBSA
(Fri Jul 08 2016 - 11:07:46 PDT)
Re: [AMBER] Amber16 tutorials
(Thu Jul 07 2016 - 08:20:39 PDT)
Re: [AMBER] Stuck somewhere using antechamber
(Wed Jul 06 2016 - 16:03:56 PDT)
Re: [AMBER] A question on SMD simulations
(Wed Jul 06 2016 - 15:11:21 PDT)
Re: [AMBER] Amber16 tutorials
(Wed Jul 06 2016 - 14:14:49 PDT)
Re: [AMBER] ParmEd
(Mon Jul 04 2016 - 08:34:12 PDT)
Re: [AMBER] MMPBSA -O: command not found
(Fri Jul 01 2016 - 13:17:11 PDT)
Re: [AMBER] Slow performance of Amber12 on cluster
(Thu Jun 30 2016 - 22:43:47 PDT)
Re: [AMBER] Help: make test fails during parallel amber installation
(Thu Jun 30 2016 - 22:34:47 PDT)
Himanshu Joshi
Re: [AMBER] how to fix COM of a group of atoms?
(Sat Jul 09 2016 - 22:02:10 PDT)
Re: [AMBER] Lipid14 with ntr=1
(Sat Jul 09 2016 - 12:49:24 PDT)
[AMBER] Lipid14 with ntr=1
(Mon Jul 04 2016 - 00:17:39 PDT)
Hirdesh Kumar
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 14:33:19 PDT)
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 14:25:26 PDT)
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 14:09:45 PDT)
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 12:52:31 PDT)
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 08:08:34 PDT)
Re: [AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 08:00:03 PDT)
[AMBER] rmsd calculations on multiple trajectories
(Fri Jul 29 2016 - 05:26:54 PDT)
Re: [AMBER] Creating topology file in MMPBSA
(Mon Jul 25 2016 - 07:25:39 PDT)
Re: [AMBER] Amber16 tutorials
(Thu Jul 07 2016 - 07:52:20 PDT)
Ibrahim Said
Re: [AMBER] SMD simulation protocols
(Sun Jul 24 2016 - 13:08:28 PDT)
[AMBER] SMD simulation protocols
(Sun Jul 24 2016 - 09:25:47 PDT)
Igor Marques
[AMBER] paramfit
(Wed Jul 27 2016 - 09:34:45 PDT)
Indrajit Deb
Re: [AMBER] NAB
(Sat Jul 23 2016 - 05:07:57 PDT)
[AMBER] Problem with Gaussian09 with B97D/def2TZVPPD basis set from EMSL
(Thu Jul 14 2016 - 05:55:07 PDT)
Iqbal, Muhammad Sajid
[AMBER] Save individual PDBs from MD trajectory
(Thu Jul 21 2016 - 06:52:50 PDT)
Irem Altan
Re: [AMBER] modified potentials
(Fri Jul 29 2016 - 08:38:13 PDT)
[AMBER] modified potentials
(Fri Jul 29 2016 - 06:52:07 PDT)
JAIME RUBIO MARTINEZ
[AMBER] InVacuoWithDielc
(Thu Jul 28 2016 - 23:38:17 PDT)
James Starlight
Re: [AMBER] Structural refinement of the protein complexed with metalo-ions
(Mon Jul 04 2016 - 04:39:50 PDT)
Re: [AMBER] Structural refinement of the protein complexed with metalo-ions
(Fri Jul 01 2016 - 01:37:14 PDT)
jandre17
[AMBER] Discrepancy between mdcrd and output files for MD run
(Sun Jul 17 2016 - 13:21:31 PDT)
Jason Swails
Re: [AMBER] MMPBSA (MD or aMD)
(Fri Jul 29 2016 - 17:43:05 PDT)
Re: [AMBER] MMPBSA (MD or aMD)
(Fri Jul 29 2016 - 12:56:39 PDT)
Re: [AMBER] CPPTRAJ
(Mon Jul 25 2016 - 08:10:08 PDT)
Re: [AMBER] Creating topology file in MMPBSA
(Mon Jul 25 2016 - 08:05:41 PDT)
Re: [AMBER] MMPBSA.py for complex or receptor or ligand only
(Fri Jul 15 2016 - 10:53:38 PDT)
Re: [AMBER] strategies to speed up MM/GBSA screening
(Thu Jul 14 2016 - 13:22:34 PDT)
Re: [AMBER] ff99SB*-ildn again
(Thu Jul 14 2016 - 06:58:00 PDT)
Re: [AMBER] carbon nanotube
(Thu Jul 14 2016 - 06:30:22 PDT)
Re: [AMBER] carbon nanotube
(Wed Jul 13 2016 - 19:12:59 PDT)
Re: [AMBER] strategies to speed up MM/GBSA screening
(Wed Jul 13 2016 - 18:38:44 PDT)
Re: [AMBER] strategies to speed up MM/GBSA screening
(Wed Jul 13 2016 - 05:14:24 PDT)
Re: [AMBER] Born Mayer Potential
(Tue Jul 12 2016 - 19:28:25 PDT)
Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein.
(Mon Jul 11 2016 - 20:13:12 PDT)
Re: [AMBER] how to fix COM of a group of atoms?
(Mon Jul 11 2016 - 10:34:35 PDT)
Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein.
(Mon Jul 11 2016 - 10:33:02 PDT)
Re: [AMBER] Multiplicity in antechamber
(Wed Jul 06 2016 - 13:35:12 PDT)
Re: [AMBER] Potential on each atom
(Wed Jul 06 2016 - 07:38:05 PDT)
Re: [AMBER] Problem to extending Simulation
(Wed Jul 06 2016 - 05:53:00 PDT)
Re: [AMBER] Amber12 or lated on POWER8 platform
(Wed Jul 06 2016 - 05:50:54 PDT)
Re: [AMBER] bad atom type decomp
(Tue Jul 05 2016 - 11:27:55 PDT)
Re: [AMBER] Potential on each atom
(Tue Jul 05 2016 - 11:17:49 PDT)
Re: [AMBER] SMD at constant force
(Mon Jul 04 2016 - 19:34:12 PDT)
Re: [AMBER] ParmEd
(Mon Jul 04 2016 - 19:30:16 PDT)
Re: [AMBER] ParmEd
(Mon Jul 04 2016 - 18:50:43 PDT)
Re: [AMBER] convert amber topology and coordinates files into gromacs topology
(Sun Jul 03 2016 - 19:57:49 PDT)
Jean-Marc Billod
Re: [AMBER] Remove rotation in postoprocess
(Wed Jul 20 2016 - 13:25:49 PDT)
Joan Torras
Re: [AMBER] QM/MM simulations with Amber/deMon2k
(Thu Jul 07 2016 - 23:18:29 PDT)
Jose Manuel
Re: [AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt
(Sat Jul 02 2016 - 01:46:09 PDT)
kenfack cyril
Re: [AMBER] average pdb distorted
(Sat Jul 30 2016 - 12:27:10 PDT)
Kenneth Huang
Re: [AMBER] Failed to solvate the molecule during the TUTORIAL A8
(Tue Jul 26 2016 - 06:14:33 PDT)
Khabiri, Morteza
[AMBER] Wierd line in amber-TI output Files
(Thu Jul 21 2016 - 10:52:53 PDT)
Kshatresh Dutta Dubey
Re: [AMBER] charmmlipid2amber not found
(Mon Jul 25 2016 - 08:26:03 PDT)
[AMBER] charmmlipid2amber not found
(Mon Jul 25 2016 - 01:08:23 PDT)
Kucharski Jr., Amir N
Re: [AMBER] Generating a HETATM database to use with reduce
(Fri Jul 15 2016 - 13:58:00 PDT)
Re: [AMBER] Generating a HETATM database to use with reduce
(Fri Jul 15 2016 - 09:51:46 PDT)
Re: [AMBER] Generating a HETATM database to use with reduce
(Thu Jul 14 2016 - 18:04:54 PDT)
[AMBER] Generating a HETATM database to use with reduce
(Wed Jul 13 2016 - 21:01:37 PDT)
Lachele Foley
Re: [AMBER] Implicit solvent with Glycam force field
(Sun Jul 24 2016 - 19:27:01 PDT)
Re: [AMBER] GLYCAM naming
(Thu Jul 07 2016 - 12:45:13 PDT)
Re: [AMBER] Question about Charge derivation for GLYCAM force field
(Mon Jul 04 2016 - 22:44:00 PDT)
Lea Natalia Toledo Carvajal
Re: [AMBER] addAtomType problem
(Fri Jul 08 2016 - 15:18:25 PDT)
Mahmood Jasim
[AMBER] RDF
(Mon Jul 18 2016 - 10:32:45 PDT)
Marc van der Kamp
Re: [AMBER] average pdb distorted
(Tue Jul 26 2016 - 00:55:05 PDT)
Marcelo Andrade Chagas
Re: [AMBER] MCPB.py
(Wed Jul 20 2016 - 06:53:33 PDT)
Re: [AMBER] MCPB
(Mon Jul 04 2016 - 13:02:54 PDT)
Marcos Serrou do Amaral
Re: [AMBER] make test.cuda failed
(Thu Jul 28 2016 - 07:53:03 PDT)
Markus Schneider
Re: [AMBER] Cpptraj - Stat bug?
(Fri Jul 29 2016 - 06:56:43 PDT)
[AMBER] Cpptraj - Stat bug?
(Fri Jul 22 2016 - 05:22:44 PDT)
Martina Devi
[AMBER] adding non-standard residue to RNA strand
(Sat Jul 09 2016 - 10:21:28 PDT)
Masoud Kazemi
[AMBER] sander QM/MM MD
(Wed Jul 20 2016 - 05:26:50 PDT)
Mijiddorj Batsaikhan
[AMBER] Create x.out and x.rst from x.mdcrd
(Sat Jul 23 2016 - 06:27:54 PDT)
Ming Tang
[AMBER] NMR restraint
(Thu Jul 28 2016 - 17:36:35 PDT)
[AMBER] NMR restraint
(Sun Jul 24 2016 - 17:51:17 PDT)
Re: [AMBER] SMD at constant force
(Thu Jul 21 2016 - 04:01:19 PDT)
Re: [AMBER] NMR restraint
(Wed Jul 20 2016 - 18:21:19 PDT)
Re: [AMBER] NMR restraint
(Wed Jul 20 2016 - 18:10:54 PDT)
[AMBER] NMR restraint
(Wed Jul 20 2016 - 06:18:07 PDT)
Re: [AMBER] how to fix COM of a group of atoms?
(Tue Jul 19 2016 - 15:50:45 PDT)
Re: [AMBER] how to fix COM of a group of atoms?
(Fri Jul 15 2016 - 00:03:56 PDT)
Re: [AMBER] how to fix COM of a group of atoms?
(Sun Jul 10 2016 - 17:45:19 PDT)
[AMBER] Restrain COM of a group of atoms
(Sat Jul 09 2016 - 18:18:11 PDT)
[AMBER] how to fix COM of a group of atoms?
(Fri Jul 08 2016 - 06:01:05 PDT)
Re: [AMBER] convert amber topology and coordinates files into gromacs topology
(Thu Jul 07 2016 - 19:21:35 PDT)
Re: [AMBER] convert amber topology and coordinates files into gromacs topology
(Thu Jul 07 2016 - 19:06:57 PDT)
[AMBER] A question on SMD simulations
(Wed Jul 06 2016 - 14:59:42 PDT)
[AMBER] Query on SMD
(Wed Jul 06 2016 - 14:49:02 PDT)
[AMBER] Question on SMD
(Wed Jul 06 2016 - 14:46:02 PDT)
[AMBER] iwrap=0
(Tue Jul 05 2016 - 04:25:13 PDT)
[AMBER] SMD at constant force
(Mon Jul 04 2016 - 19:06:25 PDT)
[AMBER] convert amber topology and coordinates files into gromacs topology
(Sun Jul 03 2016 - 17:27:47 PDT)
Morteza Chehel Amirani
[AMBER] QM/MM simulations with Amber/deMon2k
(Thu Jul 07 2016 - 14:19:53 PDT)
[AMBER] QM/MM issue
(Thu Jul 07 2016 - 14:13:10 PDT)
Muthukumaran R
[AMBER] Calculating Salt bridge interactions- Protein and RNA
(Sat Jul 30 2016 - 00:27:51 PDT)
Neha Gandhi
Re: [AMBER] parmed chamber
(Fri Jul 22 2016 - 06:14:30 PDT)
Re: [AMBER] parmed chamber
(Fri Jul 22 2016 - 05:35:23 PDT)
[AMBER] parmed chamber
(Fri Jul 22 2016 - 04:58:50 PDT)
[AMBER] selecting frames with distribution
(Thu Jul 21 2016 - 22:02:45 PDT)
[AMBER] phosphorylated residues
(Mon Jul 18 2016 - 23:40:36 PDT)
Re: [AMBER] ff99SB*-ildn again
(Thu Jul 14 2016 - 05:10:15 PDT)
Re: [AMBER] ff99SB*-ildn again
(Thu Jul 14 2016 - 02:45:37 PDT)
[AMBER] ff99SB*-ildn again
(Wed Jul 13 2016 - 23:47:07 PDT)
Re: [AMBER] carbon nanotube
(Wed Jul 13 2016 - 19:15:55 PDT)
Re: [AMBER] carbon nanotube
(Wed Jul 13 2016 - 18:43:15 PDT)
[AMBER] carbon nanotube
(Wed Jul 13 2016 - 18:18:31 PDT)
Re: [AMBER] ParmEd
(Mon Jul 04 2016 - 20:37:26 PDT)
Re: [AMBER] ParmEd
(Mon Jul 04 2016 - 19:09:06 PDT)
Re: [AMBER] ParmEd
(Mon Jul 04 2016 - 18:10:04 PDT)
[AMBER] ParmEd
(Mon Jul 04 2016 - 01:26:46 PDT)
Nhai
Re: [AMBER] selecting frames with distribution
(Thu Jul 21 2016 - 23:08:31 PDT)
Re: [AMBER] Regarding Parameter file not saved
(Mon Jul 18 2016 - 09:06:52 PDT)
Re: [AMBER] MMPBSA
(Fri Jul 08 2016 - 10:03:40 PDT)
Re: [AMBER] VMD
(Thu Jul 07 2016 - 09:57:02 PDT)
nida baig
Re: [AMBER] MDCRD
(Sat Jul 23 2016 - 00:46:45 PDT)
[AMBER] MDCRD
(Fri Jul 22 2016 - 04:19:49 PDT)
Nikolay N. Kuzmich
[AMBER] make test.cuda failed
(Thu Jul 28 2016 - 06:50:52 PDT)
[AMBER] Failed to solvate the molecule during the TUTORIAL A8
(Tue Jul 26 2016 - 04:18:49 PDT)
Osman, Roman
Re: [AMBER] EEL become ****** in minimization
(Thu Jul 28 2016 - 08:00:56 PDT)
Pengfei Li
Re: [AMBER] Error MCPB when send the input
(Tue Jul 26 2016 - 07:28:45 PDT)
Re: [AMBER] MCPB.py - coordinate sphere FE
(Wed Jul 20 2016 - 07:16:34 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Mon Jul 11 2016 - 12:18:19 PDT)
Re: [AMBER] Ambertool16 - MCPB.py angle cut off and Error with Pdbsearcher.py
(Sat Jul 09 2016 - 14:30:09 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Sat Jul 09 2016 - 08:50:56 PDT)
Re: [AMBER] MCPB
(Thu Jul 07 2016 - 13:46:35 PDT)
Re: [AMBER] Ambertool16 - MCPB.py angle cut off and Error with Pdbsearcher.py
(Tue Jul 05 2016 - 18:30:50 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Tue Jul 05 2016 - 18:21:11 PDT)
Re: [AMBER] MCPB
(Tue Jul 05 2016 - 18:17:54 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Mon Jul 04 2016 - 20:17:21 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Mon Jul 04 2016 - 20:07:43 PDT)
Re: [AMBER] MCPB
(Mon Jul 04 2016 - 20:05:39 PDT)
Re: [AMBER] MCPB
(Mon Jul 04 2016 - 16:19:57 PDT)
Re: [AMBER] can MCPB build non amino-acid containing complex?
(Fri Jul 01 2016 - 08:54:08 PDT)
Re: [AMBER] Structural refinement of the protein complexed with metalo-ions
(Fri Jul 01 2016 - 08:51:07 PDT)
Ray Luo
Re: [AMBER] MMPBSA (inp=1 or inp=2)??
(Fri Jul 15 2016 - 13:30:27 PDT)
Re: [AMBER] MMPBSA (inp=1 or inp=2)??
(Fri Jul 15 2016 - 13:27:42 PDT)
Robin Betz
Re: [AMBER] paramfit
(Fri Jul 29 2016 - 13:31:54 PDT)
Re: [AMBER] figure legend problem in the tutorial?
(Fri Jul 29 2016 - 13:25:33 PDT)
Ross Cheloha
Re: [AMBER] Proton wanders away from tryptophan and histidine sidechain carbon
(Wed Jul 20 2016 - 07:53:04 PDT)
[AMBER] Proton wanders away from tryptophan and histadine sidechain carbon
(Tue Jul 19 2016 - 07:50:53 PDT)
Ross Walker
Re: [AMBER] can amber14 be run with gtx1060
(Fri Jul 29 2016 - 05:03:59 PDT)
Re: [AMBER] Amber16 Parallel CUDA Tests
(Sat Jul 23 2016 - 15:32:59 PDT)
Re: [AMBER] Amber16 Parallel CUDA Tests
(Thu Jul 21 2016 - 02:34:19 PDT)
Re: [AMBER] Slow performance of Amber12 on cluster
(Fri Jul 01 2016 - 08:03:00 PDT)
Ruth Helena Tichauer
[AMBER] Sander bomb: how to create a larger box
(Thu Jul 28 2016 - 07:48:43 PDT)
Sally Pias
Re: [AMBER] re-imaging bilayer
(Tue Jul 19 2016 - 19:49:20 PDT)
Re: [AMBER] re-imaging bilayer
(Thu Jul 07 2016 - 06:41:17 PDT)
Saman Yousuf ali
[AMBER] hydrogen bond occupancy plot cpptraj
(Sat Jul 30 2016 - 15:15:59 PDT)
[AMBER] dssp xlabel conversion.
(Sat Jul 30 2016 - 00:38:04 PDT)
[AMBER] ntr vs ibelly.
(Tue Jul 26 2016 - 03:45:06 PDT)
[AMBER] ntr vs ibelly.
(Tue Jul 26 2016 - 02:38:42 PDT)
[AMBER] ibelly to fix protein.
(Mon Jul 25 2016 - 05:21:49 PDT)
[AMBER] MD of an elongated active site protein.
(Sat Jul 09 2016 - 07:58:02 PDT)
[AMBER] ligand bond distortion during MD run.
(Fri Jul 08 2016 - 10:48:21 PDT)
Re: [AMBER] rmsd plot error
(Fri Jul 08 2016 - 05:58:19 PDT)
Re: [AMBER] rmsd plot error
(Fri Jul 08 2016 - 05:28:28 PDT)
Re: [AMBER] rmsd plot error
(Fri Jul 08 2016 - 04:42:08 PDT)
[AMBER] rmsd plot error
(Fri Jul 08 2016 - 03:55:51 PDT)
Sanman Sabane
[AMBER] Amber12 or lated on POWER8 platform
(Wed Jul 06 2016 - 03:22:40 PDT)
Sarah Graham
Re: [AMBER] cpptraj grid command multiple trajectories
(Tue Jul 26 2016 - 13:26:12 PDT)
[AMBER] cpptraj grid command multiple trajectories
(Tue Jul 26 2016 - 10:17:47 PDT)
Scott Brozell
Re: [AMBER] Wierd line in amber-TI output Files
(Fri Jul 22 2016 - 14:10:40 PDT)
Shijie Sheng
Re: [AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d
(Wed Jul 20 2016 - 17:14:41 PDT)
Re: [AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d
(Wed Jul 20 2016 - 16:01:48 PDT)
[AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d
(Tue Jul 19 2016 - 23:14:25 PDT)
[AMBER] rism1d convergence for solvent mixtures
(Mon Jul 11 2016 - 16:30:42 PDT)
Slava Chushak
Re: [AMBER] Library errors while using NAB on Amber16
(Mon Jul 11 2016 - 07:22:52 PDT)
Re: [AMBER] Library errors while using NAB on Amber16
(Fri Jul 08 2016 - 07:15:55 PDT)
Song-Ho Chong
Re: [AMBER] parmed chamber
(Fri Jul 22 2016 - 05:57:13 PDT)
sshen004.ucr.edu
Re: [AMBER] rism1d convergence for solvent mixtures
(Mon Jul 11 2016 - 19:32:55 PDT)
Stephan Schott
[AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?)
(Thu Jul 21 2016 - 10:25:49 PDT)
[AMBER] aMD with chloroform
(Tue Jul 19 2016 - 08:19:24 PDT)
Steven Ford
Re: [AMBER] Amber16 Parallel CUDA Tests
(Mon Jul 25 2016 - 12:06:20 PDT)
[AMBER] Amber16 Parallel CUDA Tests
(Wed Jul 20 2016 - 13:19:16 PDT)
Steven Ramsey
Re: [AMBER] Regarding GIST calculation
(Fri Jul 01 2016 - 07:12:03 PDT)
Suguru ASAI
Re: [AMBER] EEL become ****** in minimization
(Thu Jul 28 2016 - 08:15:55 PDT)
[AMBER] EEL become ****** in minimization
(Thu Jul 28 2016 - 07:04:56 PDT)
Re: [AMBER] How to modify forcefield to use TIP4P-D water model
(Wed Jul 27 2016 - 20:03:17 PDT)
[AMBER] How to modify forcefield to use TIP4P-D water model
(Wed Jul 27 2016 - 03:24:29 PDT)
Thakur, Abhishek
Re: [AMBER] MMPBSA (MD or aMD)
(Fri Jul 29 2016 - 13:40:11 PDT)
Re: [AMBER] MMPBSA (MD or aMD)
(Fri Jul 29 2016 - 13:04:38 PDT)
[AMBER] MMPBSA (MD or aMD)
(Fri Jul 29 2016 - 12:27:21 PDT)
Re: [AMBER] EEL become ****** in minimization
(Thu Jul 28 2016 - 11:37:42 PDT)
Re: [AMBER] average pdb distorted
(Tue Jul 26 2016 - 11:24:29 PDT)
Re: [AMBER] average pdb distorted
(Mon Jul 25 2016 - 12:33:42 PDT)
[AMBER] average pdb distorted
(Mon Jul 25 2016 - 12:20:34 PDT)
Re: [AMBER] Regarding Parameter file not saved
(Mon Jul 18 2016 - 09:06:41 PDT)
Re: [AMBER] MMPBSA (inp=1 or inp=2)??
(Fri Jul 15 2016 - 09:16:14 PDT)
[AMBER] MMPBSA (inp=1 or inp=2)??
(Fri Jul 15 2016 - 08:53:44 PDT)
Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein.
(Mon Jul 11 2016 - 21:21:20 PDT)
Re: [AMBER] MMPBSA
(Mon Jul 11 2016 - 14:33:41 PDT)
Re: [AMBER] MMPBSA
(Mon Jul 11 2016 - 13:53:27 PDT)
Re: [AMBER] how to fix COM of a group of atoms?
(Mon Jul 11 2016 - 13:51:31 PDT)
Re: [AMBER] MMPBSA
(Mon Jul 11 2016 - 13:46:54 PDT)
[AMBER] MMPBSA
(Mon Jul 11 2016 - 13:31:32 PDT)
Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein.
(Mon Jul 11 2016 - 08:50:46 PDT)
Re: [AMBER] MMPBSA
(Fri Jul 08 2016 - 14:14:08 PDT)
Re: [AMBER] MMPBSA
(Fri Jul 08 2016 - 11:42:13 PDT)
Re: [AMBER] MMPBSA
(Fri Jul 08 2016 - 11:38:34 PDT)
Re: [AMBER] MMPBSA
(Fri Jul 08 2016 - 11:20:25 PDT)
Re: [AMBER] MMPBSA
(Fri Jul 08 2016 - 11:02:45 PDT)
[AMBER] MMPBSA
(Fri Jul 08 2016 - 09:57:16 PDT)
[AMBER] VMD
(Thu Jul 07 2016 - 09:44:53 PDT)
Re: [AMBER] MMPBSA -O: command not found
(Fri Jul 01 2016 - 13:26:51 PDT)
[AMBER] MMPBSA -O: command not found
(Fri Jul 01 2016 - 12:58:38 PDT)
Thomas Evangelidis
Re: [AMBER] restraintmask: select residues around the coordinates of a point
(Mon Jul 25 2016 - 15:02:09 PDT)
Re: [AMBER] restraintmask: select residues around the coordinates of a point
(Mon Jul 25 2016 - 11:03:11 PDT)
[AMBER] restraintmask: select residues around the coordinates of a point
(Sun Jul 24 2016 - 16:51:43 PDT)
Re: [AMBER] strategies to speed up MM/GBSA screening
(Thu Jul 14 2016 - 07:29:12 PDT)
Re: [AMBER] ff99SB*-ildn again
(Thu Jul 14 2016 - 04:40:37 PDT)
Re: [AMBER] strategies to speed up MM/GBSA screening
(Wed Jul 13 2016 - 16:09:31 PDT)
[AMBER] strategies to speed up MM/GBSA screening
(Wed Jul 13 2016 - 04:08:31 PDT)
Thomas Pochapsky
Re: [AMBER] predicting RDCs for un-restrained bonds
(Tue Jul 12 2016 - 05:36:35 PDT)
[AMBER] predicting RDCs for un-restrained bonds
(Mon Jul 11 2016 - 06:23:03 PDT)
Tiffani Rovira
[AMBER] Error MCPB when send the input
(Mon Jul 25 2016 - 10:05:23 PDT)
[AMBER] Minimization of a small molecule in gas phase
(Thu Jul 21 2016 - 08:31:38 PDT)
Tyler Luchko (Lists)
Re: [AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d
(Wed Jul 20 2016 - 16:28:46 PDT)
Re: [AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d
(Wed Jul 20 2016 - 10:48:34 PDT)
Re: [AMBER] rism1d convergence for solvent mixtures
(Mon Jul 11 2016 - 19:18:25 PDT)
Vishal Nemaysh
Re: [AMBER] Regarding Parameter file not saved
(Mon Jul 18 2016 - 08:17:02 PDT)
Re: [AMBER] Regarding Parameter file not saved
(Mon Jul 18 2016 - 03:09:37 PDT)
Re: [AMBER] Regarding Parameter file not saved
(Mon Jul 18 2016 - 02:31:42 PDT)
[AMBER] Regarding Parameter file not saved
(Sun Jul 17 2016 - 10:52:32 PDT)
Vivien Ramothe
[AMBER] Born Mayer Potential
(Tue Jul 12 2016 - 08:36:22 PDT)
Vlad Cojocaru
Re: [AMBER] ff99SB*-ildn again
(Thu Jul 14 2016 - 07:45:45 PDT)
Re: [AMBER] ff99SB*-ildn again
(Thu Jul 14 2016 - 05:21:29 PDT)
Re: [AMBER] ff99SB*-ildn again
(Thu Jul 14 2016 - 05:03:27 PDT)
Re: [AMBER] ff99SB*-ildn again
(Thu Jul 14 2016 - 04:59:25 PDT)
Re: [AMBER] ff99SB*-ildn again
(Thu Jul 14 2016 - 03:31:22 PDT)
Re: [AMBER] ff99SB*-ildn again
(Thu Jul 14 2016 - 03:28:54 PDT)
Re: [AMBER] ff99SB*-ildn again
(Thu Jul 14 2016 - 00:56:23 PDT)
Re: [AMBER] rmsd plot error
(Fri Jul 08 2016 - 08:17:34 PDT)
Re: [AMBER] rmsd plot error
(Fri Jul 08 2016 - 07:29:45 PDT)
Re: [AMBER] rmsd plot error
(Fri Jul 08 2016 - 05:47:48 PDT)
Re: [AMBER] rmsd plot error
(Fri Jul 08 2016 - 05:17:23 PDT)
Wesley Michael Botello-Smith
Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
(Tue Jul 26 2016 - 11:11:37 PDT)
Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
(Mon Jul 25 2016 - 16:17:14 PDT)
Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
(Mon Jul 25 2016 - 14:29:00 PDT)
Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
(Mon Jul 25 2016 - 10:52:11 PDT)
Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
(Mon Jul 25 2016 - 10:21:31 PDT)
Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
(Sat Jul 23 2016 - 09:39:05 PDT)
[AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
(Fri Jul 22 2016 - 16:01:12 PDT)
windy
[AMBER] Is the surf or the molsurf calculate the protein surface?
(Thu Jul 14 2016 - 19:08:02 PDT)
[AMBER] Is the surf or the molsurf calculate the protein surface?
(Thu Jul 14 2016 - 01:44:08 PDT)
Windy CC
[AMBER] Is the surf or the molsurf calculate the protein surface?
(Tue Jul 19 2016 - 19:46:15 PDT)
Xiangyu Jia
[AMBER] An attempt for TI with QM/MM Hamiltonian
(Thu Jul 07 2016 - 06:13:51 PDT)
Xiaoliu Zhang
[AMBER] Amber with Amoeba force field
(Thu Jul 21 2016 - 08:26:38 PDT)
Xiaoyu Wang
[AMBER] Stuck somewhere using antechamber
(Wed Jul 06 2016 - 16:00:37 PDT)
xjq
[AMBER] can amber14 be run with gtx1060
(Fri Jul 29 2016 - 02:43:08 PDT)
yunshi11 .
[AMBER] Implicit solvent with Glycam force field
(Sun Jul 24 2016 - 17:58:48 PDT)
[AMBER] ff14SB compatible with Glycam_06j-1?
(Sat Jul 16 2016 - 03:06:13 PDT)
Zhenyu Meng
Re: [AMBER] MCPB.py cannot recognize Cl
(Mon Jul 11 2016 - 01:16:20 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Fri Jul 08 2016 - 01:55:21 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Fri Jul 08 2016 - 00:22:47 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Mon Jul 04 2016 - 23:44:08 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Mon Jul 04 2016 - 23:29:43 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Mon Jul 04 2016 - 20:38:31 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Mon Jul 04 2016 - 20:23:43 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Mon Jul 04 2016 - 20:14:32 PDT)
[AMBER] MCPB.py cannot recognize Cl
(Mon Jul 04 2016 - 20:00:11 PDT)
Re: [AMBER] can MCPB build non amino-acid containing complex?
(Sat Jul 02 2016 - 06:49:56 PDT)
Re: [AMBER] can MCPB build non amino-acid containing complex?
(Sat Jul 02 2016 - 03:02:03 PDT)
[AMBER] can MCPB build non amino-acid containing complex?
(Fri Jul 01 2016 - 05:37:26 PDT)
ZHU JH
Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein.
(Mon Jul 11 2016 - 19:55:27 PDT)
zoran matovic
Re: [AMBER] Regarding Parameter file not saved
(Tue Jul 19 2016 - 01:00:24 PDT)
Re: [AMBER] Regarding Parameter file not saved
(Mon Jul 18 2016 - 14:10:43 PDT)
Re: [AMBER] Regarding Parameter file not saved
(Mon Jul 18 2016 - 11:58:58 PDT)
Re: [AMBER] Problem with Gaussian09 with B97D/def2TZVPPD basis set fromEMSL
(Thu Jul 14 2016 - 06:22:32 PDT)
Re: [AMBER] ligand bond distortion during MD run.
(Fri Jul 08 2016 - 11:20:04 PDT)
Re: [AMBER] rmsd plot error
(Fri Jul 08 2016 - 07:48:24 PDT)
Re: [AMBER] rmsd plot error
(Fri Jul 08 2016 - 07:13:07 PDT)
Re: [AMBER] rmsd plot error
(Fri Jul 08 2016 - 04:17:00 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Fri Jul 08 2016 - 02:10:08 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Fri Jul 08 2016 - 02:06:05 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Fri Jul 08 2016 - 01:16:13 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Mon Jul 04 2016 - 23:37:28 PDT)
Re: [AMBER] MCPB.py cannot recognize Cl
(Mon Jul 04 2016 - 23:12:58 PDT)
Re: [AMBER] can MCPB build non amino-acid containing complex?
(Fri Jul 01 2016 - 08:13:32 PDT)
乔艳
[AMBER] 回复： Re: MD simulation can not proceed normally
(Thu Jul 21 2016 - 07:28:13 PDT)
[AMBER] MD simulation can not proceed normally
(Thu Jul 21 2016 - 04:31:22 PDT)
康宁
[AMBER] NMode binding entropy Error -- Line minimizer aborted
(Sat Jul 23 2016 - 03:16:24 PDT)
朱 婧涵
[AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein.
(Mon Jul 11 2016 - 02:19:28 PDT)
Last message date
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Sun Jul 31 2016 - 07:00:03 PDT
Archived on
: Mon Apr 22 2024 - 05:55:17 PDT
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