Amber Archive Mar 2014 by author
563 messages
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Starting
Sat Mar 01 2014 - 03:30:02 PST,
Ending
Mon Mar 31 2014 - 14:00:04 PDT
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. mirage
[AMBER] question about mmpbsa result
(Mon Mar 03 2014 - 22:47:55 PST)
ABEL Stephane 175950
Re: [AMBER] modeling glucoside
(Sat Mar 08 2014 - 04:44:35 PST)
Aditya Sarkar
[AMBER] Fwd: MMGBSA of protein DNA complex
(Wed Mar 26 2014 - 03:40:01 PDT)
Ahmed Ayoub
Re: [AMBER] MMPBSA TrajError
(Thu Mar 13 2014 - 13:27:30 PDT)
Re: [AMBER] MMPBSA TrajError
(Tue Mar 11 2014 - 13:14:30 PDT)
Re: [AMBER] MMPBSA TrajError
(Fri Mar 07 2014 - 11:32:16 PST)
Re: [AMBER] MMPBSA TrajError
(Wed Mar 05 2014 - 20:46:59 PST)
Re: [AMBER] MMPBSA TrajError
(Tue Mar 04 2014 - 12:58:58 PST)
[AMBER] MMPBSA TrajError
(Mon Mar 03 2014 - 15:08:31 PST)
Ahmet yıldırım
[AMBER] deprotonated histidine parameters
(Tue Mar 04 2014 - 01:12:11 PST)
Akashdeep Biswas
[AMBER] Problem in configuring the amber
(Tue Mar 25 2014 - 23:55:59 PDT)
Aldo Segura
Re: [AMBER] antechamber for two ligands
(Thu Mar 27 2014 - 06:40:23 PDT)
almarques
Re: [AMBER] MMPBSA.py error
(Mon Mar 03 2014 - 03:06:13 PST)
Andreas Goetz
Re: [AMBER] Including amino acid backbone into QM part during QM/MM
(Thu Mar 06 2014 - 11:50:31 PST)
Antoine Marion
Re: [AMBER] Water cap without MM-PBSA
(Fri Mar 14 2014 - 10:09:32 PDT)
Re: [AMBER] Water cap without MM-PBSA
(Fri Mar 14 2014 - 08:46:59 PDT)
Re: [AMBER] Water cap without MM-PBSA
(Fri Mar 14 2014 - 07:22:20 PDT)
[AMBER] Water cap without MM-PBSA
(Fri Mar 14 2014 - 06:29:06 PDT)
Antonios Kolocouris
[AMBER] ΑΠ: cpptraj h-bond: error
(Sat Mar 22 2014 - 14:35:01 PDT)
Arun Kumar Somavarapu
[AMBER] MMPBSA calculation with entropy
(Thu Mar 27 2014 - 22:02:02 PDT)
Arunima Shilpi
[AMBER] error in running density coomand
(Wed Mar 26 2014 - 23:33:11 PDT)
[AMBER] Positive value of delta G
(Sun Mar 23 2014 - 20:58:51 PDT)
[AMBER] delta G calculation in MMPBSA
(Sat Mar 22 2014 - 23:01:26 PDT)
[AMBER] protein-ligand tutorial
(Thu Mar 20 2014 - 04:15:18 PDT)
[AMBER] error in MMPBSA.py
(Tue Mar 18 2014 - 21:06:10 PDT)
[AMBER] error in running MMPBSA.py
(Mon Mar 17 2014 - 19:55:55 PDT)
[AMBER] error in executing pmemd
(Mon Mar 10 2014 - 21:33:29 PDT)
[AMBER] error in running Antechamber
(Sun Mar 09 2014 - 08:27:28 PDT)
[AMBER] sander command
(Tue Mar 04 2014 - 23:09:54 PST)
[AMBER] calculate charge and spin multiplicity
(Tue Mar 04 2014 - 03:17:43 PST)
[AMBER] error in running antechamber
(Sat Mar 01 2014 - 03:11:59 PST)
Asaminew Haile
Re: [AMBER] QM/MM
(Mon Mar 24 2014 - 09:25:01 PDT)
[AMBER] charges for QM/MM simulations
(Tue Mar 11 2014 - 07:10:57 PDT)
Ayesha Fatima
[AMBER] GPU not being recognised
(Mon Mar 31 2014 - 03:38:58 PDT)
Re: [AMBER] Compilation error on Ubuntu 13.10
(Thu Mar 20 2014 - 03:21:48 PDT)
Re: [AMBER] linker error
(Sat Mar 15 2014 - 01:23:25 PDT)
Re: [AMBER] linker error
(Sat Mar 15 2014 - 01:14:25 PDT)
[AMBER] linker error
(Fri Mar 14 2014 - 23:30:15 PDT)
Baifan Wang
Re: [AMBER] Problem in using xleap
(Thu Mar 06 2014 - 22:50:41 PST)
Benjamin Madej
Re: [AMBER] Lipid14 falling apart
(Thu Mar 20 2014 - 14:19:42 PDT)
Re: [AMBER] Lipid14 falling apart
(Thu Mar 20 2014 - 11:13:05 PDT)
BERGY
Re: [AMBER] Error: Prmtop appears to contain modified off-diagonal elements for VDW A coef
(Fri Mar 21 2014 - 04:44:39 PDT)
Re: [AMBER] Error: Prmtop appears to contain modified off-diagonal elements for VDW A coef
(Thu Mar 20 2014 - 02:37:05 PDT)
[AMBER] Error: Prmtop appears to contain modified off-diagonal elements for VDW A coef
(Wed Mar 19 2014 - 08:55:06 PDT)
Bill Ross
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 19 2014 - 19:43:04 PDT)
Re: [AMBER] generating topology
(Wed Mar 19 2014 - 19:22:47 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 19 2014 - 19:01:12 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Fri Mar 14 2014 - 19:23:48 PDT)
Brian Radak
[AMBER] data overflow in dx output from rism3d
(Thu Mar 27 2014 - 14:02:03 PDT)
Re: [AMBER] repulsive restraints
(Thu Mar 27 2014 - 09:43:53 PDT)
Re: [AMBER] QM/MM
(Mon Mar 24 2014 - 09:46:33 PDT)
Re: [AMBER] Energy unit in sqm
(Tue Mar 18 2014 - 07:03:12 PDT)
[AMBER] 3DRISM and orientationally averaged 3D pair distribution functions
(Wed Mar 12 2014 - 11:34:46 PDT)
[AMBER] rism3d.snglpnt output in dx format
(Mon Mar 10 2014 - 07:09:55 PDT)
Re: [AMBER] Mutating residues in an RNA
(Sun Mar 09 2014 - 12:56:00 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 05 2014 - 07:00:10 PST)
Re: [AMBER] Unable to restrain A-DNA conformation
(Wed Mar 05 2014 - 06:46:31 PST)
Re: [AMBER] print molecular orbitals
(Wed Mar 05 2014 - 06:28:51 PST)
Browning, Nicholas
Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types
(Thu Mar 20 2014 - 03:52:04 PDT)
Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types
(Thu Mar 20 2014 - 02:47:04 PDT)
Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types
(Wed Mar 19 2014 - 11:11:50 PDT)
Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types
(Tue Mar 18 2014 - 09:25:09 PDT)
[AMBER] tleap output of mol2 format incorrect bond order/atom types
(Tue Mar 18 2014 - 07:59:47 PDT)
Carlos Simmerling
Re: [AMBER] Problem with REMD simulation
(Thu Mar 27 2014 - 09:08:23 PDT)
Re: [AMBER] repulsive restraints
(Thu Mar 27 2014 - 09:03:34 PDT)
Re: [AMBER] Fwd: MMGBSA of protein DNA complex
(Wed Mar 26 2014 - 05:32:12 PDT)
Re: [AMBER] Open Source Drug Design and In Silico Molecules Pledge to AMBER developers
(Mon Mar 24 2014 - 06:53:19 PDT)
Re: [AMBER] strain/energy of backbone atoms
(Wed Mar 19 2014 - 11:43:57 PDT)
Re: [AMBER] strain/energy of backbone atoms
(Wed Mar 19 2014 - 09:42:47 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 19 2014 - 07:50:58 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Mon Mar 17 2014 - 04:31:25 PDT)
Re: [AMBER] Unable to restrain A-DNA conformation
(Wed Mar 05 2014 - 06:52:35 PST)
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 05 2014 - 06:46:10 PST)
Chris McClendon
[AMBER] how to get around "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable"
(Sat Mar 08 2014 - 17:52:45 PST)
CHRISTOPHER PATRICK MCNARY
[AMBER] Antechamber not converting HyperChem .hin files correctly
(Thu Mar 20 2014 - 10:50:56 PDT)
Daniel Roe
Re: [AMBER] restart MD from arbitrary snapshot
(Sun Mar 30 2014 - 19:30:25 PDT)
Re: [AMBER] restart MD from arbitrary snapshot
(Sun Mar 30 2014 - 13:42:17 PDT)
Re: [AMBER] cpptraj hbond analysis cutoff angle
(Sat Mar 29 2014 - 12:06:18 PDT)
Re: [AMBER] Replica exchange restart file
(Fri Mar 28 2014 - 07:48:21 PDT)
Re: [AMBER] error in running density coomand
(Thu Mar 27 2014 - 07:57:07 PDT)
Re: [AMBER] combining trajectories with diff. number of residues for same protein
(Wed Mar 26 2014 - 13:15:31 PDT)
Re: [AMBER] Possible bug in xleap
(Wed Mar 26 2014 - 08:16:07 PDT)
Re: [AMBER] How to update cpptraj and setting donor/acceptormask
(Wed Mar 26 2014 - 07:40:58 PDT)
Re: [AMBER] cpptraj grid function
(Tue Mar 25 2014 - 12:11:55 PDT)
Re: [AMBER] ibelly
(Tue Mar 25 2014 - 07:31:18 PDT)
Re: [AMBER] cpptraj grid function
(Mon Mar 24 2014 - 07:22:18 PDT)
Re: [AMBER] cpptraj grid function
(Sat Mar 22 2014 - 15:01:12 PDT)
Re: [AMBER] cpptraj h-bond: error
(Sat Mar 22 2014 - 14:54:54 PDT)
Re: [AMBER] Cuda compilation problems with Ubuntu 13.10
(Fri Mar 21 2014 - 07:58:05 PDT)
Re: [AMBER] strip_mask syntax error
(Fri Mar 21 2014 - 07:56:58 PDT)
Re: [AMBER] Cpptraj hbond bridgeout segmentation fault
(Thu Mar 20 2014 - 15:30:36 PDT)
Re: [AMBER] the combination ntb != 0, ntp != 0, ifbox == 0 is not supported!
(Thu Mar 20 2014 - 08:43:55 PDT)
Re: [AMBER] Percentage of secondary structure determination
(Tue Mar 18 2014 - 07:23:07 PDT)
Re: [AMBER] rdf around atom
(Mon Mar 17 2014 - 16:47:23 PDT)
Re: [AMBER] rdf around atom
(Mon Mar 17 2014 - 12:46:39 PDT)
Re: [AMBER] MMPBSA.py not generating specified frames for analysis
(Sat Mar 15 2014 - 21:08:18 PDT)
Re: [AMBER] iRED: relaxation rates and NOEs with ptraj
(Sat Mar 15 2014 - 09:34:14 PDT)
Re: [AMBER] linker error
(Sat Mar 15 2014 - 00:43:27 PDT)
Re: [AMBER] Water cap without MM-PBSA
(Fri Mar 14 2014 - 08:39:46 PDT)
Re: [AMBER] Compilation of amber12 on GRAY XE6
(Fri Mar 14 2014 - 08:08:42 PDT)
Re: [AMBER] Specifying a particular angle in ptraj when there is more than one residue with the same residue number
(Fri Mar 14 2014 - 07:07:22 PDT)
Re: [AMBER] Water cap without MM-PBSA
(Fri Mar 14 2014 - 07:00:52 PDT)
Re: [AMBER] AmberTools update 24 for CPPTRAJ
(Fri Mar 14 2014 - 06:56:18 PDT)
Re: [AMBER] MMPBSA TrajError
(Thu Mar 13 2014 - 07:37:30 PDT)
[AMBER] AmberTools update 24 for CPPTRAJ
(Thu Mar 13 2014 - 07:35:58 PDT)
Re: [AMBER] MMPBSA TrajError
(Tue Mar 11 2014 - 21:41:19 PDT)
Re: [AMBER] MMPBSA TrajError
(Tue Mar 11 2014 - 21:07:47 PDT)
Re: [AMBER] cpptraj -fixatomorder
(Tue Mar 11 2014 - 05:54:55 PDT)
Re: [AMBER] problem in "re-image" and "unwarp"
(Mon Mar 10 2014 - 07:43:15 PDT)
Re: [AMBER] problem when performing the ired anaysis
(Sat Mar 08 2014 - 08:04:36 PST)
Re: [AMBER] Fwd: cpptraj -fixatomorder
(Sat Mar 08 2014 - 08:02:17 PST)
Re: [AMBER] problem when performing the ired anaysis
(Fri Mar 07 2014 - 16:26:48 PST)
Re: [AMBER] MMPBSA TrajError
(Fri Mar 07 2014 - 12:02:04 PST)
Re: [AMBER] amber trajectory to gromacs trajectory conversion
(Mon Mar 03 2014 - 15:28:14 PST)
Re: [AMBER] MMPBSA TrajError
(Mon Mar 03 2014 - 15:16:02 PST)
Re: [AMBER] Cpptraj bridge
(Mon Mar 03 2014 - 07:42:48 PST)
Re: [AMBER] PairwiseDistance file after clustering analysis
(Mon Mar 03 2014 - 07:34:03 PST)
Re: [AMBER] extracting selected lipids from bilayer
(Mon Mar 03 2014 - 07:16:16 PST)
David A Case
Re: [AMBER] GPU not being recognised
(Mon Mar 31 2014 - 04:39:15 PDT)
Re: [AMBER] reg: the charges for methylated cytosine atoms
(Sat Mar 29 2014 - 12:23:52 PDT)
Re: [AMBER] reg: the charges for methylated cytosine atoms
(Fri Mar 28 2014 - 13:44:38 PDT)
Re: [AMBER] non-protonated and protonated phosphate
(Thu Mar 27 2014 - 09:26:25 PDT)
Re: [AMBER] antechamber for two ligands
(Thu Mar 27 2014 - 06:35:39 PDT)
Re: [AMBER] antechamber for two ligands
(Thu Mar 27 2014 - 06:19:28 PDT)
Re: [AMBER] Regarding SPC/E water model
(Thu Mar 27 2014 - 06:16:13 PDT)
Re: [AMBER] Regarding SPC/E water model
(Wed Mar 26 2014 - 12:46:25 PDT)
Re: [AMBER] Possible bug in xleap
(Wed Mar 26 2014 - 10:33:18 PDT)
Re: [AMBER] ibelly
(Tue Mar 25 2014 - 08:19:04 PDT)
Re: [AMBER] tleap cannot handle dummies in the middle?
(Tue Mar 25 2014 - 06:48:53 PDT)
Re: [AMBER] ibelly
(Tue Mar 25 2014 - 06:41:46 PDT)
Re: [AMBER] igb=1
(Tue Mar 25 2014 - 04:56:09 PDT)
Re: [AMBER] Open Source Drug Design and In Silico Molecules Pledge to AMBER developers
(Mon Mar 24 2014 - 13:23:30 PDT)
Re: [AMBER] Incomplete frcmod from parmchk
(Fri Mar 21 2014 - 11:48:55 PDT)
Re: [AMBER] Antechamber not converting HyperChem .hin files correctly
(Thu Mar 20 2014 - 11:25:40 PDT)
Re: [AMBER] problem in generating .prmtop and .inpcrd file using amber9
(Thu Mar 20 2014 - 04:45:59 PDT)
Re: [AMBER] RESTRAINT FILE
(Wed Mar 19 2014 - 18:54:03 PDT)
Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types
(Wed Mar 19 2014 - 18:44:12 PDT)
Re: [AMBER] generating topology
(Wed Mar 19 2014 - 07:01:34 PDT)
Re: [AMBER] Hbond
(Tue Mar 18 2014 - 13:16:09 PDT)
Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types
(Tue Mar 18 2014 - 09:45:40 PDT)
Re: [AMBER] Energy unit in sqm
(Tue Mar 18 2014 - 08:16:37 PDT)
Re: [AMBER] iRED: relaxation rates and NOEs with ptraj
(Sat Mar 15 2014 - 05:25:48 PDT)
Re: [AMBER] Question about Ambertools 1.5 installation
(Fri Mar 14 2014 - 11:44:12 PDT)
Re: [AMBER] Arsenic co-ordinates
(Fri Mar 14 2014 - 06:14:09 PDT)
Re: [AMBER] Specifying a particular angle in ptraj when there is more than one residue with the same residue number
(Thu Mar 13 2014 - 19:08:58 PDT)
Re: [AMBER] reg: the charges for methylated cytosine atoms
(Wed Mar 12 2014 - 12:33:59 PDT)
Re: [AMBER] problem in "re-image" and "unwarp"
(Mon Mar 10 2014 - 08:52:26 PDT)
Re: [AMBER] Antechamber add new parameter
(Sat Mar 08 2014 - 10:00:48 PST)
Re: [AMBER] Modified RNA frcmod error
(Sat Mar 08 2014 - 09:56:15 PST)
Re: [AMBER] FF10 Error
(Sat Mar 08 2014 - 06:17:10 PST)
Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron
(Fri Mar 07 2014 - 10:33:00 PST)
Re: [AMBER] Request for help in using Amberlite
(Fri Mar 07 2014 - 05:51:32 PST)
Re: [AMBER] Problem in using xleap
(Fri Mar 07 2014 - 05:48:27 PST)
Re: [AMBER] Trouble obtaining force field parameters via Antechamber
(Wed Mar 05 2014 - 10:58:56 PST)
Re: [AMBER] Unable to restrain A-DNA conformation
(Wed Mar 05 2014 - 05:17:39 PST)
Re: [AMBER] how to produce the prmtop of 'ch3cn'
(Wed Mar 05 2014 - 05:11:02 PST)
Re: [AMBER] sander command
(Wed Mar 05 2014 - 05:07:05 PST)
Re: [AMBER] deprotonated histidine parameters
(Tue Mar 04 2014 - 10:58:19 PST)
Re: [AMBER] calculate charge and spin multiplicity
(Tue Mar 04 2014 - 04:59:01 PST)
Re: [AMBER] error in running antechamber
(Sat Mar 01 2014 - 06:46:35 PST)
de Waal, Parker
Re: [AMBER] tleap lipid residue splitting warnings
(Mon Mar 17 2014 - 07:52:38 PDT)
[AMBER] tleap lipid residue splitting warnings
(Sun Mar 16 2014 - 09:35:19 PDT)
Debayan Chakraborty
Re: [AMBER] Generalized Born subroutines
(Mon Mar 24 2014 - 07:15:02 PDT)
[AMBER] Generalized Born subroutines
(Mon Mar 24 2014 - 06:41:19 PDT)
Re: [AMBER] Mutating residues in an RNA
(Sat Mar 08 2014 - 08:02:18 PST)
DEBOSTUTI GHOSHDASTIDAR
Re: [AMBER] Generating frc and prep files
(Mon Mar 31 2014 - 06:56:52 PDT)
[AMBER] cpptraj hbond analysis cutoff angle
(Fri Mar 28 2014 - 22:37:22 PDT)
[AMBER] Generating frc and prep files
(Tue Mar 25 2014 - 07:38:52 PDT)
Re: [AMBER] Unable to restrain A-DNA conformation
(Wed Mar 05 2014 - 05:48:48 PST)
[AMBER] Unable to restrain A-DNA conformation
(Wed Mar 05 2014 - 02:23:56 PST)
Dickson, Callum J
Re: [AMBER] PgP protein and amber14 lipid FF
(Thu Mar 20 2014 - 16:07:49 PDT)
Re: [AMBER] Lipid14 falling apart
(Thu Mar 20 2014 - 14:56:56 PDT)
Re: [AMBER] extracting selected lipids from bilayer
(Mon Mar 03 2014 - 02:02:14 PST)
Dongshan Wei
Re: [AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file?
(Thu Mar 27 2014 - 03:05:56 PDT)
Re: [AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file?
(Thu Mar 27 2014 - 03:01:07 PDT)
Re: [AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file?
(Thu Mar 27 2014 - 02:06:35 PDT)
[AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file?
(Wed Mar 26 2014 - 20:04:58 PDT)
Elisa Frezza
[AMBER] PairwiseDistance file after clustering analysis
(Mon Mar 03 2014 - 04:15:16 PST)
Entomology Research Institute
[AMBER] Amber settings in pymol
(Tue Mar 04 2014 - 22:54:40 PST)
Fabian Glaser
Re: [AMBER] antechamber for two ligands
(Sun Mar 30 2014 - 03:49:37 PDT)
Re: [AMBER] antechamber for two ligands
(Thu Mar 27 2014 - 07:50:12 PDT)
Re: [AMBER] antechamber for two ligands
(Thu Mar 27 2014 - 06:22:31 PDT)
[AMBER] antechamber for two ligands
(Thu Mar 27 2014 - 05:40:15 PDT)
[AMBER] libgfortran.2.dylib
(Tue Mar 25 2014 - 00:54:05 PDT)
filip fratev
Re: [AMBER] PgP protein and amber14 lipid FF
(Thu Mar 20 2014 - 16:04:04 PDT)
Re: [AMBER] Lipid14 falling apart
(Thu Mar 20 2014 - 15:29:24 PDT)
Re: [AMBER] Lipid14 falling apart
(Thu Mar 20 2014 - 11:38:46 PDT)
Re: [AMBER] PgP protein and amber14 lipid FF
(Mon Mar 17 2014 - 04:10:49 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Mon Mar 17 2014 - 03:57:38 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Mon Mar 17 2014 - 03:56:15 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Mon Mar 17 2014 - 03:55:14 PDT)
Re: [AMBER] Help for system configuration
(Tue Mar 11 2014 - 15:31:44 PDT)
Re: [AMBER] how to get around "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable"
(Sat Mar 08 2014 - 18:21:35 PST)
Re: [AMBER] PgP protein and amber14 lipid FF
(Thu Mar 06 2014 - 21:14:27 PST)
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 05 2014 - 08:21:53 PST)
Filip Lankas
Re: [AMBER] reg: the charges for methylated cytosine atoms
(Mon Mar 31 2014 - 01:53:31 PDT)
Florent Barbault
[AMBER] print molecular orbitals
(Wed Mar 05 2014 - 05:01:48 PST)
FyD
Re: [AMBER] antechamber for two ligands
(Sun Mar 30 2014 - 10:11:59 PDT)
Re: [AMBER] non-protonated and protonated phosphate
(Sat Mar 29 2014 - 00:20:38 PDT)
Re: [AMBER] Generating frc and prep files
(Wed Mar 26 2014 - 05:16:44 PDT)
Re: [AMBER] Generating frc and prep files
(Wed Mar 26 2014 - 00:24:56 PDT)
Re: [AMBER] Adenine parameters and topology files
(Mon Mar 24 2014 - 13:19:51 PDT)
Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types
(Thu Mar 20 2014 - 00:36:07 PDT)
Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron
(Fri Mar 07 2014 - 09:30:12 PST)
Re: [AMBER] Trouble obtaining force field parameters via Antechamber
(Wed Mar 05 2014 - 22:50:12 PST)
Re: [AMBER] how to produce the prmtop of 'ch3cn'
(Wed Mar 05 2014 - 22:29:52 PST)
Gargi Borgohai
[AMBER] Problem with REMD simulation
(Thu Mar 27 2014 - 08:03:15 PDT)
Geoffrey Gray
Re: [AMBER] AMOEBA force field in amber
(Thu Mar 20 2014 - 14:52:20 PDT)
[AMBER] AMOEBA force field in amber
(Thu Mar 20 2014 - 11:50:21 PDT)
George Tzotzos
Re: [AMBER] Positive value of delta G
(Mon Mar 24 2014 - 08:24:52 PDT)
[AMBER] cpptraj h-bond: error
(Sat Mar 22 2014 - 13:13:00 PDT)
[AMBER] strip_mask syntax error
(Fri Mar 21 2014 - 07:35:05 PDT)
[AMBER] MMPBSA.py.MPI - Runtime error cont.d
(Mon Mar 10 2014 - 14:16:56 PDT)
[AMBER] MMPBSA.py.MPI - Runtime error
(Mon Mar 10 2014 - 14:02:18 PDT)
[AMBER] Updater problems
(Mon Mar 10 2014 - 08:32:48 PDT)
Gerald Monard
Re: [AMBER] ibelly
(Tue Mar 25 2014 - 08:17:33 PDT)
Re: [AMBER] ibelly
(Tue Mar 25 2014 - 06:27:20 PDT)
Ghulam Mustafa
Re: [AMBER] Lipid14 falling apart
(Fri Mar 21 2014 - 09:28:41 PDT)
[AMBER] Lipid14 falling apart
(Thu Mar 20 2014 - 08:50:28 PDT)
Gmail2
Re: [AMBER] deprotonated histidine parameters
(Tue Mar 04 2014 - 09:11:18 PST)
Re: [AMBER] deprotonated histidine parameters
(Tue Mar 04 2014 - 08:42:02 PST)
Gustavo Seabra
Re: [AMBER] Help for system configuration
(Wed Mar 12 2014 - 06:50:19 PDT)
Hai Nguyen
Re: [AMBER] Multiple vs Continuous MD opinion
(Mon Mar 17 2014 - 15:38:34 PDT)
Hannes Loeffler
[AMBER] central atom always 3rd in improper
(Mon Mar 31 2014 - 07:45:21 PDT)
Re: [AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file?
(Thu Mar 27 2014 - 03:29:57 PDT)
Re: [AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file?
(Thu Mar 27 2014 - 02:24:49 PDT)
Re: [AMBER] tleap cannot handle dummies in the middle?
(Tue Mar 25 2014 - 07:32:27 PDT)
Re: [AMBER] tleap cannot handle dummies in the middle?
(Mon Mar 24 2014 - 05:10:11 PDT)
Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types
(Thu Mar 20 2014 - 03:07:08 PDT)
Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types
(Tue Mar 18 2014 - 09:57:22 PDT)
Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types
(Tue Mar 18 2014 - 08:23:15 PDT)
hannes.loeffler.stfc.ac.uk
Re: [AMBER] setangle in parmed API
(Wed Mar 26 2014 - 09:24:47 PDT)
[AMBER] setangle in parmed API
(Wed Mar 26 2014 - 08:01:11 PDT)
Re: [AMBER] tleap cannot handle dummies in the middle?
(Wed Mar 26 2014 - 01:36:47 PDT)
Re: [AMBER] error in running antechamber
(Sat Mar 01 2014 - 06:40:41 PST)
Hyun-seok Kim
[AMBER] Trouble obtaining force field parameters via Antechamber
(Wed Mar 05 2014 - 10:43:49 PST)
Ignacio Faustino
[AMBER] iRED: relaxation rates and NOEs with ptraj
(Sat Mar 15 2014 - 03:43:52 PDT)
Ilias Patmanidis
Re: [AMBER] Possible bug in xleap
(Thu Mar 27 2014 - 03:54:25 PDT)
Re: [AMBER] Possible bug in xleap
(Wed Mar 26 2014 - 08:49:36 PDT)
[AMBER] Possible bug in xleap
(Wed Mar 26 2014 - 08:10:11 PDT)
Ivanov, Maxim
Re: [AMBER] How to get the ESP on the grid point
(Wed Mar 19 2014 - 07:00:13 PDT)
Jacopo Sgrignani
[AMBER] Energy unit in sqm
(Tue Mar 18 2014 - 02:12:33 PDT)
[AMBER] qm/mm
(Sun Mar 16 2014 - 10:57:54 PDT)
Jan-Philip Gehrcke
Re: [AMBER] GPU not being recognised
(Mon Mar 31 2014 - 12:11:25 PDT)
Re: [AMBER] Help for system configuration
(Tue Mar 11 2014 - 10:02:57 PDT)
Re: [AMBER] pmemd.cuda segfaults
(Mon Mar 03 2014 - 08:44:29 PST)
Jason Swails
Re: [AMBER] central atom always 3rd in improper
(Mon Mar 31 2014 - 08:40:06 PDT)
Re: [AMBER] Generating frc and prep files
(Mon Mar 31 2014 - 07:20:42 PDT)
Re: [AMBER] Problem regarding running job in AMBER 12
(Sat Mar 29 2014 - 10:23:26 PDT)
Re: [AMBER] Replica exchange restart file
(Fri Mar 28 2014 - 07:53:02 PDT)
Re: [AMBER] Replica exchange restart file
(Fri Mar 28 2014 - 05:48:14 PDT)
Re: [AMBER] MMPBSA calculation with entropy
(Fri Mar 28 2014 - 04:14:19 PDT)
Re: [AMBER] How is ZN treated in AMBER14
(Thu Mar 27 2014 - 09:16:55 PDT)
Re: [AMBER] antechamber for two ligands
(Thu Mar 27 2014 - 08:22:26 PDT)
Re: [AMBER] Problem with REMD simulation
(Thu Mar 27 2014 - 08:14:43 PDT)
Re: [AMBER] antechamber for two ligands
(Thu Mar 27 2014 - 06:37:40 PDT)
Re: [AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file?
(Thu Mar 27 2014 - 03:12:03 PDT)
Re: [AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file?
(Thu Mar 27 2014 - 03:04:34 PDT)
Re: [AMBER] combining trajectories with diff. number of residues for same protein
(Wed Mar 26 2014 - 11:18:10 PDT)
Re: [AMBER] setangle in parmed API
(Wed Mar 26 2014 - 10:19:23 PDT)
Re: [AMBER] setangle in parmed API
(Wed Mar 26 2014 - 09:00:34 PDT)
Re: [AMBER] combining trajectories with diff. number of residues for same protein
(Wed Mar 26 2014 - 07:27:01 PDT)
Re: [AMBER] Generating frc and prep files
(Wed Mar 26 2014 - 03:00:44 PDT)
Re: [AMBER] Problem in configuring the amber
(Wed Mar 26 2014 - 02:55:21 PDT)
Re: [AMBER] Generating frc and prep files
(Tue Mar 25 2014 - 10:22:50 PDT)
Re: [AMBER] ibelly
(Tue Mar 25 2014 - 06:54:37 PDT)
Re: [AMBER] tleap cannot handle dummies in the middle?
(Tue Mar 25 2014 - 07:54:44 PDT)
Re: [AMBER] ibelly
(Tue Mar 25 2014 - 07:36:45 PDT)
Re: [AMBER] libgfortran.2.dylib
(Tue Mar 25 2014 - 05:16:51 PDT)
Re: [AMBER] QM/MM
(Mon Mar 24 2014 - 09:35:58 PDT)
Re: [AMBER] Positive value of delta G
(Mon Mar 24 2014 - 08:41:53 PDT)
Re: [AMBER] Generalized Born subroutines
(Mon Mar 24 2014 - 06:56:15 PDT)
Re: [AMBER] error during installation of AMBERtools13
(Mon Mar 24 2014 - 06:43:51 PDT)
Re: [AMBER] Positive value of delta G
(Mon Mar 24 2014 - 05:15:14 PDT)
Re: [AMBER] Problem with Decomposition of Binding Free Energy
(Mon Mar 24 2014 - 04:59:13 PDT)
Re: [AMBER] aMD error for the coordinates file
(Sun Mar 23 2014 - 19:34:52 PDT)
Re: [AMBER] Error: EOF when searching for tprmtop
(Fri Mar 21 2014 - 21:10:00 PDT)
Re: [AMBER] Error: EOF when searching for tprmtop
(Fri Mar 21 2014 - 18:35:33 PDT)
Re: [AMBER] AMOEBA force field in amber
(Thu Mar 20 2014 - 12:26:18 PDT)
Re: [AMBER] trajectory concatenation using cpptraj
(Thu Mar 20 2014 - 04:52:48 PDT)
Re: [AMBER] Compilation error on Ubuntu 13.10
(Thu Mar 20 2014 - 04:47:39 PDT)
Re: [AMBER] protein-ligand tutorial
(Thu Mar 20 2014 - 04:44:50 PDT)
Re: [AMBER] Error: Prmtop appears to contain modified off-diagonal elements for VDW A coef
(Thu Mar 20 2014 - 04:40:17 PDT)
Re: [AMBER] problem in generating .prmtop and .inpcrd file using amber9
(Thu Mar 20 2014 - 04:37:49 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 19 2014 - 19:13:39 PDT)
Re: [AMBER] RESTRAINT FILE
(Wed Mar 19 2014 - 18:40:33 PDT)
Re: [AMBER] RESTRAINT FILE
(Wed Mar 19 2014 - 16:20:33 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 19 2014 - 12:53:56 PDT)
Re: [AMBER] Error: Prmtop appears to contain modified off-diagonal elements for VDW A coef
(Wed Mar 19 2014 - 09:05:17 PDT)
Re: [AMBER] generating topology
(Wed Mar 19 2014 - 09:01:58 PDT)
Re: [AMBER] error in MMPBSA.py
(Wed Mar 19 2014 - 06:05:15 PDT)
Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types
(Tue Mar 18 2014 - 09:49:57 PDT)
Re: [AMBER] error in running MMPBSA.py
(Tue Mar 18 2014 - 02:46:01 PDT)
Re: [AMBER] calculating binding free energy using MM-GBSA FOR ZIF268-DNA complex
(Mon Mar 17 2014 - 10:04:01 PDT)
Re: [AMBER] calculating binding free energy using MM-GBSA FOR ZIF268-DNA complex
(Mon Mar 17 2014 - 09:28:37 PDT)
Re: [AMBER] pmf -Equilibration termination
(Mon Mar 17 2014 - 05:56:00 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Mon Mar 17 2014 - 05:28:53 PDT)
Re: [AMBER] (no subject)
(Mon Mar 17 2014 - 05:10:14 PDT)
Re: [AMBER] tleap lipid residue splitting warnings
(Sun Mar 16 2014 - 11:32:27 PDT)
Re: [AMBER] qm/mm
(Sun Mar 16 2014 - 11:22:42 PDT)
Re: [AMBER] Question about Ambertools 1.5 installation
(Fri Mar 14 2014 - 12:25:38 PDT)
Re: [AMBER] Question about Ambertools 1.5 installation
(Fri Mar 14 2014 - 10:14:47 PDT)
Re: [AMBER] electric field
(Fri Mar 14 2014 - 05:51:34 PDT)
Re: [AMBER] Problem in rst file
(Fri Mar 14 2014 - 04:54:37 PDT)
Re: [AMBER] unsubscribe mailing list
(Fri Mar 14 2014 - 04:45:58 PDT)
Re: [AMBER] electric field
(Fri Mar 14 2014 - 04:43:41 PDT)
Re: [AMBER] problem with -make-mdins mode in entropy MMPBSA.py.MPI calculations
(Thu Mar 13 2014 - 10:44:15 PDT)
Re: [AMBER] problem with -make-mdins mode in entropy MMPBSA.py.MPI calculations
(Wed Mar 12 2014 - 18:24:35 PDT)
Re: [AMBER] MutateError: Mismatch in atom # in residue VAL
(Wed Mar 12 2014 - 05:07:58 PDT)
Re: [AMBER] MutateError: Mismatch in atom
(Wed Mar 12 2014 - 03:28:03 PDT)
Re: [AMBER] cpptraj -fixatomorder
(Tue Mar 11 2014 - 06:33:20 PDT)
Re: [AMBER] PM6-DH+ QM/MM-GBSA
(Tue Mar 11 2014 - 05:28:57 PDT)
Re: [AMBER] cpptraj -fixatomorder
(Tue Mar 11 2014 - 04:59:22 PDT)
Re: [AMBER] problem in "re-image" and "unwarp"
(Tue Mar 11 2014 - 04:45:55 PDT)
Re: [AMBER] Updater problems
(Mon Mar 10 2014 - 09:59:02 PDT)
Re: [AMBER] problem in "re-image" and "unwarp"
(Mon Mar 10 2014 - 09:45:09 PDT)
Re: [AMBER] problem in "re-image" and "unwarp"
(Mon Mar 10 2014 - 08:04:36 PDT)
Re: [AMBER] problem in "re-image" and "unwarp"
(Mon Mar 10 2014 - 08:00:28 PDT)
Re: [AMBER] rism3d.snglpnt output in dx format
(Mon Mar 10 2014 - 07:34:34 PDT)
Re: [AMBER] cpptraj -fixatomorder
(Mon Mar 10 2014 - 05:01:36 PDT)
Re: [AMBER] error in running Antechamber
(Sun Mar 09 2014 - 09:21:30 PDT)
Re: [AMBER] How can I create input for two molecule?
(Sun Mar 09 2014 - 09:19:42 PDT)
Re: [AMBER] How can I create input for two molecule?
(Sun Mar 09 2014 - 06:39:57 PDT)
Re: [AMBER] pmemd.cuda segfaults
(Sat Mar 08 2014 - 11:09:25 PST)
Re: [AMBER] Mutating residues in an RNA
(Sat Mar 08 2014 - 07:20:26 PST)
Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron
(Fri Mar 07 2014 - 10:34:24 PST)
Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron
(Fri Mar 07 2014 - 08:26:54 PST)
Re: [AMBER] Request for help in using Amberlite
(Fri Mar 07 2014 - 05:58:03 PST)
Re: [AMBER] MMPBSA TrajError
(Thu Mar 06 2014 - 04:58:53 PST)
Re: [AMBER] pmemd.cuda segfaults
(Wed Mar 05 2014 - 12:20:55 PST)
Re: [AMBER] pmf-plane to plane restrain
(Wed Mar 05 2014 - 05:12:29 PST)
Re: [AMBER] how to produce the prmtop of 'ch3cn'
(Wed Mar 05 2014 - 04:56:33 PST)
Re: [AMBER] Unable to restrain A-DNA conformation
(Wed Mar 05 2014 - 04:53:02 PST)
Re: [AMBER] MMPBSA alanine scanning
(Tue Mar 04 2014 - 18:08:54 PST)
Re: [AMBER] MMPBSA TrajError
(Tue Mar 04 2014 - 13:41:31 PST)
Re: [AMBER] deprotonated histidine parameters
(Tue Mar 04 2014 - 08:51:05 PST)
Re: [AMBER] deprotonated histidine parameters
(Tue Mar 04 2014 - 05:17:39 PST)
Re: [AMBER] question about mmpbsa result
(Tue Mar 04 2014 - 05:10:30 PST)
Re: [AMBER] format of FINAL_DECOMP_MMPBSA.dat
(Mon Mar 03 2014 - 09:24:08 PST)
Re: [AMBER] pmemd.cuda segfaults
(Mon Mar 03 2014 - 09:01:04 PST)
Re: [AMBER] mass
(Mon Mar 03 2014 - 06:45:28 PST)
Re: [AMBER] MMPBSA.py error
(Mon Mar 03 2014 - 05:14:02 PST)
Jean-Paul Becker
Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron
(Thu Mar 06 2014 - 06:47:14 PST)
Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron
(Wed Mar 05 2014 - 13:11:51 PST)
[AMBER] non-bonded parameters for ferric iron and ferrous iron
(Tue Mar 04 2014 - 09:08:48 PST)
Jio M
Re: [AMBER] cpptraj grid function
(Wed Mar 26 2014 - 19:04:43 PDT)
Re: [AMBER] cpptraj grid function
(Wed Mar 26 2014 - 15:21:13 PDT)
Re: [AMBER] cpptraj grid function
(Tue Mar 25 2014 - 13:11:11 PDT)
Re: [AMBER] cpptraj grid function
(Tue Mar 25 2014 - 12:02:18 PDT)
Re: [AMBER] cpptraj grid function
(Mon Mar 24 2014 - 14:06:11 PDT)
Re: [AMBER] cpptraj grid function
(Sat Mar 22 2014 - 19:35:11 PDT)
[AMBER] cpptraj grid function
(Sat Mar 22 2014 - 11:43:02 PDT)
Re: [AMBER] strain/energy of backbone atoms
(Fri Mar 21 2014 - 12:03:23 PDT)
Re: [AMBER] strain/energy of backbone atoms
(Wed Mar 19 2014 - 10:14:05 PDT)
[AMBER] strain/energy of backbone atoms
(Wed Mar 19 2014 - 09:14:21 PDT)
Re: [AMBER] rdf around atom
(Mon Mar 17 2014 - 16:16:17 PDT)
[AMBER] rdf around atom
(Mon Mar 17 2014 - 12:18:24 PDT)
Re: [AMBER] AmberTools update 24 for CPPTRAJ
(Thu Mar 13 2014 - 16:21:40 PDT)
John Chuang莊曜遠
[AMBER] unsubscribe mailing list
(Fri Mar 14 2014 - 02:09:38 PDT)
John Smith
Re: [AMBER] QM/MM
(Mon Mar 24 2014 - 10:18:27 PDT)
[AMBER] QM/MM
(Mon Mar 24 2014 - 09:17:32 PDT)
Jonathan Sheehan
Re: [AMBER] antechamber for two ligands
(Sun Mar 30 2014 - 07:03:06 PDT)
Jose Borreguero
[AMBER] anybody knows how Langevin dynamics affects time-correlation functions?
(Fri Mar 28 2014 - 12:27:41 PDT)
JPB
Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron
(Mon Mar 10 2014 - 01:03:05 PDT)
Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron
(Fri Mar 07 2014 - 08:07:49 PST)
Juan.Aranda.uv.es
[AMBER] Cpptraj hbond bridgeout segmentation fault
(Thu Mar 20 2014 - 14:01:12 PDT)
Kanin Wichapong
[AMBER] PM6-DH+ QM/MM-GBSA
(Tue Mar 11 2014 - 02:38:56 PDT)
Ken Merz
Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron
(Fri Mar 07 2014 - 08:27:05 PST)
Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron
(Fri Mar 07 2014 - 08:19:11 PST)
Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron
(Tue Mar 04 2014 - 13:45:57 PST)
Re: [AMBER] deprotonated histidine parameters
(Tue Mar 04 2014 - 13:25:25 PST)
Kim TaeHwan
Re: [AMBER] How to get the ESP on the grid point
(Wed Mar 19 2014 - 07:24:55 PDT)
[AMBER] How to get the ESP on the grid point
(Wed Mar 19 2014 - 00:19:13 PDT)
Kshatresh Dutta Dubey
Re: [AMBER] MMPBSA.py: decomposition error
(Sun Mar 23 2014 - 13:43:36 PDT)
[AMBER] MMPBSA.py: decomposition error
(Sun Mar 23 2014 - 10:57:46 PDT)
Re: [AMBER] Help for system configuration
(Fri Mar 14 2014 - 00:24:28 PDT)
Re: [AMBER] Help for system configuration
(Tue Mar 11 2014 - 21:39:24 PDT)
Re: [AMBER] Help for system configuration
(Tue Mar 11 2014 - 14:35:24 PDT)
[AMBER] Help for system configuration
(Tue Mar 11 2014 - 09:46:10 PDT)
Lachele Foley
Re: [AMBER] Parameters for a residue
(Fri Mar 14 2014 - 08:39:25 PDT)
Re: [AMBER] modeling glucoside
(Fri Mar 14 2014 - 08:33:32 PDT)
lnubbs2014
[AMBER] MutateError: Mismatch in atom # in residue VAL
(Wed Mar 12 2014 - 04:49:28 PDT)
[AMBER] MutateError: Mismatch in atom
(Wed Mar 12 2014 - 04:06:27 PDT)
[AMBER] MutateError: Mismatch in atom
(Wed Mar 12 2014 - 01:43:11 PDT)
lnubbs2014
[AMBER] MutateError: Mismatch in atom
(Wed Mar 12 2014 - 03:07:27 PDT)
lnubbs2014.163.com
Re: [AMBER] MutateError: Mismatch in atom # in residue VAL
(Wed Mar 12 2014 - 05:17:37 PDT)
loue chen
[AMBER] Problem with Decomposition of Binding Free Energy
(Sun Mar 23 2014 - 20:31:25 PDT)
Manikanthan Bhavaraju
Re: [AMBER] error in MMPBSA.py
(Tue Mar 18 2014 - 21:42:25 PDT)
Re: [AMBER] MMPBSA.py not generating specified frames for analysis
(Sat Mar 15 2014 - 21:50:30 PDT)
[AMBER] MMPBSA.py not generating specified frames for analysis
(Sat Mar 15 2014 - 19:34:44 PDT)
Marcus Arieno
Re: [AMBER] MMPBSA
(Mon Mar 17 2014 - 04:08:06 PDT)
Marek Maly
Re: [AMBER] problem with -make-mdins mode in entropy MMPBSA.py.MPI calculations
(Fri Mar 14 2014 - 03:53:09 PDT)
Re: [AMBER] problem with -make-mdins mode in entropy MMPBSA.py.MPI calculations
(Thu Mar 13 2014 - 06:58:05 PDT)
[AMBER] problem with -make-mdins mode in entropy MMPBSA.py.MPI calculations
(Wed Mar 12 2014 - 17:40:12 PDT)
Mary Varughese
Re: [AMBER] MMPBSA
(Mon Mar 17 2014 - 11:10:06 PDT)
[AMBER] MMPBSA
(Mon Mar 17 2014 - 03:51:51 PDT)
Maryam Azimzadeh Irani
Re: [AMBER] MMPBSA alanine scanning
(Thu Mar 06 2014 - 23:35:50 PST)
[AMBER] MMPBSA alanine scanning
(Tue Mar 04 2014 - 17:56:40 PST)
maryam azimzadehirani
[AMBER] aMD error for the coordinates file
(Sun Mar 23 2014 - 19:24:23 PDT)
Massimiliano Porrini
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 19 2014 - 10:40:12 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 19 2014 - 10:10:17 PDT)
Mele N.
Re: [AMBER] Replica exchange restart file
(Fri Mar 28 2014 - 06:20:05 PDT)
[AMBER] Replica exchange restart file
(Fri Mar 28 2014 - 05:15:17 PDT)
Mengyuan Zhu
Re: [AMBER] Antechamber add new parameter
(Sat Mar 08 2014 - 10:09:25 PST)
[AMBER] Antechamber add new parameter
(Sat Mar 08 2014 - 09:40:54 PST)
Milo Westler
Re: [AMBER] restart MD from arbitrary snapshot
(Mon Mar 31 2014 - 05:59:56 PDT)
Re: [AMBER] restart MD from arbitrary snapshot
(Sun Mar 30 2014 - 16:27:14 PDT)
[AMBER] restart MD from arbitrary snapshot
(Sun Mar 30 2014 - 13:29:35 PDT)
MOHD HOMAIDUR RAHMAN
Re: [AMBER] Regarding SPC/E water model
(Thu Mar 27 2014 - 11:35:45 PDT)
Re: [AMBER] Regarding SPC/E water model
(Wed Mar 26 2014 - 22:27:31 PDT)
[AMBER] Regarding SPC/E water model
(Wed Mar 26 2014 - 11:07:01 PDT)
nalini chauhan
[AMBER] ERROR in sidechain.bcl file in MCPB
(Thu Mar 06 2014 - 00:29:32 PST)
[AMBER] Error : while running force field modification files
(Wed Mar 05 2014 - 23:23:26 PST)
Neha Gandhi
[AMBER] running amber on multigpu
(Wed Mar 26 2014 - 07:17:52 PDT)
[AMBER] trajectory concatenation using cpptraj
(Thu Mar 20 2014 - 01:32:12 PDT)
Re: [AMBER] electric field
(Sat Mar 15 2014 - 04:32:52 PDT)
Re: [AMBER] electric field
(Fri Mar 14 2014 - 04:48:47 PDT)
[AMBER] electric field
(Fri Mar 14 2014 - 03:50:52 PDT)
Nelson Max
Re: [AMBER] Error: EOF when searching for tprmtop
(Fri Mar 21 2014 - 20:57:16 PDT)
[AMBER] Error: EOF when searching for tprmtop
(Fri Mar 21 2014 - 17:32:04 PDT)
nhai.wn
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 19 2014 - 01:00:37 PDT)
Nitin Sharma
Re: [AMBER] combining trajectories with diff. number of residues for same protein
(Thu Mar 27 2014 - 20:13:57 PDT)
Re: [AMBER] combining trajectories with diff. number of residues for same protein
(Thu Mar 27 2014 - 00:57:11 PDT)
Re: [AMBER] combining trajectories with diff. number of residues for same protein
(Wed Mar 26 2014 - 12:38:38 PDT)
Re: [AMBER] combining trajectories with diff. number of residues for same protein
(Wed Mar 26 2014 - 10:42:35 PDT)
[AMBER] combining trajectories with diff. number of residues for same protein
(Wed Mar 26 2014 - 06:29:37 PDT)
Re: [AMBER] Hbond
(Tue Mar 18 2014 - 21:42:20 PDT)
[AMBER] Hbond
(Tue Mar 18 2014 - 12:47:37 PDT)
[AMBER] format of FINAL_DECOMP_MMPBSA.dat
(Mon Mar 03 2014 - 08:29:00 PST)
pavel.banas.upol.cz
Re: [AMBER] pmemd.cuda segfaults
(Tue Mar 11 2014 - 07:54:23 PDT)
Re: [AMBER] pmemd.cuda segfaults
(Tue Mar 11 2014 - 07:50:51 PDT)
Re: [AMBER] pmemd.cuda segfaults
(Sat Mar 08 2014 - 00:39:13 PST)
Re: [AMBER] pmemd.cuda segfaults
(Wed Mar 05 2014 - 12:09:15 PST)
Re: [AMBER] pmemd.cuda segfaults
(Tue Mar 04 2014 - 00:10:51 PST)
Re: [AMBER] pmemd.cuda segfaults
(Mon Mar 03 2014 - 12:44:24 PST)
[AMBER] pmemd.cuda segfaults
(Mon Mar 03 2014 - 08:09:38 PST)
Pengfei Li
Re: [AMBER] How is ZN treated in AMBER14
(Thu Mar 27 2014 - 15:43:41 PDT)
Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron
(Thu Mar 13 2014 - 08:31:44 PDT)
Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron
(Thu Mar 06 2014 - 14:22:14 PST)
Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron
(Wed Mar 05 2014 - 13:38:47 PST)
Pete Kekenes-Huskey
[AMBER] small box changes still fail with 'Nonbond cells need to be recalculated'
(Thu Mar 27 2014 - 21:46:34 PDT)
[AMBER] using chamber with vmd-generated psf (after reformatting to extended format)
(Mon Mar 24 2014 - 11:42:18 PDT)
Prema Mallipeddi
[AMBER] Incomplete frcmod from parmchk
(Fri Mar 21 2014 - 11:11:43 PDT)
psu4.uic.edu
[AMBER] rescue amd.log
(Thu Mar 20 2014 - 16:49:41 PDT)
[AMBER] scale molecular dynamic / GPU available in Amber 12?
(Tue Mar 11 2014 - 12:57:18 PDT)
Re: [AMBER] pmemd.CUDA.mpi micro-second long simulation
(Tue Mar 04 2014 - 10:40:14 PST)
R R S Pissurlenkar
[AMBER] How is ZN treated in AMBER14
(Thu Mar 27 2014 - 08:46:17 PDT)
Re: [AMBER] AMBER Digest, Vol 793, Issue 1
(Fri Mar 14 2014 - 20:40:09 PDT)
[AMBER] Parameters for a residue
(Fri Mar 14 2014 - 05:55:08 PDT)
Rajiv Gandhi
Re: [AMBER] (no subject)
(Sun Mar 16 2014 - 23:43:40 PDT)
Rasha Alqus
[AMBER] pmf -Equilibration termination
(Mon Mar 17 2014 - 05:25:04 PDT)
[AMBER] pmf-plane to plane restrain
(Wed Mar 05 2014 - 00:02:13 PST)
[AMBER] Pmf-plane to plane restrain
(Tue Mar 04 2014 - 09:03:19 PST)
Raviprasad Aduri
[AMBER] Mutating residues in an RNA
(Fri Mar 07 2014 - 23:14:36 PST)
Ray Luo, Ph.D.
Re: [AMBER] Positive value of delta G
(Mon Mar 24 2014 - 12:31:08 PDT)
Re: [AMBER] How to get the ESP on the grid point
(Wed Mar 19 2014 - 10:19:32 PDT)
Robert McGibbon
Re: [AMBER] Generalized Born subroutines
(Tue Mar 25 2014 - 04:12:24 PDT)
Re: [AMBER] electric field
(Sat Mar 15 2014 - 13:46:21 PDT)
Robert Molt
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 19 2014 - 10:16:37 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 19 2014 - 08:32:30 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 05 2014 - 08:09:02 PST)
Robin Jain
[AMBER] Request for help in using Amberlite
(Thu Mar 06 2014 - 23:02:33 PST)
Ross Walker
[AMBER] AMBER on GTX-Titan Black
(Mon Mar 31 2014 - 09:51:09 PDT)
Re: [AMBER] GPU not being recognised
(Mon Mar 31 2014 - 09:37:16 PDT)
Re: [AMBER] Lipid14 falling apart
(Thu Mar 20 2014 - 15:02:20 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 19 2014 - 10:25:44 PDT)
Re: [AMBER] tleap lipid residue splitting warnings
(Mon Mar 17 2014 - 08:45:09 PDT)
Re: [AMBER] tleap lipid residue splitting warnings
(Sun Mar 16 2014 - 20:29:21 PDT)
Re: [AMBER] Help for system configuration
(Thu Mar 13 2014 - 16:22:12 PDT)
Re: [AMBER] Help for system configuration
(Thu Mar 13 2014 - 08:50:09 PDT)
Re: [AMBER] Help for system configuration
(Tue Mar 11 2014 - 16:57:32 PDT)
Re: [AMBER] Help for system configuration
(Tue Mar 11 2014 - 15:22:22 PDT)
Re: [AMBER] scale molecular dynamic / GPU available in Amber 12?
(Tue Mar 11 2014 - 13:10:31 PDT)
Re: [AMBER] Help for system configuration
(Tue Mar 11 2014 - 12:31:26 PDT)
Re: [AMBER] Help for system configuration
(Tue Mar 11 2014 - 12:32:09 PDT)
Re: [AMBER] how to get around "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable"
(Sat Mar 08 2014 - 18:39:14 PST)
Re: [AMBER] pmemd.cuda segfaults
(Sat Mar 08 2014 - 10:00:00 PST)
Re: [AMBER] pmemd.cuda segfaults
(Wed Mar 05 2014 - 12:49:26 PST)
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 05 2014 - 09:08:35 PST)
Re: [AMBER] pmemd.CUDA.mpi micro-second long simulation
(Tue Mar 04 2014 - 10:49:14 PST)
Re: [AMBER] pmemd.cuda segfaults
(Mon Mar 03 2014 - 13:43:45 PST)
Re: [AMBER] pmemd.cuda segfaults
(Mon Mar 03 2014 - 09:03:02 PST)
Re: [AMBER] pmemd.cuda segfaults
(Mon Mar 03 2014 - 08:49:31 PST)
Re: [AMBER] pmemd.cuda segfaults
(Mon Mar 03 2014 - 08:43:12 PST)
Roza M
Re: [AMBER] calculating binding free energy using MM-GBSA FOR ZIF268-DNA complex
(Mon Mar 17 2014 - 09:52:35 PDT)
[AMBER] calculating binding free energy using MM-GBSA FOR ZIF268-DNA complex
(Mon Mar 17 2014 - 07:58:00 PDT)
Saeed Nasiri
[AMBER] the combination ntb != 0, ntp != 0, ifbox == 0 is not supported!
(Thu Mar 20 2014 - 08:31:10 PDT)
[AMBER] cpptraj -fixatomorder
(Tue Mar 11 2014 - 02:15:30 PDT)
[AMBER] cpptraj -fixatomorder
(Mon Mar 10 2014 - 00:01:00 PDT)
[AMBER] Fwd: cpptraj -fixatomorder
(Sat Mar 08 2014 - 01:42:59 PST)
Sajeewa Pemasinghe
Re: [AMBER] Specifying a particular angle in ptraj when there is more than one residue with the same residue number
(Thu Mar 13 2014 - 18:03:46 PDT)
[AMBER] Specifying a particular angle in ptraj when there is more than one residue with the same residue number
(Thu Mar 13 2014 - 18:00:42 PDT)
Scott Brozell
[AMBER] bugzilla searches
(Tue Mar 18 2014 - 08:52:47 PDT)
Setyanto Md
[AMBER] How to update cpptraj and setting donor/acceptormask
(Wed Mar 26 2014 - 01:34:38 PDT)
Sidney Elmer
Re: [AMBER] reg: the charges for methylated cytosine atoms
(Mon Mar 31 2014 - 13:45:01 PDT)
Re: [AMBER] reg: the charges for methylated cytosine atoms
(Fri Mar 28 2014 - 15:03:34 PDT)
Re: [AMBER] reg: the charges for methylated cytosine atoms
(Fri Mar 28 2014 - 12:21:26 PDT)
Re: [AMBER] reg: the charges for methylated cytosine atoms
(Wed Mar 12 2014 - 17:01:58 PDT)
Re: [AMBER] reg: the charges for methylated cytosine atoms
(Wed Mar 12 2014 - 11:46:08 PDT)
Sohag Biswas
[AMBER] amber trajectory to gromacs trajectory conversion
(Sat Mar 01 2014 - 22:55:23 PST)
Sorensen, Jesper
Re: [AMBER] FF10 Error
(Sat Mar 08 2014 - 10:30:12 PST)
[AMBER] Modified RNA frcmod error
(Fri Mar 07 2014 - 16:51:49 PST)
[AMBER] FF10 Error
(Fri Mar 07 2014 - 16:47:59 PST)
Soumendranath Bhakat
[AMBER] Open Source Drug Design and In Silico Molecules Pledge to AMBER developers
(Mon Mar 24 2014 - 06:35:19 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 19 2014 - 00:30:34 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Mon Mar 17 2014 - 04:45:46 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Mon Mar 17 2014 - 04:25:51 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Sun Mar 16 2014 - 23:40:23 PDT)
Re: [AMBER] Multiple vs Continuous MD opinion
(Wed Mar 05 2014 - 07:58:58 PST)
[AMBER] Multiple vs Continuous MD opinion
(Wed Mar 05 2014 - 06:33:50 PST)
Sourav Purohit
Re: [AMBER] RESTRAINT FILE
(Thu Mar 20 2014 - 08:20:54 PDT)
Re: [AMBER] RESTRAINT FILE
(Wed Mar 19 2014 - 16:28:09 PDT)
[AMBER] RESTRAINT FILE
(Wed Mar 19 2014 - 16:16:32 PDT)
Souvik Sur
[AMBER] Problem regarding running job in AMBER 12
(Sat Mar 29 2014 - 04:16:29 PDT)
Stefan Richter
[AMBER] Compilation of amber12 on GRAY XE6
(Fri Mar 14 2014 - 07:29:56 PDT)
Sushi Shilpa
[AMBER] Problem in rst file
(Thu Mar 13 2014 - 23:33:35 PDT)
[AMBER] Arsenic co-ordinates
(Thu Mar 13 2014 - 23:17:05 PDT)
Sushil Mishra
Re: [AMBER] delta G calculation in MMPBSA
(Sun Mar 23 2014 - 00:52:50 PDT)
T Luchko (Lists)
Re: [AMBER] 3DRISM and orientationally averaged 3D pair distribution functions
(Wed Mar 12 2014 - 13:07:12 PDT)
Re: [AMBER] rism3d.snglpnt output in dx format
(Mon Mar 10 2014 - 09:33:54 PDT)
Tanmoy Paul
[AMBER] Percentage of secondary structure determination
(Tue Mar 18 2014 - 04:23:19 PDT)
Thomas Cheatham
[AMBER] Call for participation: ISQBP Meeting, Telluride 15-19.06.2014
(Mon Mar 10 2014 - 09:27:42 PDT)
Re: [AMBER] problem in "re-image" and "unwarp"
(Mon Mar 10 2014 - 08:57:45 PDT)
Re: [AMBER] problem in "re-image" and "unwarp"
(Mon Mar 10 2014 - 08:27:02 PDT)
Thomas Evangelidis
[AMBER] repulsive restraints
(Thu Mar 27 2014 - 08:34:12 PDT)
Thomas Exner
[AMBER] non-protonated and protonated phosphate
(Thu Mar 27 2014 - 08:47:14 PDT)
Tru Huynh
Re: [AMBER] GPU not being recognised
(Mon Mar 31 2014 - 09:26:32 PDT)
Re: [AMBER] pmemd.cuda segfaults
(Thu Mar 06 2014 - 11:25:01 PST)
Urszula Uciechowska
Re: [AMBER] ibelly
(Tue Mar 25 2014 - 07:16:15 PDT)
Re: [AMBER] ibelly
(Tue Mar 25 2014 - 06:39:14 PDT)
[AMBER] ibelly
(Tue Mar 25 2014 - 06:13:06 PDT)
[AMBER] igb=1
(Tue Mar 25 2014 - 03:11:42 PDT)
[AMBER] error during installation of AMBERtools13
(Mon Mar 24 2014 - 06:35:31 PDT)
Valentina Romano
Re: [AMBER] Adenine parameters and topology files
(Tue Mar 25 2014 - 03:09:05 PDT)
[AMBER] Adenine without ribose ring and/or phosphate groups
(Mon Mar 24 2014 - 09:46:20 PDT)
[AMBER] Adenine parameters and topology files
(Mon Mar 24 2014 - 08:20:29 PDT)
Vijay Manickam Achari
[AMBER] generating topology
(Wed Mar 19 2014 - 06:47:05 PDT)
Re: [AMBER] problem in "re-image" and "unwarp"
(Mon Mar 10 2014 - 23:37:38 PDT)
[AMBER] problem in "re-image" and "unwarp"
(Mon Mar 10 2014 - 07:18:49 PDT)
Re: [AMBER] modeling glucoside
(Sun Mar 09 2014 - 01:37:48 PST)
[AMBER] modeling glucoside
(Sat Mar 08 2014 - 02:29:36 PST)
[AMBER] extracting selected lipids from bilayer
(Mon Mar 03 2014 - 00:57:07 PST)
Vijay Singh
Re: [AMBER] Ptraj's "NO ATOMS DETECTED" problem
(Sat Mar 15 2014 - 20:33:05 PDT)
Re: [AMBER] MMPBSA
(Sat Mar 15 2014 - 20:33:05 PDT)
Vijayalaxmi Sahoo
[AMBER] problem in generating .prmtop and .inpcrd file using amber9
(Thu Mar 20 2014 - 03:47:32 PDT)
[AMBER] problem in generating .prmtop and .inpcrd file using amber9
(Wed Mar 19 2014 - 20:08:47 PDT)
Vlad Cojocaru
Re: [AMBER] Positive value of delta G
(Mon Mar 24 2014 - 08:52:02 PDT)
Weinzierl, Robert O J
[AMBER] Cuda compilation problems with Ubuntu 13.10
(Fri Mar 21 2014 - 07:55:06 PDT)
[AMBER] Compilation error on Ubuntu 13.10
(Thu Mar 20 2014 - 00:57:50 PDT)
wmsmith.uci.edu
Re: [AMBER] data overflow in dx output from rism3d
(Thu Mar 27 2014 - 23:40:30 PDT)
Re: [AMBER] data overflow in dx output from rism3d
(Thu Mar 27 2014 - 23:31:39 PDT)
Wook Lee
Re: [AMBER] Question about Ambertools 1.5 installation
(Fri Mar 14 2014 - 12:53:56 PDT)
Re: [AMBER] Question about Ambertools 1.5 installation
(Fri Mar 14 2014 - 10:37:30 PDT)
[AMBER] Question about Ambertools 1.5 installation
(Fri Mar 14 2014 - 09:53:04 PDT)
Yeng-Tseng Wang
Re: [AMBER] Generating frc and prep files
(Tue Mar 25 2014 - 09:27:15 PDT)
Re: [AMBER] QM/MM
(Mon Mar 24 2014 - 09:19:47 PDT)
Zahra Khatti
Re: [AMBER] How can I create input for two molecule?
(Sun Mar 09 2014 - 08:58:16 PDT)
[AMBER] How can I create input for two molecule?
(Sun Mar 09 2014 - 06:18:48 PDT)
[AMBER] mass
(Mon Mar 03 2014 - 06:13:13 PST)
肖立
Re: [AMBER] problem when performing the ired anaysis
(Fri Mar 07 2014 - 16:31:51 PST)
[AMBER] problem when performing the ired anaysis
(Fri Mar 07 2014 - 15:18:46 PST)
[AMBER] Problem in using xleap
(Thu Mar 06 2014 - 21:07:53 PST)
闫玉娜
[AMBER] how to produce the prmtop of 'ch3cn'
(Wed Mar 05 2014 - 00:16:25 PST)
Last message date
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Mon Mar 31 2014 - 14:00:04 PDT
Archived on
: Fri Nov 22 2024 - 05:54:52 PST
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