Amber Archive Jul 2014 by author
537 messages
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Starting
Mon Jun 30 2014 - 21:30:02 PDT,
Ending
Thu Jul 31 2014 - 21:00:03 PDT
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ABEL Stephane 175950
Re: [AMBER] Solvating the system with polyethylene glycol PEG
(Mon Jul 28 2014 - 11:01:04 PDT)
Abhishek Mukhopadhyay
[AMBER] Visualizing average solvent-oxygen density/occupancy from an MD trajectory
(Tue Jul 01 2014 - 17:34:10 PDT)
Ahmed Ayoub
Re: [AMBER] MMPBSA Energy between system and its image
(Fri Jul 04 2014 - 14:15:44 PDT)
[AMBER] MMPBSA Energy between system and its image
(Thu Jul 03 2014 - 12:41:17 PDT)
Alegrete, Matthew
[AMBER] cpptraj rotdif parameters
(Thu Jul 10 2014 - 12:34:29 PDT)
Alessandro Contini
[AMBER] R: Re: ATP and Mg2+ parameters
(Tue Jul 08 2014 - 08:21:14 PDT)
Re: [AMBER] ATP and Mg2+ parameters
(Tue Jul 08 2014 - 03:50:50 PDT)
Re: [AMBER] errors in compiling AmberTools14
(Mon Jul 07 2014 - 07:42:51 PDT)
[AMBER] errors in compiling AmberTools14
(Mon Jul 07 2014 - 02:21:40 PDT)
[AMBER] errors in compiling AmberTools14
(Fri Jul 04 2014 - 00:26:19 PDT)
Allen, Scott Edward
Re: [AMBER] imin=5, maxcyc>1 stalls
(Tue Jul 08 2014 - 08:56:08 PDT)
[AMBER] imin=5, maxcyc>1 stalls
(Tue Jul 08 2014 - 06:59:59 PDT)
amor san juan
Re: [AMBER] graph energy check after minimization
(Sat Jul 12 2014 - 03:03:44 PDT)
[AMBER] graph energy check after minimization
(Fri Jul 11 2014 - 11:59:47 PDT)
anu chandra
[AMBER] Tool in PTRAJ/CPPTRAJ to analyse residue movement
(Wed Jul 16 2014 - 05:00:25 PDT)
Arthur Roberts
[AMBER] How is temperature in Amber MD simulations calculated?
(Thu Jul 10 2014 - 13:04:20 PDT)
Asmita Gupta
[AMBER] ncsu_smd support in pmemd amber12
(Thu Jul 03 2014 - 06:31:56 PDT)
Re: [AMBER] sander error "Could not find cntrl namelist"
(Wed Jul 02 2014 - 07:20:21 PDT)
Re: [AMBER] sander error "Could not find cntrl namelist"
(Tue Jul 01 2014 - 09:22:06 PDT)
[AMBER] sander error "Could not find cntrl namelist"
(Tue Jul 01 2014 - 08:31:36 PDT)
Baptiste Legrand
Re: [AMBER] To get resp charges of a modified central residue (not an integer).
(Thu Jul 17 2014 - 00:47:04 PDT)
[AMBER] To get resp charges of a modified central residue (not an integer).
(Tue Jul 15 2014 - 08:24:52 PDT)
Re: [AMBER] Build Xleap
(Mon Jul 07 2014 - 08:35:51 PDT)
Re: [AMBER] Build Xleap
(Mon Jul 07 2014 - 06:15:14 PDT)
[AMBER] Build Xleap
(Mon Jul 07 2014 - 01:24:32 PDT)
Bill Miller III
Re: [AMBER] Free Binding Energy Calculation
(Thu Jul 10 2014 - 06:11:28 PDT)
Blake Mertz
[AMBER] pmemdTI test failure
(Tue Jul 08 2014 - 10:32:49 PDT)
Blatter Markus
Re: [AMBER] RNA covalent bond angles
(Wed Jul 16 2014 - 08:38:07 PDT)
Re: [AMBER] RNA covalent bond angles
(Wed Jul 16 2014 - 08:11:37 PDT)
[AMBER] RNA covalent bond angles
(Wed Jul 16 2014 - 02:33:35 PDT)
Bob Healey
[AMBER] Attempting to compile fresh version of Amber 11, bugfixes > 17 won't apply cleanly
(Wed Jul 02 2014 - 08:22:11 PDT)
Brian Radak
Re: [AMBER] How to calculate the parameters of metal ions?
(Thu Jul 31 2014 - 07:17:05 PDT)
Re: [AMBER] Parameters for SulfoTyrosine
(Wed Jul 30 2014 - 08:08:31 PDT)
Re: [AMBER] PMF by WHAM
(Mon Jul 28 2014 - 06:53:57 PDT)
Re: [AMBER] Berendsen vs. Monte Carlo
(Fri Jul 25 2014 - 07:49:06 PDT)
Re: [AMBER] On the values of boost potential for aMD based on amd.log
(Wed Jul 23 2014 - 08:28:35 PDT)
Re: [AMBER] sander.APBS: automatic grid adjustments in output?
(Wed Jul 23 2014 - 05:35:21 PDT)
[AMBER] sander.APBS: automatic grid adjustments in output?
(Tue Jul 22 2014 - 09:55:47 PDT)
Re: [AMBER] imin=5
(Thu Jul 17 2014 - 08:31:44 PDT)
Re: [AMBER] How is temperature in Amber MD simulations calculated?
(Thu Jul 10 2014 - 13:40:11 PDT)
Re: [AMBER] RDF
(Tue Jul 01 2014 - 09:13:43 PDT)
Brittany Boykin
[AMBER] Question
(Thu Jul 10 2014 - 14:01:53 PDT)
[AMBER] Question
(Wed Jul 09 2014 - 09:51:19 PDT)
Carlos Simmerling
Re: [AMBER] Equilibirum/System convergence
(Thu Jul 31 2014 - 10:33:38 PDT)
Re: [AMBER] On the ussage of the langevens thermostat with the gb models
(Sat Jul 26 2014 - 04:50:10 PDT)
Re: [AMBER] Implicit solvent and membrane protein
(Thu Jul 17 2014 - 12:55:41 PDT)
Re: [AMBER] Loop refirement
(Thu Jul 17 2014 - 10:06:50 PDT)
Re: [AMBER] Loop refirement
(Thu Jul 17 2014 - 10:05:47 PDT)
Re: [AMBER] imin=5
(Thu Jul 17 2014 - 08:24:44 PDT)
Re: [AMBER] Loop refirement
(Thu Jul 17 2014 - 05:00:04 PDT)
Re: [AMBER] Loop refirement
(Wed Jul 16 2014 - 08:37:04 PDT)
Re: [AMBER] Finding a good REMD temperature ladder
(Wed Jul 09 2014 - 13:13:51 PDT)
Changqing Yan
[AMBER] Fwd: AMBER Digest, Vol 926, Issue 1
(Fri Jul 25 2014 - 19:22:45 PDT)
Re: [AMBER] element symbol error in tleap
(Fri Jul 25 2014 - 02:19:16 PDT)
[AMBER] element symbol error in tleap
(Fri Jul 25 2014 - 01:52:40 PDT)
Charu Suri
[AMBER] Error installing Ambertools on Centos 6.3 and open suse 12.3
(Thu Jul 17 2014 - 05:45:58 PDT)
Christina Bergonzo
Re: [AMBER] How to calculate the parameters of metal ions?
(Thu Jul 31 2014 - 07:07:58 PDT)
Re: [AMBER] RNA covalent bond angles
(Wed Jul 16 2014 - 07:44:06 PDT)
Re: [AMBER] QM on Adenosine
(Wed Jul 02 2014 - 07:50:33 PDT)
Christy Lee
Re: [AMBER] ZAFF-CCCH Histidine charge problem
(Thu Jul 10 2014 - 11:39:50 PDT)
Re: [AMBER] ZAFF-CCCH Histidine charge problem
(Mon Jul 07 2014 - 14:54:24 PDT)
Re: [AMBER] ZAFF-CCCH Histidine charge problem
(Mon Jul 07 2014 - 10:18:35 PDT)
Re: [AMBER] ZAFF-CCCH Histidine charge problem
(Thu Jul 03 2014 - 16:11:30 PDT)
Re: [AMBER] ZAFF-CCCH Histidine charge problem
(Wed Jul 02 2014 - 14:07:43 PDT)
[AMBER] ZAFF-CCCH Histidine charge problem
(Tue Jul 01 2014 - 14:00:09 PDT)
cq y
[AMBER] element symbol error in tleap
(Fri Jul 25 2014 - 01:35:03 PDT)
cye927.mail.ustc.edu.cn
[AMBER] AMP Parameters
(Tue Jul 22 2014 - 01:40:26 PDT)
Daniel Roe
Re: [AMBER] this a very green neophyte's question.
(Thu Jul 31 2014 - 15:05:03 PDT)
Re: [AMBER] Problem with atommap in cpptraj
(Thu Jul 31 2014 - 13:31:15 PDT)
Re: [AMBER] erro na criação do complexo
(Wed Jul 30 2014 - 12:53:50 PDT)
Re: [AMBER] Running PCA
(Wed Jul 30 2014 - 07:05:04 PDT)
Re: [AMBER] Running PCA
(Tue Jul 29 2014 - 07:31:20 PDT)
Re: [AMBER] Running PCA
(Tue Jul 29 2014 - 07:16:28 PDT)
Re: [AMBER] cpptraj not processing all mdcrd files
(Fri Jul 25 2014 - 09:25:50 PDT)
Re: [AMBER] ptraj binary missing from AmberTools 13 install?
(Wed Jul 23 2014 - 13:42:48 PDT)
Re: [AMBER] On the values of boost potential for aMD based on amd.log
(Wed Jul 23 2014 - 07:02:03 PDT)
Re: [AMBER] Z-axis coordinates
(Wed Jul 23 2014 - 06:57:57 PDT)
Re: [AMBER] atom number same as line number for cpptraj
(Tue Jul 22 2014 - 19:12:25 PDT)
Re: [AMBER] Hydrogen bond analysis
(Tue Jul 22 2014 - 08:13:35 PDT)
Re: [AMBER] Regarding LIE in cpptraj
(Tue Jul 22 2014 - 07:43:25 PDT)
Re: [AMBER] How do I apply cpptraj.timecorr to the output dataset of cpptraj.dihedral?
(Wed Jul 16 2014 - 21:56:39 PDT)
Re: [AMBER] Problem with atommap in cpptraj
(Wed Jul 16 2014 - 21:47:52 PDT)
Re: [AMBER] nativecontacts by amber14 cpptraj
(Tue Jul 15 2014 - 09:47:33 PDT)
Re: [AMBER] hydrogen bond evaluation
(Mon Jul 14 2014 - 09:05:51 PDT)
Re: [AMBER] diffusion path length
(Mon Jul 14 2014 - 08:51:13 PDT)
Re: [AMBER] cpptraj help
(Mon Jul 14 2014 - 05:38:20 PDT)
Re: [AMBER] diffusion path length
(Sat Jul 12 2014 - 11:02:19 PDT)
Re: [AMBER] diffusion path length
(Fri Jul 11 2014 - 12:57:34 PDT)
Re: [AMBER] DCCP analysis
(Thu Jul 10 2014 - 06:57:43 PDT)
Re: [AMBER] Finding a good REMD temperature ladder
(Wed Jul 09 2014 - 12:47:16 PDT)
Re: [AMBER] autoimage doesn't work
(Wed Jul 09 2014 - 12:09:18 PDT)
Re: [AMBER] Question
(Wed Jul 09 2014 - 09:58:10 PDT)
Re: [AMBER] atomiccorr: glibc detected *** cpptraj: malloc(): memory corruption:
(Tue Jul 08 2014 - 19:46:20 PDT)
Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories
(Tue Jul 08 2014 - 19:42:03 PDT)
Re: [AMBER] cpptraj hbond
(Tue Jul 08 2014 - 12:31:28 PDT)
Re: [AMBER] imaging problem
(Tue Jul 08 2014 - 12:21:16 PDT)
Re: [AMBER] imaging problem
(Tue Jul 08 2014 - 10:52:03 PDT)
Re: [AMBER] imaging problem
(Mon Jul 07 2014 - 07:16:24 PDT)
Re: [AMBER] questions on output files of hbond analysis
(Mon Jul 07 2014 - 07:10:37 PDT)
Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories
(Sat Jul 05 2014 - 07:57:04 PDT)
Re: [AMBER] Fwd: neighbours around an atom
(Sat Jul 05 2014 - 07:49:40 PDT)
Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories
(Fri Jul 04 2014 - 11:05:53 PDT)
Re: [AMBER] Fwd: neighbours around an atom
(Fri Jul 04 2014 - 10:59:31 PDT)
Re: [AMBER] Time information lost.
(Thu Jul 03 2014 - 09:52:14 PDT)
Re: [AMBER] neighbours around an atom
(Thu Jul 03 2014 - 09:46:43 PDT)
Re: [AMBER] Debug amber energy parameters
(Thu Jul 03 2014 - 08:46:10 PDT)
Re: [AMBER] grid analysis
(Wed Jul 02 2014 - 12:11:54 PDT)
Re: [AMBER] Understand the AMBER coordinate files
(Wed Jul 02 2014 - 07:23:13 PDT)
Re: [AMBER] Extracting total energy and other enegy componenets of ligand
(Wed Jul 02 2014 - 07:20:21 PDT)
Re: [AMBER] grid analysis
(Wed Jul 02 2014 - 07:03:25 PDT)
Re: [AMBER] Visualizing average solvent-oxygen density/occupancy from an MD trajectory
(Wed Jul 02 2014 - 06:52:28 PDT)
Re: [AMBER] cpptraj: arithmetic on data sets?
(Tue Jul 01 2014 - 09:24:47 PDT)
David A Case
Re: [AMBER] this a very green neophyte's question.
(Wed Jul 30 2014 - 18:18:55 PDT)
Re: [AMBER] NONBONDED_PARM_INDEX
(Tue Jul 29 2014 - 05:09:09 PDT)
Re: [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process
(Mon Jul 28 2014 - 05:58:15 PDT)
Re: [AMBER] Problem on making inpcrd file
(Sun Jul 27 2014 - 20:52:27 PDT)
Re: [AMBER] Fwd: AMBER Digest, Vol 926, Issue 1
(Sat Jul 26 2014 - 06:21:12 PDT)
Re: [AMBER] element symbol error in tleap
(Fri Jul 25 2014 - 04:23:54 PDT)
Re: [AMBER] values of λ in Thermodynamic Integration
(Fri Jul 25 2014 - 04:17:04 PDT)
Re: [AMBER] pbc problem
(Thu Jul 24 2014 - 13:38:53 PDT)
Re: [AMBER] CYM charges in amino14ipq.lib wrong?
(Thu Jul 24 2014 - 06:00:11 PDT)
Re: [AMBER] renumber all residues in prmtop
(Thu Jul 24 2014 - 05:02:33 PDT)
Re: [AMBER] Hello
(Wed Jul 23 2014 - 04:51:12 PDT)
Re: [AMBER] help
(Tue Jul 22 2014 - 16:28:16 PDT)
Re: [AMBER] Lipid and protein - error reading group during heat
(Mon Jul 21 2014 - 03:46:17 PDT)
Re: [AMBER] memory allocation error for *bond
(Sun Jul 20 2014 - 05:05:57 PDT)
Re: [AMBER] X11 error
(Sat Jul 19 2014 - 09:04:31 PDT)
Re: [AMBER] Fwd: problem in installation of ambertools14
(Sat Jul 19 2014 - 05:36:59 PDT)
Re: [AMBER] memory allocation error for *bond
(Sat Jul 19 2014 - 05:34:05 PDT)
Re: [AMBER] Fwd: problem in installation of ambertools14
(Fri Jul 18 2014 - 04:50:21 PDT)
Re: [AMBER] installation of AMBER 12 in MAC 10.7 lion
(Wed Jul 16 2014 - 05:23:11 PDT)
Re: [AMBER] cpptraj rotdif parameters
(Thu Jul 10 2014 - 17:17:44 PDT)
Re: [AMBER] Switch function in Amber
(Thu Jul 10 2014 - 04:46:45 PDT)
Re: [AMBER] pmemdTI test failure
(Tue Jul 08 2014 - 11:55:01 PDT)
Re: [AMBER] questions on output files of hbond analysis
(Tue Jul 08 2014 - 04:46:32 PDT)
Re: [AMBER] Build Xleap
(Mon Jul 07 2014 - 07:20:22 PDT)
Re: [AMBER] Imaging issue
(Mon Jul 07 2014 - 04:47:12 PDT)
Re: [AMBER] Build Xleap
(Mon Jul 07 2014 - 04:43:39 PDT)
Re: [AMBER] Wrong number of restrained atoms
(Thu Jul 03 2014 - 05:22:47 PDT)
Re: [AMBER] Failed to generate parameter file
(Thu Jul 03 2014 - 05:19:33 PDT)
Re: [AMBER] NMR distance restrains
(Wed Jul 02 2014 - 08:04:32 PDT)
Re: [AMBER] NMR distance restrains
(Wed Jul 02 2014 - 07:14:29 PDT)
Re: [AMBER] MM-PBSA
(Wed Jul 02 2014 - 04:55:18 PDT)
Re: [AMBER] periodic box drifted during NVE run
(Wed Jul 02 2014 - 04:40:16 PDT)
Re: [AMBER] sander error "Could not find cntrl namelist"
(Tue Jul 01 2014 - 12:10:54 PDT)
Re: [AMBER] AmberTools parallel test experienced errors
(Tue Jul 01 2014 - 04:22:22 PDT)
David Minh
Re: [AMBER] Bug in tleap savemol2?
(Wed Jul 23 2014 - 13:05:22 PDT)
[AMBER] Bug in tleap savemol2?
(Wed Jul 23 2014 - 09:41:59 PDT)
Dickson, Callum J
Re: [AMBER] No parameters for PGR in lipid14
(Wed Jul 02 2014 - 03:52:50 PDT)
Domenico Marson
[AMBER] Time information lost.
(Thu Jul 03 2014 - 08:52:34 PDT)
Eric Pettersen
Re: [AMBER] Visualizing average solvent-oxygen density/occupancy from an MD trajectory
(Thu Jul 03 2014 - 12:37:29 PDT)
Eugene Yedvabny
[AMBER] Finding a good REMD temperature ladder
(Wed Jul 09 2014 - 11:01:39 PDT)
Faez Iqbal khan
[AMBER] Error output file
(Tue Jul 15 2014 - 01:17:49 PDT)
Fengxue Li
[AMBER] Could not find cntrl namelist
(Tue Jul 15 2014 - 06:19:27 PDT)
FyD
Re: [AMBER] How to calculate the parameters of metal ions?
(Thu Jul 31 2014 - 07:20:03 PDT)
Re: [AMBER] Solvating the system with polyethylene glycol PEG
(Wed Jul 30 2014 - 02:16:30 PDT)
Re: [AMBER] AMP Parameters
(Wed Jul 23 2014 - 01:52:52 PDT)
Re: [AMBER] parameterizing a connected moiety
(Fri Jul 18 2014 - 06:38:11 PDT)
Re: [AMBER] To get resp charges of a modified central residue (not an integer).
(Thu Jul 17 2014 - 09:03:29 PDT)
Re: [AMBER] To get resp charges of a modified central residue (not an integer).
(Tue Jul 15 2014 - 23:20:58 PDT)
Re: [AMBER] ATP and Mg2+ parameters
(Tue Jul 15 2014 - 04:05:20 PDT)
Re: [AMBER] coordinate and topology files using tleap from RED server output files
(Tue Jul 15 2014 - 04:01:41 PDT)
[AMBER] Fwd: Re: [q4md-fft] URGENT:Orbital Hessian Not Positive Definite
(Thu Jul 10 2014 - 02:57:12 PDT)
Re: [AMBER] Parameter file for polyethyleglycol PEG
(Thu Jul 10 2014 - 02:53:39 PDT)
[AMBER] Fwd: Re: [q4md-fft] Issues Running, missing Ante_RED 2
(Thu Jul 10 2014 - 02:43:55 PDT)
Re: [AMBER] RESP fitting with group restraint
(Tue Jul 08 2014 - 08:24:04 PDT)
Re: [AMBER] ATP and Mg2+ parameters
(Tue Jul 08 2014 - 08:20:01 PDT)
Re: [AMBER] inositol hexakisphosphate
(Tue Jul 08 2014 - 08:18:24 PDT)
George Patargias
Re: [AMBER] ATP parameters: tleap error
(Wed Jul 16 2014 - 23:21:19 PDT)
Gustavo Seabra
Re: [AMBER] support of "center of mass restraint"
(Wed Jul 02 2014 - 10:11:10 PDT)
Hai Long
Re: [AMBER] PMEMD running on Intel Xeon Phi
(Mon Jul 07 2014 - 09:52:18 PDT)
[AMBER] PMEMD running on Intel Xeon Phi
(Thu Jul 03 2014 - 12:22:29 PDT)
Hannes Loeffler
Re: [AMBER] parmchk2 segfaults
(Fri Jul 25 2014 - 02:48:01 PDT)
Re: [AMBER] parmchk2 segfaults
(Thu Jul 24 2014 - 07:47:27 PDT)
Re: [AMBER] Thermodynamic Integration by using pmemd
(Fri Jul 11 2014 - 03:01:57 PDT)
Harmeet Kaur
[AMBER] Fwd: error: unable to generate parameter file
(Wed Jul 02 2014 - 00:07:45 PDT)
Hector A. Baldoni
Re: [AMBER] Solvating the system with polyethylene glycol PEG
(Mon Jul 28 2014 - 11:08:00 PDT)
Re: [AMBER] ATP and Mg2+ parameters
(Tue Jul 08 2014 - 03:50:37 PDT)
[AMBER] inositol hexakisphosphate
(Mon Jul 07 2014 - 14:12:39 PDT)
Him Shweta
[AMBER] NONBONDED_PARM_INDEX
(Tue Jul 29 2014 - 00:37:39 PDT)
[AMBER] Hi
(Fri Jul 25 2014 - 02:19:46 PDT)
Re: [AMBER] Z-axis coordinates
(Wed Jul 23 2014 - 07:44:00 PDT)
[AMBER] Z-axis coordinates
(Wed Jul 23 2014 - 02:34:25 PDT)
Re: [AMBER] problem in "re-image" and "unwarp"
(Wed Jul 16 2014 - 04:13:42 PDT)
Re: [AMBER] entropy Calculation
(Thu Jul 10 2014 - 20:50:31 PDT)
Re: [AMBER] entropy Calculation
(Thu Jul 10 2014 - 09:30:56 PDT)
Re: [AMBER] Free Binding Energy Calculation
(Thu Jul 10 2014 - 06:20:39 PDT)
[AMBER] Free Binding Energy Calculation
(Thu Jul 10 2014 - 05:58:01 PDT)
Re: [AMBER] entropy Calculation
(Thu Jul 10 2014 - 05:52:06 PDT)
[AMBER] entropy Calculation
(Tue Jul 08 2014 - 22:12:06 PDT)
Hirdesh Kumar
Re: [AMBER] Fwd: problem in installation of ambertools14
(Sat Jul 19 2014 - 04:38:29 PDT)
Iqbal, Muhammad Sajid
[AMBER] Solvating the system with polyethylene glycol PEG
(Mon Jul 28 2014 - 10:07:35 PDT)
[AMBER] coordinate and topology files using tleap from RED server output files
(Mon Jul 14 2014 - 14:17:40 PDT)
[AMBER] Parameter file for polyethyleglycol PEG
(Tue Jul 08 2014 - 11:03:04 PDT)
J.W. Halley
Re: [AMBER] this a very green neophyte's question.
(Thu Jul 31 2014 - 17:29:53 PDT)
Re: [AMBER] this a very green neophyte's question.
(Thu Jul 31 2014 - 15:31:23 PDT)
Re: [AMBER] this a very green neophyte's question.
(Thu Jul 31 2014 - 14:47:08 PDT)
[AMBER] this a very green neophyte's question.
(Wed Jul 30 2014 - 17:56:49 PDT)
James Starlight
Re: [AMBER] On the ussage of the langevens thermostat with the gb models
(Mon Jul 28 2014 - 04:22:05 PDT)
[AMBER] On the ussage of the langevens thermostat with the gb models
(Sat Jul 26 2014 - 00:03:20 PDT)
[AMBER] Cpptraj clustering
(Thu Jul 24 2014 - 08:13:19 PDT)
Re: [AMBER] On the values of boost potential for aMD based on amd.log
(Wed Jul 23 2014 - 12:20:45 PDT)
Re: [AMBER] On the values of boost potential for aMD based on amd.log
(Wed Jul 23 2014 - 07:54:56 PDT)
[AMBER] On the values of boost potential for aMD based on amd.log
(Wed Jul 23 2014 - 02:08:40 PDT)
Re: [AMBER] bash scripting for MD tasks
(Mon Jul 21 2014 - 04:54:00 PDT)
Re: [AMBER] Implicit solvent and membrane protein
(Fri Jul 18 2014 - 03:31:26 PDT)
Re: [AMBER] Implicit solvent and membrane protein
(Fri Jul 18 2014 - 03:05:20 PDT)
Re: [AMBER] Implicit solvent and membrane protein
(Fri Jul 18 2014 - 02:06:33 PDT)
Re: [AMBER] Implicit solvent and membrane protein
(Thu Jul 17 2014 - 12:51:15 PDT)
Re: [AMBER] Loop refirement
(Thu Jul 17 2014 - 10:31:19 PDT)
Re: [AMBER] Loop refirement
(Thu Jul 17 2014 - 09:32:19 PDT)
Re: [AMBER] Loop refirement
(Thu Jul 17 2014 - 09:01:59 PDT)
Re: [AMBER] Loop refirement
(Thu Jul 17 2014 - 04:47:53 PDT)
Re: [AMBER] Loop refirement
(Thu Jul 17 2014 - 00:27:46 PDT)
[AMBER] Implicit solvent and membrane protein
(Thu Jul 17 2014 - 00:21:29 PDT)
Re: [AMBER] Loop refirement
(Thu Jul 10 2014 - 02:44:21 PDT)
Re: [AMBER] Loop refirement
(Wed Jul 09 2014 - 03:01:15 PDT)
Jason Swails
Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop
(Thu Jul 31 2014 - 20:33:05 PDT)
Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop
(Thu Jul 31 2014 - 19:51:54 PDT)
Re: [AMBER] this a very green neophyte's question.
(Thu Jul 31 2014 - 19:49:52 PDT)
Re: [AMBER] this a very green neophyte's question.
(Thu Jul 31 2014 - 16:31:26 PDT)
Re: [AMBER] this a very green neophyte's question.
(Thu Jul 31 2014 - 14:52:28 PDT)
Re: [AMBER] HELP Needed: AMBER12 cuda compilation ERROR
(Wed Jul 30 2014 - 05:26:08 PDT)
Re: [AMBER] !Help!: Normal Mode Analysis
(Tue Jul 29 2014 - 08:22:03 PDT)
Re: [AMBER] Problem on making inpcrd file
(Mon Jul 28 2014 - 16:24:02 PDT)
Re: [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process
(Mon Jul 28 2014 - 06:58:21 PDT)
Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
(Mon Jul 28 2014 - 06:42:09 PDT)
Re: [AMBER] Problem on making inpcrd file
(Mon Jul 28 2014 - 06:36:55 PDT)
Re: [AMBER] Berendsen vs. Monte Carlo
(Thu Jul 24 2014 - 22:20:29 PDT)
Re: [AMBER] GPU error Attempting MC barostat change: Failed
(Thu Jul 24 2014 - 22:01:04 PDT)
Re: [AMBER] parmchk2 segfaults
(Thu Jul 24 2014 - 14:36:24 PDT)
Re: [AMBER] GPU error Attempting MC barostat change: Failed
(Thu Jul 24 2014 - 11:03:58 PDT)
Re: [AMBER] renumber all residues in prmtop
(Wed Jul 23 2014 - 19:04:41 PDT)
Re: [AMBER] ptraj binary missing from AmberTools 13 install?
(Wed Jul 23 2014 - 18:58:30 PDT)
Re: [AMBER] Bug in tleap savemol2?
(Wed Jul 23 2014 - 10:39:24 PDT)
Re: [AMBER] atom number same as line number for cpptraj
(Wed Jul 23 2014 - 09:03:02 PDT)
Re: [AMBER] atom number same as line number for cpptraj
(Tue Jul 22 2014 - 19:12:03 PDT)
Re: [AMBER] help
(Tue Jul 22 2014 - 16:17:53 PDT)
Re: [AMBER] Unable to compile cuda version of amber14
(Tue Jul 22 2014 - 12:57:56 PDT)
Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA
(Fri Jul 18 2014 - 14:48:16 PDT)
Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA
(Fri Jul 18 2014 - 14:17:38 PDT)
Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA
(Fri Jul 18 2014 - 13:45:00 PDT)
Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA
(Fri Jul 18 2014 - 13:18:46 PDT)
Re: [AMBER] ScaledMD for proline dipeptide
(Fri Jul 18 2014 - 02:05:08 PDT)
Re: [AMBER] ScaledMD for proline dipeptide
(Thu Jul 17 2014 - 23:35:03 PDT)
Re: [AMBER] parameterizing a connected moiety
(Thu Jul 17 2014 - 14:51:14 PDT)
Re: [AMBER] Error installing Ambertools on Centos 6.3 and open suse 12.3
(Thu Jul 17 2014 - 08:11:46 PDT)
Re: [AMBER] ATP parameters: tleap error
(Wed Jul 16 2014 - 09:51:37 PDT)
Re: [AMBER] gpu and cpu runs
(Tue Jul 15 2014 - 19:08:14 PDT)
Re: [AMBER] pressure tensor
(Tue Jul 15 2014 - 10:36:47 PDT)
Re: [AMBER] Downloading old versions of AMBERTools
(Tue Jul 15 2014 - 10:09:06 PDT)
Re: [AMBER] To get resp charges of a modified central residue (not an integer).
(Tue Jul 15 2014 - 09:02:00 PDT)
Re: [AMBER] Error while running tleap
(Tue Jul 15 2014 - 08:55:24 PDT)
Re: [AMBER] Error output file
(Tue Jul 15 2014 - 08:47:21 PDT)
Re: [AMBER] gpu and cpu runs
(Tue Jul 15 2014 - 08:43:55 PDT)
Re: [AMBER] hydrogen bond evaluation
(Tue Jul 15 2014 - 08:35:16 PDT)
Re: [AMBER] Downloading old versions of AMBERTools
(Mon Jul 14 2014 - 16:10:50 PDT)
Re: [AMBER] update amber12
(Mon Jul 14 2014 - 14:35:07 PDT)
Re: [AMBER] hydrogen bond evaluation
(Mon Jul 14 2014 - 08:49:28 PDT)
Re: [AMBER] Query about QM/MM scanning using amber
(Sun Jul 13 2014 - 09:15:58 PDT)
Re: [AMBER] graph energy check after minimization
(Fri Jul 11 2014 - 12:19:44 PDT)
Re: [AMBER] parmchk2 segfaults
(Fri Jul 11 2014 - 08:16:55 PDT)
Re: [AMBER] Question
(Thu Jul 10 2014 - 14:11:50 PDT)
Re: [AMBER] How is temperature in Amber MD simulations calculated?
(Thu Jul 10 2014 - 13:53:30 PDT)
Re: [AMBER] Sander of Amber11, Amber12 and AmberTools14
(Thu Jul 10 2014 - 11:13:46 PDT)
Re: [AMBER] entropy Calculation
(Thu Jul 10 2014 - 11:11:17 PDT)
Re: [AMBER] tinker to amber format
(Thu Jul 10 2014 - 03:11:50 PDT)
Re: [AMBER] Problem with MMPBSA.py
(Tue Jul 08 2014 - 22:50:50 PDT)
Re: [AMBER] entropy Calculation
(Tue Jul 08 2014 - 22:38:40 PDT)
Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories
(Tue Jul 08 2014 - 21:01:01 PDT)
Re: [AMBER] atomiccorr: glibc detected *** cpptraj: malloc(): memory corruption:
(Tue Jul 08 2014 - 16:06:14 PDT)
Re: [AMBER] atomiccorr: glibc detected *** cpptraj: malloc(): memory corruption:
(Tue Jul 08 2014 - 15:05:14 PDT)
Re: [AMBER] Parameter file for polyethyleglycol PEG
(Tue Jul 08 2014 - 11:16:04 PDT)
Re: [AMBER] Problem with MMPBSA.py
(Tue Jul 08 2014 - 08:44:03 PDT)
Re: [AMBER] ATP and Mg2+ parameters
(Tue Jul 08 2014 - 08:38:13 PDT)
Re: [AMBER] imin=5, maxcyc>1 stalls
(Tue Jul 08 2014 - 08:21:26 PDT)
Re: [AMBER] errors in compiling AmberTools14
(Mon Jul 07 2014 - 07:35:22 PDT)
Re: [AMBER] Fwd: neighbours around an atom
(Sat Jul 05 2014 - 07:31:39 PDT)
Re: [AMBER] MMPBSA Energy between system and its image
(Fri Jul 04 2014 - 15:29:16 PDT)
Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories
(Fri Jul 04 2014 - 12:58:02 PDT)
Re: [AMBER] MMPBSA
(Fri Jul 04 2014 - 12:04:41 PDT)
Re: [AMBER] MMPBSA Energy between system and its image
(Thu Jul 03 2014 - 13:02:20 PDT)
Re: [AMBER] amoeba into ambertools
(Thu Jul 03 2014 - 12:48:54 PDT)
Re: [AMBER] neighbours around an atom
(Thu Jul 03 2014 - 09:21:57 PDT)
Re: [AMBER] ncsu_smd support in pmemd amber12
(Thu Jul 03 2014 - 07:38:34 PDT)
Re: [AMBER] Issues Compiling AmberTools13
(Wed Jul 02 2014 - 12:54:20 PDT)
Re: [AMBER] Attempting to compile fresh version of Amber 11, bugfixes > 17 won't apply cleanly
(Wed Jul 02 2014 - 09:47:50 PDT)
Re: [AMBER] MM-PBSA
(Wed Jul 02 2014 - 09:19:10 PDT)
Re: [AMBER] MM-PBSA
(Wed Jul 02 2014 - 07:13:37 PDT)
Re: [AMBER] No parameters for PGR in lipid14
(Wed Jul 02 2014 - 07:00:59 PDT)
Re: [AMBER] about setting nscm
(Tue Jul 01 2014 - 17:28:51 PDT)
Re: [AMBER] Cuda tests failure on GeForce GTX 780
(Tue Jul 01 2014 - 09:50:51 PDT)
Re: [AMBER] sander error "Could not find cntrl namelist"
(Tue Jul 01 2014 - 08:40:20 PDT)
Re: [AMBER] support of "center of mass restraint"
(Tue Jul 01 2014 - 08:29:11 PDT)
Jinfeng Huang
[AMBER] How to calculate the parameters of metal ions?
(Thu Jul 31 2014 - 06:58:50 PDT)
Jonathan Gough
[AMBER] question about lipid tutorial
(Thu Jul 31 2014 - 13:15:57 PDT)
[AMBER] Lipid and protein - error reading group during heat
(Sun Jul 20 2014 - 20:50:39 PDT)
Re: [AMBER] cuda.test errors
(Sat Jul 12 2014 - 06:10:45 PDT)
[AMBER] cuda.test errors
(Fri Jul 11 2014 - 14:53:28 PDT)
Re: [AMBER] imaging problem
(Tue Jul 08 2014 - 11:17:18 PDT)
Re: [AMBER] imaging problem
(Tue Jul 08 2014 - 07:12:06 PDT)
[AMBER] imaging problem
(Sun Jul 06 2014 - 14:41:48 PDT)
Jorgen Simonsen
[AMBER] tinker to amber format
(Wed Jul 09 2014 - 21:44:14 PDT)
[AMBER] amoeba into ambertools
(Thu Jul 03 2014 - 11:35:18 PDT)
Jose Borreguero
Re: [AMBER] How do I apply cpptraj.timecorr to the output dataset of cpptraj.dihedral?
(Thu Jul 17 2014 - 11:36:54 PDT)
Re: [AMBER] How do I apply cpptraj.timecorr to the output dataset of cpptraj.dihedral?
(Thu Jul 17 2014 - 06:50:44 PDT)
[AMBER] How do I apply cpptraj.timecorr to the output dataset of cpptraj.dihedral?
(Wed Jul 16 2014 - 16:40:48 PDT)
Ken Merz
Re: [AMBER] How to calculate the parameters of metal ions?
(Thu Jul 31 2014 - 07:36:39 PDT)
kirtana S
[AMBER] pressure tensor
(Sat Jul 12 2014 - 10:45:23 PDT)
[AMBER] high energy output
(Wed Jul 02 2014 - 11:52:58 PDT)
[AMBER] about setting nscm
(Tue Jul 01 2014 - 09:27:58 PDT)
Krisztina Feher
[AMBER] atomiccorr: glibc detected *** cpptraj: malloc(): memory corruption:
(Tue Jul 08 2014 - 14:26:53 PDT)
Re: [AMBER] Fwd: neighbours around an atom
(Fri Jul 04 2014 - 05:20:09 PDT)
[AMBER] neighbours around an atom
(Thu Jul 03 2014 - 07:16:14 PDT)
Krisztina Fehér
Re: [AMBER] Fwd: neighbours around an atom
(Sat Jul 05 2014 - 08:15:07 PDT)
Re: [AMBER] Fwd: neighbours around an atom
(Sat Jul 05 2014 - 08:10:02 PDT)
Re: [AMBER] Fwd: neighbours around an atom
(Sat Jul 05 2014 - 07:18:55 PDT)
[AMBER] Fwd: neighbours around an atom
(Fri Jul 04 2014 - 04:49:44 PDT)
[AMBER] Fwd: neighbours around an atom
(Fri Jul 04 2014 - 02:48:08 PDT)
Kshatresh Dutta Dubey
[AMBER] cpptraj not processing all mdcrd files
(Thu Jul 24 2014 - 14:50:24 PDT)
[AMBER] Regarding LIE in cpptraj
(Tue Jul 22 2014 - 00:23:50 PDT)
[AMBER] Query about QM/MM scanning using amber
(Sun Jul 13 2014 - 04:24:50 PDT)
Lachele Foley
Re: [AMBER] Not integer charge for glycoprotein
(Thu Jul 24 2014 - 10:27:46 PDT)
Lara rajam
Re: [AMBER] imin=5
(Thu Jul 17 2014 - 09:19:57 PDT)
[AMBER] imin=5
(Thu Jul 17 2014 - 08:12:13 PDT)
Lorenzo Gontrani
Re: [AMBER] Amber12 CUDA problems
(Mon Jul 21 2014 - 07:20:25 PDT)
Re: [AMBER] Amber12 CUDA problems
(Mon Jul 21 2014 - 07:18:36 PDT)
[AMBER] Amber12 CUDA problems
(Mon Jul 21 2014 - 03:45:05 PDT)
Malachi Phillips
[AMBER] Orbital Hessian Not Positive Definite Error
(Tue Jul 08 2014 - 14:49:17 PDT)
[AMBER] Issues running RED ESP software
(Tue Jul 08 2014 - 10:25:40 PDT)
[AMBER] Issues Compiling AmberTools13
(Wed Jul 02 2014 - 12:20:15 PDT)
Manikanthan Bhavaraju
[AMBER] Unable to compile cuda version of amber14
(Tue Jul 22 2014 - 12:45:48 PDT)
Marawan Hussien
Re: [AMBER] Downloading old versions of AMBERTools
(Tue Jul 15 2014 - 09:09:30 PDT)
[AMBER] Downloading old versions of AMBERTools
(Mon Jul 14 2014 - 14:55:19 PDT)
Marc van der Kamp
Re: [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process
(Mon Jul 28 2014 - 04:49:23 PDT)
[AMBER] CYM charges in amino14ipq.lib wrong?
(Thu Jul 24 2014 - 05:27:11 PDT)
Re: [AMBER] Hi
(Thu Jul 24 2014 - 01:23:28 PDT)
Marek Maly
Re: [AMBER] problems with paramfit
(Wed Jul 30 2014 - 13:29:56 PDT)
Re: [AMBER] problems with paramfit
(Mon Jul 28 2014 - 18:25:16 PDT)
Re: [AMBER] problems with paramfit
(Mon Jul 28 2014 - 13:51:11 PDT)
Re: [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process
(Mon Jul 28 2014 - 07:17:18 PDT)
Re: [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process
(Mon Jul 28 2014 - 05:56:07 PDT)
[AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process
(Sun Jul 27 2014 - 09:35:39 PDT)
Re: [AMBER] problems with paramfit
(Sun Jul 27 2014 - 09:12:35 PDT)
Re: [AMBER] problems with paramfit
(Fri Jul 25 2014 - 08:52:48 PDT)
[AMBER] problems with paramfit
(Thu Jul 24 2014 - 14:56:00 PDT)
Marta Wisniewska
[AMBER] PMF by WHAM
(Mon Jul 28 2014 - 06:22:46 PDT)
Mary Varughese
Re: [AMBER] gpu and cpu runs
(Wed Jul 16 2014 - 21:31:14 PDT)
Re: [AMBER] gpu and cpu runs
(Tue Jul 15 2014 - 20:29:02 PDT)
Re: [AMBER] gpu and cpu runs
(Tue Jul 15 2014 - 18:57:47 PDT)
[AMBER] gpu and cpu runs
(Tue Jul 15 2014 - 00:23:24 PDT)
Re: [AMBER] grid analysis
(Wed Jul 02 2014 - 21:48:29 PDT)
Re: [AMBER] grid analysis
(Wed Jul 02 2014 - 11:19:12 PDT)
[AMBER] grid analysis
(Tue Jul 01 2014 - 19:04:44 PDT)
Massimiliano Porrini
Re: [AMBER] Sander of Amber11, Amber12 and AmberTools14
(Fri Jul 11 2014 - 03:30:43 PDT)
[AMBER] Sander of Amber11, Amber12 and AmberTools14
(Thu Jul 10 2014 - 10:59:30 PDT)
Mele N.
Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories
(Sun Jul 06 2014 - 02:20:00 PDT)
Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories
(Sat Jul 05 2014 - 02:48:42 PDT)
Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories
(Fri Jul 04 2014 - 13:22:05 PDT)
Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories
(Fri Jul 04 2014 - 12:23:56 PDT)
[AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories
(Fri Jul 04 2014 - 06:19:41 PDT)
menwer momo
[AMBER] Hydrogen bond analysis
(Sat Jul 19 2014 - 03:56:41 PDT)
Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA
(Fri Jul 18 2014 - 14:53:04 PDT)
Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA
(Fri Jul 18 2014 - 13:38:42 PDT)
[AMBER] Electrostatic energy calculated by MD in MM/GBSA
(Fri Jul 18 2014 - 13:06:08 PDT)
Michael Criddle
[AMBER] Imaging issue
(Mon Jul 07 2014 - 02:24:49 PDT)
Mohammad Salem
[AMBER] parameterizing a connected moiety
(Thu Jul 17 2014 - 14:31:15 PDT)
Nadia Li
Re: [AMBER] Zinc parameterization
(Thu Jul 31 2014 - 15:37:37 PDT)
[AMBER] Zinc parameterization
(Thu Jul 31 2014 - 09:55:01 PDT)
Neha Gandhi
Re: [AMBER] cpptraj hbond
(Wed Jul 09 2014 - 07:34:47 PDT)
[AMBER] cpptraj hbond
(Mon Jul 07 2014 - 23:55:34 PDT)
newamber list
Re: [AMBER] atom number same as line number for cpptraj
(Wed Jul 23 2014 - 09:30:55 PDT)
Re: [AMBER] atom number same as line number for cpptraj
(Wed Jul 23 2014 - 08:23:42 PDT)
[AMBER] atom number same as line number for cpptraj
(Tue Jul 22 2014 - 17:02:54 PDT)
Re: [AMBER] diffusion path length
(Mon Jul 14 2014 - 09:52:48 PDT)
Re: [AMBER] diffusion path length
(Sat Jul 12 2014 - 13:54:31 PDT)
Re: [AMBER] diffusion path length
(Sat Jul 12 2014 - 09:01:27 PDT)
Re: [AMBER] diffusion path length
(Fri Jul 11 2014 - 13:41:00 PDT)
[AMBER] diffusion path length
(Fri Jul 11 2014 - 12:11:03 PDT)
Nicole Ippolito
Re: [AMBER] Running PCA
(Wed Jul 30 2014 - 06:46:55 PDT)
Re: [AMBER] Running PCA
(Tue Jul 29 2014 - 08:07:55 PDT)
[AMBER] Fwd: Running PCA
(Tue Jul 29 2014 - 06:24:45 PDT)
[AMBER] Running PCA
(Fri Jul 25 2014 - 10:56:31 PDT)
Niel Henriksen
Re: [AMBER] RNA covalent bond angles
(Wed Jul 16 2014 - 08:19:38 PDT)
Niels Geudens
Re: [AMBER] ScaledMD for proline dipeptide
(Fri Jul 18 2014 - 00:55:36 PDT)
[AMBER] ScaledMD for proline dipeptide
(Thu Jul 17 2014 - 23:02:37 PDT)
[AMBER] RESP fitting with group restraint
(Tue Jul 08 2014 - 06:08:17 PDT)
Re: [AMBER] No parameters for PGR in lipid14
(Wed Jul 02 2014 - 05:12:33 PDT)
[AMBER] No parameters for PGR in lipid14
(Wed Jul 02 2014 - 03:41:19 PDT)
niels.geudens.ugent.be
Re: [AMBER] RESP fitting with group restraint
(Mon Jul 07 2014 - 11:09:34 PDT)
Niloofar Nayebi
[AMBER] pbc problem
(Thu Jul 24 2014 - 09:21:24 PDT)
Pablo Ródenas
[AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
(Mon Jul 28 2014 - 06:04:14 PDT)
Parker de Waal
Re: [AMBER] this a very green neophyte's question.
(Thu Jul 31 2014 - 14:52:34 PDT)
[AMBER] Equilibirum/System convergence
(Thu Jul 31 2014 - 10:15:37 PDT)
Re: [AMBER] this a very green neophyte's question.
(Wed Jul 30 2014 - 18:26:32 PDT)
Re: [AMBER] Berendsen vs. Monte Carlo
(Fri Jul 25 2014 - 05:23:21 PDT)
[AMBER] Berendsen vs. Monte Carlo
(Thu Jul 24 2014 - 19:14:06 PDT)
Re: [AMBER] bash scripting for MD tasks
(Mon Jul 21 2014 - 06:32:19 PDT)
Pedro Swagger
[AMBER] Could not find vdW (or other) parameters for type
(Wed Jul 30 2014 - 16:38:35 PDT)
Pengfei Li
Re: [AMBER] Zinc parameterization
(Thu Jul 31 2014 - 18:28:59 PDT)
Re: [AMBER] Zinc parameterization
(Thu Jul 31 2014 - 14:34:40 PDT)
Re: [AMBER] Hello
(Tue Jul 22 2014 - 19:59:08 PDT)
Re: [AMBER] Could not find cntrl namelist
(Tue Jul 15 2014 - 07:41:55 PDT)
Re: [AMBER] Ag+ ion parameters
(Fri Jul 11 2014 - 07:41:43 PDT)
Re: [AMBER] ZAFF-CCCH Histidine charge problem
(Thu Jul 10 2014 - 14:46:16 PDT)
Re: [AMBER] ZAFF-CCCH Histidine charge problem
(Tue Jul 08 2014 - 08:12:51 PDT)
Re: [AMBER] ZAFF-CCCH Histidine charge problem
(Mon Jul 07 2014 - 14:03:24 PDT)
Re: [AMBER] ZAFF-CCCH Histidine charge problem
(Sun Jul 06 2014 - 09:37:26 PDT)
Re: [AMBER] ZAFF-CCCH Histidine charge problem
(Wed Jul 02 2014 - 14:12:03 PDT)
Re: [AMBER] ZAFF-CCCH Histidine charge problem
(Tue Jul 01 2014 - 14:10:36 PDT)
Pierpaolo Cacciotto
Re: [AMBER] Setting up z-constraint
(Tue Jul 01 2014 - 03:22:17 PDT)
Quynh Vo
Re: [AMBER] periodic box drifted during NVE run
(Thu Jul 03 2014 - 13:19:34 PDT)
Re: [AMBER] periodic box drifted during NVE run
(Tue Jul 01 2014 - 13:11:10 PDT)
Raik Grünberg
Re: [AMBER] ptraj binary missing from AmberTools 13 install?
(Wed Jul 23 2014 - 17:59:21 PDT)
Re: [AMBER] ptraj binary missing from AmberTools 13 install?
(Wed Jul 23 2014 - 13:23:08 PDT)
[AMBER] ptraj binary missing from AmberTools 13 install?
(Wed Jul 23 2014 - 13:14:41 PDT)
Rajeswari A.
[AMBER] Problem with atommap in cpptraj
(Wed Jul 16 2014 - 07:04:15 PDT)
Re: [AMBER] nativecontacts by amber14 cpptraj
(Tue Jul 15 2014 - 21:52:43 PDT)
[AMBER] nativecontacts by amber14 cpptraj
(Tue Jul 15 2014 - 04:36:00 PDT)
Re: [AMBER] Problem with MMPBSA.py
(Tue Jul 08 2014 - 22:32:09 PDT)
[AMBER] Problem with MMPBSA.py
(Tue Jul 08 2014 - 07:07:03 PDT)
Raman Parkesh
Re: [AMBER] GPU error Attempting MC barostat change: Failed
(Thu Jul 24 2014 - 17:35:49 PDT)
Re: [AMBER] GPU error Attempting MC barostat change: Failed
(Thu Jul 24 2014 - 07:10:07 PDT)
Re: [AMBER] NVT and NPT ensemble
(Tue Jul 22 2014 - 19:54:46 PDT)
Re: [AMBER] Fwd: problem in installation of ambertools14
(Fri Jul 18 2014 - 04:25:17 PDT)
Ramuntcho Moretti
[AMBER] Switch function in Amber
(Thu Jul 10 2014 - 01:04:43 PDT)
[AMBER] Debug amber energy parameters
(Thu Jul 03 2014 - 02:17:08 PDT)
Ray Luo, Ph.D.
Re: [AMBER] Implicit solvent and membrane protein
(Thu Jul 17 2014 - 11:27:50 PDT)
Rebeca García Fandiño
[AMBER] Ag+ ion parameters
(Thu Jul 10 2014 - 01:35:03 PDT)
renatoac.ufpa.br
Re: [AMBER] erro na criação do complexo
(Wed Jul 30 2014 - 13:00:15 PDT)
[AMBER] erro na criação do complexo
(Wed Jul 30 2014 - 12:50:07 PDT)
[AMBER] erro na criação do complexo
(Wed Jul 30 2014 - 12:43:10 PDT)
[AMBER] AMBER
(Wed Jul 30 2014 - 12:15:24 PDT)
Robert Konecny
Re: [AMBER] sander.APBS: automatic grid adjustments in output?
(Tue Jul 22 2014 - 20:47:46 PDT)
Robin Betz
Re: [AMBER] problems with paramfit
(Mon Jul 28 2014 - 17:52:14 PDT)
Re: [AMBER] problems with paramfit
(Mon Jul 28 2014 - 13:12:58 PDT)
Re: [AMBER] problems with paramfit
(Fri Jul 25 2014 - 08:33:37 PDT)
Ross Walker
Re: [AMBER] error in md simulation in pmemd.cuda.MPI
(Mon Jul 21 2014 - 08:32:16 PDT)
Re: [AMBER] Amber12 CUDA problems
(Mon Jul 21 2014 - 06:39:04 PDT)
Re: [AMBER] gpu and cpu runs
(Wed Jul 16 2014 - 10:03:59 PDT)
Re: [AMBER] cuda.test errors
(Fri Jul 11 2014 - 15:03:54 PDT)
Re: [AMBER] PMEMD running on Intel Xeon Phi
(Thu Jul 03 2014 - 20:22:02 PDT)
Re: [AMBER] high energy output
(Wed Jul 02 2014 - 12:06:13 PDT)
Re: [AMBER] support of "center of mass restraint"
(Wed Jul 02 2014 - 09:18:33 PDT)
Re: [AMBER] Understand the AMBER coordinate files
(Tue Jul 01 2014 - 19:33:36 PDT)
SaeeD PourasaD
[AMBER] Hi
(Thu Jul 24 2014 - 00:14:15 PDT)
[AMBER] Hello
(Tue Jul 22 2014 - 19:34:13 PDT)
Saikat Dutta chowdhury
[AMBER] HELP Needed: AMBER12 cuda compilation ERROR
(Wed Jul 30 2014 - 04:18:19 PDT)
Re: [AMBER] cpptraj help
(Mon Jul 14 2014 - 06:21:38 PDT)
[AMBER] cpptraj help
(Mon Jul 14 2014 - 04:40:16 PDT)
Sangita Kachhap
Re: [AMBER] NVT and NPT ensemble
(Tue Jul 22 2014 - 21:20:00 PDT)
[AMBER] NVT and NPT ensemble
(Mon Jul 21 2014 - 01:17:41 PDT)
Scott Le Grand
Re: [AMBER] gpu and cpu runs
(Wed Jul 16 2014 - 10:21:52 PDT)
Re: [AMBER] PMEMD running on Intel Xeon Phi
(Thu Jul 03 2014 - 19:17:57 PDT)
Serzhan Sakipov
[AMBER] Cuda tests failure on GeForce GTX 780
(Tue Jul 01 2014 - 09:17:10 PDT)
Shweta
Re: [AMBER] NONBONDED_PARM_INDEX
(Wed Jul 30 2014 - 05:31:28 PDT)
Soumendranath Bhakat
Re: [AMBER] NVT and NPT ensemble
(Mon Jul 21 2014 - 01:55:47 PDT)
Re: [AMBER] Tool in PTRAJ/CPPTRAJ to analyse residue movement
(Wed Jul 16 2014 - 05:10:22 PDT)
Re: [AMBER] Error output file
(Tue Jul 15 2014 - 01:59:07 PDT)
Re: [AMBER] Error output file
(Tue Jul 15 2014 - 01:51:27 PDT)
[AMBER] DCCP analysis
(Thu Jul 10 2014 - 02:04:18 PDT)
Re: [AMBER] ATP and Mg2+ parameters
(Tue Jul 08 2014 - 03:48:49 PDT)
Re: [AMBER] How to strip water from .mdcrd file?
(Fri Jul 04 2014 - 00:06:25 PDT)
Re: [AMBER] Failed to generate parameter file
(Thu Jul 03 2014 - 04:45:38 PDT)
Re: [AMBER] MM-PBSA
(Wed Jul 02 2014 - 07:32:03 PDT)
Re: [AMBER] MM-PBSA
(Wed Jul 02 2014 - 05:05:15 PDT)
[AMBER] How to Extract Energy Contribution of Ligand Only
(Wed Jul 02 2014 - 02:57:38 PDT)
[AMBER] Extracting total energy and other enegy componenets of ligand
(Wed Jul 02 2014 - 02:51:27 PDT)
Re: [AMBER] Fwd: error: unable to generate parameter file
(Wed Jul 02 2014 - 00:19:00 PDT)
Sourav Purohit
[AMBER] iwrap
(Thu Jul 17 2014 - 10:03:43 PDT)
[AMBER] MMPBSA
(Fri Jul 04 2014 - 02:10:46 PDT)
Stephane Azoulay
[AMBER] Parameters for SulfoTyrosine
(Wed Jul 30 2014 - 07:52:19 PDT)
Steven M. Graham
Re: [AMBER] QM on Adenosine
(Wed Jul 02 2014 - 07:25:51 PDT)
Subrata Paul
[AMBER] Fwd: error in md simulation in pmemd.cuda.MPI
(Mon Jul 21 2014 - 07:10:16 PDT)
[AMBER] error in md simulation in pmemd.cuda.MPI
(Mon Jul 21 2014 - 07:07:05 PDT)
Suchetana Gupta
Re: [AMBER] Error while running tleap
(Tue Jul 15 2014 - 09:00:09 PDT)
[AMBER] Error while running tleap
(Tue Jul 15 2014 - 02:13:20 PDT)
Sun
[AMBER] values of λ in Thermodynamic Integration
(Thu Jul 24 2014 - 19:25:16 PDT)
[AMBER] Thermodynamic Integration by using pmemd
(Fri Jul 11 2014 - 02:33:21 PDT)
sunita.tifrh.res.in
[AMBER] AmberTools parallel test experienced errors
(Mon Jun 30 2014 - 21:01:27 PDT)
Sushil Mishra
Re: [AMBER] parmchk2 segfaults
(Fri Jul 11 2014 - 01:41:28 PDT)
Takeshi Baba
Re: [AMBER] support of "center of mass restraint"
(Wed Jul 02 2014 - 09:42:25 PDT)
Re: [AMBER] support of "center of mass restraint"
(Wed Jul 02 2014 - 08:52:30 PDT)
[AMBER] support of "center of mass restraint"
(Tue Jul 01 2014 - 05:53:02 PDT)
Teerapong Pirojsirikul
Re: [AMBER] iwrap
(Thu Jul 17 2014 - 10:33:51 PDT)
Thomas Evangelidis
Re: [AMBER] renumber all residues in prmtop
(Thu Jul 24 2014 - 00:09:06 PDT)
[AMBER] renumber all residues in prmtop
(Wed Jul 23 2014 - 16:33:01 PDT)
Re: [AMBER] On the values of boost potential for aMD based on amd.log
(Wed Jul 23 2014 - 08:26:56 PDT)
Re: [AMBER] Implicit solvent and membrane protein
(Fri Jul 18 2014 - 03:22:00 PDT)
Re: [AMBER] Implicit solvent and membrane protein
(Fri Jul 18 2014 - 02:18:59 PDT)
[AMBER] cholesterol with lipid14
(Fri Jul 11 2014 - 00:44:33 PDT)
[AMBER] how to quantify and visualize the flow of water into a protein
(Tue Jul 08 2014 - 16:20:14 PDT)
Tommaso Casalini
[AMBER] Not integer charge for glycoprotein
(Thu Jul 24 2014 - 09:28:52 PDT)
Valentina Romano
[AMBER] ATP parameters: tleap error
(Wed Jul 16 2014 - 09:41:55 PDT)
Re: [AMBER] ATP and Mg2+ parameters
(Tue Jul 15 2014 - 03:27:55 PDT)
Re: [AMBER] ATP and Mg2+ parameters
(Tue Jul 08 2014 - 07:54:33 PDT)
[AMBER] ATP and Mg2+ parameters
(Tue Jul 08 2014 - 03:41:26 PDT)
[AMBER] Wrong number of restrained atoms
(Thu Jul 03 2014 - 02:45:01 PDT)
Re: [AMBER] NMR distance restrains
(Thu Jul 03 2014 - 00:39:14 PDT)
Re: [AMBER] NMR distance restrains
(Wed Jul 02 2014 - 07:50:16 PDT)
[AMBER] NMR distance restrains
(Wed Jul 02 2014 - 06:28:55 PDT)
Vidushi Sharma
[AMBER] X11 error
(Sat Jul 19 2014 - 07:00:53 PDT)
[AMBER] mailing list problem
(Sat Jul 19 2014 - 04:04:34 PDT)
[AMBER] Fwd: problem in installation of ambertools14
(Fri Jul 18 2014 - 04:13:12 PDT)
Vijay Manickam Achari
[AMBER] hydrogen bond evaluation
(Mon Jul 14 2014 - 02:28:26 PDT)
[AMBER] evaluating hydrogen bond using ptraj
(Thu Jul 10 2014 - 23:31:05 PDT)
Vishal Nemaysh
[AMBER] memory allocation error for *bond
(Sun Jul 20 2014 - 02:38:17 PDT)
Re: [AMBER] memory allocation error for *bond
(Sat Jul 19 2014 - 09:36:00 PDT)
[AMBER] memory allocation error for *bond
(Sat Jul 19 2014 - 03:18:57 PDT)
[AMBER] installation of AMBER 12 in MAC 10.7 lion
(Wed Jul 16 2014 - 00:14:42 PDT)
[AMBER] Failed to generate parameter file
(Thu Jul 03 2014 - 02:45:46 PDT)
Vivek Shankar Bharadwaj
Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop
(Thu Jul 31 2014 - 20:55:52 PDT)
Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop
(Thu Jul 31 2014 - 20:46:39 PDT)
Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop
(Thu Jul 31 2014 - 20:07:35 PDT)
Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop
(Thu Jul 31 2014 - 19:59:29 PDT)
[AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop
(Thu Jul 31 2014 - 18:23:43 PDT)
Waldner, Birgit
[AMBER] GIST - unusually high water-water energies
(Tue Jul 22 2014 - 23:13:33 PDT)
Wujie Wang
Re: [AMBER] How to strip water from .mdcrd file?
(Fri Jul 04 2014 - 09:56:07 PDT)
Re: [AMBER] How to strip water from .mdcrd file?
(Fri Jul 04 2014 - 09:48:06 PDT)
[AMBER] How to strip water from .mdcrd file?
(Thu Jul 03 2014 - 18:36:13 PDT)
Re: [AMBER] Understand the AMBER coordinate files
(Wed Jul 02 2014 - 06:32:42 PDT)
[AMBER] Understand the AMBER coordinate files
(Tue Jul 01 2014 - 18:52:13 PDT)
xy21hb
[AMBER] !Help!: Normal Mode Analysis
(Tue Jul 29 2014 - 07:56:24 PDT)
Ying-Chieh Sun
Re: [AMBER] values of λ in Thermodynamic Integration
(Thu Jul 24 2014 - 19:50:01 PDT)
Re: [AMBER] Thermodynamic Integration by using pmemd
(Fri Jul 11 2014 - 05:54:19 PDT)
Yue
Re: [AMBER] ZAFF-CCCH Histidine charge problem
(Thu Jul 10 2014 - 15:01:15 PDT)
zahra khatti
[AMBER] update amber12
(Mon Jul 14 2014 - 14:05:56 PDT)
[AMBER] RDF
(Tue Jul 01 2014 - 03:04:24 PDT)
Zeinab Tavasoli
[AMBER] MM-PBSA
(Wed Jul 02 2014 - 03:08:44 PDT)
Zeynep Topdemir
[AMBER] help
(Tue Jul 22 2014 - 16:01:20 PDT)
zhangmk
Re: [AMBER] questions on output files of hbond analysis
(Mon Jul 07 2014 - 21:00:12 PDT)
[AMBER] questions on output files of hbond analysis
(Mon Jul 07 2014 - 03:01:23 PDT)
肖立
Re: [AMBER] Problem on making inpcrd file
(Mon Jul 28 2014 - 16:13:26 PDT)
[AMBER] Problem on making inpcrd file
(Sun Jul 27 2014 - 13:06:34 PDT)
Re: [AMBER] autoimage doesn't work
(Wed Jul 09 2014 - 12:38:56 PDT)
Re: [AMBER] autoimage doesn't work
(Wed Jul 09 2014 - 12:36:19 PDT)
[AMBER] autoimage doesn't work
(Wed Jul 09 2014 - 12:03:25 PDT)
Last message date
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Thu Jul 31 2014 - 21:00:03 PDT
Archived on
: Fri Dec 20 2024 - 05:55:01 PST
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