Amber Archive Nov 2017 by author
391 messages
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Starting
Wed Nov 01 2017 - 04:00:03 PDT,
Ending
Thu Nov 30 2017 - 18:30:03 PST
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Aashish Bhatt
[AMBER] Regarding Resp charge
(Sat Nov 25 2017 - 06:18:09 PST)
Re: [AMBER] Query about the Glucose Parameters
(Thu Nov 23 2017 - 21:48:32 PST)
Re: [AMBER] Query about the Glucose Parameters
(Tue Nov 21 2017 - 20:48:15 PST)
[AMBER] Query about the Glucose Parameters
(Mon Nov 20 2017 - 04:00:08 PST)
Re: [AMBER] Regarding Glucose dynamics
(Tue Nov 14 2017 - 07:27:59 PST)
Re: [AMBER] Regarding Glucose dynamics
(Tue Nov 14 2017 - 07:14:10 PST)
Re: [AMBER] Regarding Glucose dynamics
(Tue Nov 14 2017 - 07:02:29 PST)
[AMBER] Regarding Glucose dynamics
(Tue Nov 14 2017 - 06:48:06 PST)
[AMBER] Regarding MCPB.py error
(Mon Nov 13 2017 - 07:42:25 PST)
Abdul-Rashid III Sampaco
Re: [AMBER] Post processing of trajectory
(Wed Nov 29 2017 - 05:22:37 PST)
Re: [AMBER] Batch Minimization
(Sat Nov 25 2017 - 19:44:54 PST)
[AMBER] Batch Minimization
(Sat Nov 25 2017 - 19:24:56 PST)
Abhilash J
Re: [AMBER] Query regarding MCPB.py force constant
(Thu Nov 16 2017 - 01:48:26 PST)
[AMBER] Query regarding MCPB.py force constant
(Thu Nov 16 2017 - 00:20:56 PST)
Adebayo Adeniyi
[AMBER] No torsion terms error even though I specified them in frcmod file
(Wed Nov 08 2017 - 03:10:05 PST)
Alonso Martinez, Diego
[AMBER] MMPBSA.py error: “Could not set up '_MMPBSA_receptor.mdcrd.0' for reading”
(Mon Nov 13 2017 - 06:16:56 PST)
Andreas Tosstorff
[AMBER] REMD jobs slowing down unexpectedly
(Fri Nov 10 2017 - 00:47:36 PST)
Re: [AMBER] Wrong connectivity after antechamber/Gaussian16
(Tue Nov 07 2017 - 02:22:39 PST)
Andrew Schaub
Re: [AMBER] how to generate the force fied file of AsO3H3?
(Wed Nov 29 2017 - 08:57:55 PST)
[AMBER] T.I. - single topology HIP <-> HIE
(Tue Nov 21 2017 - 08:53:39 PST)
Antonija Tomić
Re: [AMBER] restrain charge during MCPB.py parametrization
(Tue Nov 14 2017 - 23:10:30 PST)
[AMBER] restrain charge during MCPB.py parametrization
(Tue Nov 14 2017 - 08:22:00 PST)
anu chandra
Re: [AMBER] Analysis of percentage contact in residue-ligand interaction with CPPTRAJ
(Mon Nov 20 2017 - 20:51:40 PST)
[AMBER] Analysis of percentage contact in residue-ligand interaction with CPPTRAJ
(Wed Nov 15 2017 - 21:36:19 PST)
Ashok Kumar
[AMBER] Computer for running MD simulation using Amber
(Thu Nov 09 2017 - 03:26:05 PST)
Bill Ross
Re: [AMBER] mpirun Error opening unit 5
(Wed Nov 29 2017 - 02:13:55 PST)
Re: [AMBER] how to generate the force fied file of AsO3H3?
(Wed Nov 29 2017 - 00:05:41 PST)
Re: [AMBER] APR error
(Tue Nov 28 2017 - 03:34:12 PST)
Re: [AMBER] structure minimization
(Tue Nov 28 2017 - 03:27:10 PST)
Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib
(Tue Nov 28 2017 - 02:35:35 PST)
Re: [AMBER] PCA eigenvalues
(Mon Nov 27 2017 - 02:20:09 PST)
Re: [AMBER] PCA eigenvalues
(Mon Nov 27 2017 - 00:58:19 PST)
Re: [AMBER] Can we study the bond breaking event through Md simulation
(Thu Nov 23 2017 - 23:40:45 PST)
Re: [AMBER] Equilibration
(Wed Nov 22 2017 - 22:39:42 PST)
Re: [AMBER] Equilibration
(Wed Nov 22 2017 - 01:51:30 PST)
Re: [AMBER] problem in minimization
(Mon Nov 20 2017 - 00:27:36 PST)
Re: [AMBER] Equilibration
(Mon Nov 20 2017 - 00:25:09 PST)
Re: [AMBER] How to extract one frame from a trajectory to use as input file for new MD run?
(Thu Nov 16 2017 - 18:32:15 PST)
Re: [AMBER] Regarding Glucose dynamics
(Tue Nov 14 2017 - 07:26:29 PST)
Re: [AMBER] Regarding Glucose dynamics
(Tue Nov 14 2017 - 07:24:09 PST)
Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations
(Mon Nov 13 2017 - 12:50:24 PST)
Re: [AMBER] cpptraj error
(Mon Nov 13 2017 - 05:41:11 PST)
Re: [AMBER] cpptraj error
(Mon Nov 13 2017 - 04:39:01 PST)
Re: [AMBER] cpptraj error
(Mon Nov 13 2017 - 04:24:37 PST)
Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations
(Mon Nov 13 2017 - 04:04:57 PST)
[AMBER] Cross-vendor GPU layer for Machine Learning
(Mon Nov 13 2017 - 03:58:16 PST)
Re: [AMBER] cpptraj error
(Mon Nov 13 2017 - 03:33:48 PST)
Re: [AMBER] cpptraj error
(Mon Nov 13 2017 - 03:26:42 PST)
Re: [AMBER] ntxo option in amber
(Sat Nov 11 2017 - 02:48:00 PST)
Re: [AMBER] ntxo option in amber
(Sat Nov 11 2017 - 02:39:57 PST)
Re: [AMBER] UREA PDB file from xleap
(Fri Nov 10 2017 - 23:40:44 PST)
Re: [AMBER] Computer for running MD simulation using Amber
(Thu Nov 09 2017 - 03:40:26 PST)
Re: [AMBER] solvation box
(Thu Nov 09 2017 - 02:02:55 PST)
Re: [AMBER] error: Atom does not have type
(Tue Nov 07 2017 - 23:42:16 PST)
Re: [AMBER] Automatic rotation of the protein by LEAP to minimize the periodic cell dimensions?
(Sat Nov 04 2017 - 02:38:54 PDT)
Re: [AMBER] Acetate ion using xleap
(Thu Nov 02 2017 - 22:37:11 PDT)
Re: [AMBER] Acetate ion using xleap
(Thu Nov 02 2017 - 21:55:35 PDT)
Re: [AMBER] Acetate ion using xleap
(Thu Nov 02 2017 - 21:36:45 PDT)
Biplab Ghosh
[AMBER] Miniconda gives error while compiling AmberTools-17
(Thu Nov 02 2017 - 04:46:21 PDT)
Carlos Romero
Re: [AMBER] problem in minimization
(Mon Nov 20 2017 - 08:12:36 PST)
[AMBER] problem in minimization
(Sun Nov 19 2017 - 23:16:28 PST)
Carlos Simmerling
Re: [AMBER] Protein-Ligand Energy Minimization
(Thu Nov 30 2017 - 12:10:42 PST)
Re: [AMBER] Distorted peptide
(Thu Nov 16 2017 - 08:26:50 PST)
Re: [AMBER] Regarding Glucose dynamics
(Tue Nov 14 2017 - 07:23:36 PST)
Re: [AMBER] Regarding Glucose dynamics
(Tue Nov 14 2017 - 07:03:40 PST)
Re: [AMBER] chloride as anion
(Fri Nov 03 2017 - 03:35:45 PDT)
Re: [AMBER] protein && DNA in implicit solvents
(Wed Nov 01 2017 - 07:31:57 PDT)
Chetna Tyagi
[AMBER] Distorted peptide
(Thu Nov 16 2017 - 07:12:27 PST)
Re: [AMBER] Fwd: Can't load MEOHBOX as solvent
(Thu Nov 09 2017 - 04:29:13 PST)
[AMBER] Fwd: Can't load MEOHBOX as solvent
(Wed Nov 08 2017 - 08:08:50 PST)
Chitrak Gupta
Re: [AMBER] lipid 14 compatibility with FF14SB
(Thu Nov 30 2017 - 08:53:40 PST)
[AMBER] lipid 14 compatibility with FF14SB
(Wed Nov 29 2017 - 10:05:31 PST)
Cruzeiro,Vinicius Wilian D
Re: [AMBER] imin=5 not working in AMBER16?
(Wed Nov 29 2017 - 09:04:46 PST)
Re: [AMBER] imin=5 not working in AMBER16?
(Wed Nov 29 2017 - 07:27:03 PST)
Re: [AMBER] Running Explicit pH MD
(Thu Nov 16 2017 - 12:00:27 PST)
Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations
(Mon Nov 13 2017 - 08:20:29 PST)
Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations
(Mon Nov 13 2017 - 06:51:07 PST)
Re: [AMBER] Running Explicit pH MD
(Fri Nov 10 2017 - 12:54:10 PST)
Re: [AMBER] Running Explicit pH MD
(Fri Nov 10 2017 - 08:00:38 PST)
Daniel Roe
Re: [AMBER] Protein-Ligand Energy Minimization
(Thu Nov 30 2017 - 12:02:59 PST)
Re: [AMBER] imin=5 not working in AMBER16?
(Thu Nov 30 2017 - 10:57:44 PST)
Re: [AMBER] Trouble installing amber tools on new OSX 10.13.1
(Wed Nov 29 2017 - 05:25:54 PST)
Re: [AMBER] Centriod in clustering
(Tue Nov 28 2017 - 07:27:25 PST)
Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib
(Tue Nov 28 2017 - 05:49:44 PST)
Re: [AMBER] cpptraj: partial charges missing from mol2 file
(Mon Nov 27 2017 - 08:29:34 PST)
Re: [AMBER] Hydrogen bond analysis Through CPPTRAJ
(Mon Nov 27 2017 - 08:27:28 PST)
Re: [AMBER] PCA eigenvalues
(Mon Nov 27 2017 - 08:24:03 PST)
Re: [AMBER] PCA eigenvalues
(Mon Nov 27 2017 - 08:09:18 PST)
Re: [AMBER] Batch Minimization
(Sat Nov 25 2017 - 19:34:43 PST)
Re: [AMBER] cpptraj: partial charges missing from mol2 file
(Wed Nov 22 2017 - 09:44:43 PST)
Re: [AMBER] Analysis of percentage contact in residue-ligand interaction with CPPTRAJ
(Tue Nov 21 2017 - 05:48:08 PST)
Re: [AMBER] How to extract one frame from a trajectory to use as input file for new MD run?
(Mon Nov 20 2017 - 08:28:44 PST)
Re: [AMBER] Fwd: simulations of enzyme with ligand
(Mon Nov 20 2017 - 07:59:11 PST)
Re: [AMBER] PCA eigenvalues
(Mon Nov 20 2017 - 07:53:21 PST)
Re: [AMBER] pdb snapshots
(Wed Nov 15 2017 - 08:22:32 PST)
Re: [AMBER] Cpptraj
(Wed Nov 15 2017 - 07:31:36 PST)
Re: [AMBER] cpptraj error
(Tue Nov 14 2017 - 09:36:47 PST)
Re: [AMBER] Help
(Tue Nov 14 2017 - 09:33:36 PST)
Re: [AMBER] Amber GCC 6.4.0 and MKL 2017.3.196 build failing
(Tue Nov 14 2017 - 09:27:09 PST)
Re: [AMBER] Energy Calculations by cpptraj
(Thu Nov 09 2017 - 06:36:47 PST)
Re: [AMBER] H-bond analysis
(Wed Nov 08 2017 - 08:31:32 PST)
daniele selli
Re: [AMBER] AMBER QM/MM Point charges
(Fri Nov 17 2017 - 05:10:56 PST)
[AMBER] AMBER QM/MM Point charges
(Fri Nov 17 2017 - 02:05:11 PST)
Darrin Y
Re: [AMBER] Free Energy GPU
(Mon Nov 06 2017 - 13:30:51 PST)
David A Case
Re: [AMBER] Trouble installing amber tools on new OSX 10.13.1
(Wed Nov 29 2017 - 10:43:13 PST)
Re: [AMBER] how to generate the force fied file of AsO3H3?
(Wed Nov 29 2017 - 04:38:49 PST)
Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib
(Wed Nov 29 2017 - 04:28:08 PST)
Re: [AMBER] structure minimization
(Tue Nov 28 2017 - 05:44:57 PST)
Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib
(Tue Nov 28 2017 - 05:41:45 PST)
Re: [AMBER] any opportunity of using the pmemd.cuda if one cannot afford the fee
(Mon Nov 27 2017 - 04:30:59 PST)
Re: [AMBER] Query about the Glucose Parameters
(Fri Nov 24 2017 - 14:11:03 PST)
Re: [AMBER] how to set hetrodimer for MD Simulation
(Thu Nov 23 2017 - 05:21:54 PST)
Re: [AMBER] SCEE/SCNB zeros
(Wed Nov 22 2017 - 04:33:05 PST)
Re: [AMBER] SHAKEH problem in GPU calculation
(Tue Nov 21 2017 - 05:17:11 PST)
Re: [AMBER] Is GAFF polarizable forcefield ??
(Fri Nov 17 2017 - 04:54:15 PST)
Re: [AMBER] How to extract one frame from a trajectory to use as input file for new MD run?
(Thu Nov 16 2017 - 19:20:54 PST)
Re: [AMBER] Confusion in urea Model
(Wed Nov 15 2017 - 04:26:15 PST)
Re: [AMBER] pdb snapshots
(Tue Nov 14 2017 - 05:26:08 PST)
Re: [AMBER] Convert prmtop
(Mon Nov 13 2017 - 07:18:09 PST)
Re: [AMBER] Cpptraj pdb snapshots
(Mon Nov 13 2017 - 05:01:41 PST)
Re: [AMBER] ntxo option in amber
(Sat Nov 11 2017 - 06:27:21 PST)
Re: [AMBER] UREA PDB file from xleap
(Fri Nov 10 2017 - 05:18:22 PST)
Re: [AMBER] solvation box
(Thu Nov 09 2017 - 04:44:40 PST)
Re: [AMBER] Fwd: Can't load MEOHBOX as solvent
(Wed Nov 08 2017 - 17:15:44 PST)
Re: [AMBER] New ligand [antechamber->prepgen->parmchk2->xLeap]
(Wed Nov 08 2017 - 00:31:04 PST)
Re: [AMBER] Distance restrain usage for fixing distance between two atoms
(Mon Nov 06 2017 - 00:33:37 PST)
Re: [AMBER] How to generate inpcrd and prmtop files for A and B mixed solution
(Thu Nov 02 2017 - 11:13:45 PDT)
Re: [AMBER] How to generate inpcrd and prmtop files for A and B mixed solution
(Thu Nov 02 2017 - 04:51:15 PDT)
Re: [AMBER] the best APS is not zero, bonds involved by this atom are frozen
(Wed Nov 01 2017 - 14:06:04 PDT)
Re: [AMBER] energy minimum vs binding pose for charge calculation
(Wed Nov 01 2017 - 10:56:07 PDT)
David Cerutti
Re: [AMBER] What forcefield does the DHFR JAC benchmark system use?
(Sat Nov 25 2017 - 12:46:06 PST)
Re: [AMBER] What forcefield does the DHFR JAC benchmark system use?
(Sat Nov 25 2017 - 12:44:19 PST)
Re: [AMBER] The strange way of paramfit working process
(Fri Nov 17 2017 - 13:45:10 PST)
Re: [AMBER] The strange way of paramfit working process
(Thu Nov 16 2017 - 16:42:28 PST)
Re: [AMBER] MC barostat
(Wed Nov 15 2017 - 00:27:34 PST)
Re: [AMBER] The strange way of paramfit working process
(Wed Nov 15 2017 - 00:08:10 PST)
Re: [AMBER] MC barostat
(Tue Nov 14 2017 - 11:18:26 PST)
Dmitry Suplatov
[AMBER] Automatic rotation of the protein by LEAP to minimize the periodic cell dimensions?
(Sat Nov 04 2017 - 02:34:58 PDT)
Dr. MANAS MONDAL
Re: [AMBER] H-REMD
(Fri Nov 03 2017 - 20:29:17 PDT)
[AMBER] H-REMD
(Fri Nov 03 2017 - 03:53:22 PDT)
Eiros Zamora, Juan
[AMBER] Trouble installing amber tools on new OSX 10.13.1
(Wed Nov 29 2017 - 04:35:00 PST)
Elisa Pieri
[AMBER] About PCA and pi-stacking
(Tue Nov 28 2017 - 08:51:43 PST)
Elvis Martis
Re: [AMBER] aMD- alphaD- what does solute residues mean?
(Wed Nov 29 2017 - 03:45:57 PST)
Re: [AMBER] STOP PMEMD Terminated Abnormally
(Mon Nov 27 2017 - 08:10:36 PST)
Re: [AMBER] PCA eigenvalues
(Mon Nov 27 2017 - 04:05:47 PST)
Re: [AMBER] PCA eigenvalues
(Fri Nov 24 2017 - 04:15:33 PST)
Re: [AMBER] Can we study the bond breaking event through Md simulation
(Thu Nov 23 2017 - 22:52:44 PST)
Emmanuel
[AMBER] MMPBSA's output: Which atoms are treated as Backbone Atoms (and Side Chain Atoms) for Nucleic Acids?
(Fri Nov 17 2017 - 00:22:24 PST)
Ercig Bogac (BIOCH)
Re: [AMBER] Can we study the bond breaking event through Md simulation
(Fri Nov 24 2017 - 00:58:37 PST)
Re: [AMBER] cudaGetDeviceCount failed unknown error
(Thu Nov 23 2017 - 14:29:35 PST)
Re: [AMBER] cudaGetDeviceCount failed unknown error
(Thu Nov 23 2017 - 10:51:25 PST)
[AMBER] cudaGetDeviceCount failed unknown error
(Thu Nov 23 2017 - 05:29:42 PST)
Eric Lang
Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations
(Tue Nov 14 2017 - 03:20:27 PST)
Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations
(Mon Nov 13 2017 - 08:07:46 PST)
Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations
(Mon Nov 13 2017 - 08:00:47 PST)
[AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations
(Mon Nov 13 2017 - 03:46:01 PST)
Eugene Cha
[AMBER] MCPB.py step 1 help please
(Wed Nov 01 2017 - 12:14:31 PDT)
Feng Pan
Re: [AMBER] Free Energy GPU
(Mon Nov 06 2017 - 09:55:06 PST)
Re: [AMBER] H-REMD
(Fri Nov 03 2017 - 20:48:14 PDT)
Re: [AMBER] H-REMD
(Fri Nov 03 2017 - 17:47:37 PDT)
filip
Re: [AMBER] MC barostat
(Wed Nov 15 2017 - 01:39:55 PST)
Re: [AMBER] MC barostat
(Wed Nov 15 2017 - 00:13:14 PST)
[AMBER] MC barostat
(Tue Nov 14 2017 - 03:09:59 PST)
Gustavo Seabra
Re: [AMBER] AMBER QM/MM Point charges
(Fri Nov 17 2017 - 13:46:52 PST)
Re: [AMBER] AMBER QM/MM Point charges
(Fri Nov 17 2017 - 03:49:08 PST)
Hai Nguyen
Re: [AMBER] Trouble installing amber tools on new OSX 10.13.1
(Wed Nov 29 2017 - 05:40:17 PST)
Re: [AMBER] STOP PMEMD Terminated Abnormally
(Mon Nov 27 2017 - 16:27:48 PST)
Re: [AMBER] Can't find pad4amber module.
(Mon Nov 20 2017 - 22:21:38 PST)
Re: [AMBER] the CYX problem of generation parm7 crd files by AT17
(Sun Nov 12 2017 - 16:43:44 PST)
Re: [AMBER] the CYX problem of generation parm7 crd files by AT17
(Sun Nov 12 2017 - 16:40:35 PST)
Re: [AMBER] the CYX problem of generation parm7 crd files by AT17
(Sun Nov 12 2017 - 16:33:40 PST)
Re: [AMBER] error of pdb4amber
(Sun Nov 12 2017 - 16:23:54 PST)
Re: [AMBER] error of pdb4amber
(Sun Nov 12 2017 - 08:44:56 PST)
Re: [AMBER] Unknown flag error - sander
(Mon Nov 06 2017 - 06:20:27 PST)
Re: [AMBER] Unknown flag error - sander
(Mon Nov 06 2017 - 06:18:48 PST)
Re: [AMBER] Miniconda gives error while compiling AmberTools-17
(Thu Nov 02 2017 - 05:47:34 PDT)
Hector A. Baldoni
Re: [AMBER] force field for xylose
(Sun Nov 12 2017 - 14:58:57 PST)
Holger Kruse
[AMBER] DFTB3
(Thu Nov 16 2017 - 04:10:18 PST)
ilhan.yavuz
Re: [AMBER] suggestion for a GTX 1080
(Mon Nov 13 2017 - 00:29:34 PST)
[AMBER] suggestion for a GTX 1080
(Sat Nov 11 2017 - 10:41:04 PST)
jacky zhao
Re: [AMBER] error of pdb4amber
(Mon Nov 13 2017 - 09:14:05 PST)
[AMBER] the CYX problem of generation parm7 crd files by AT17
(Sun Nov 12 2017 - 15:14:49 PST)
Re: [AMBER] error of pdb4amber
(Sun Nov 12 2017 - 13:51:19 PST)
[AMBER] error of pdb4amber
(Sun Nov 12 2017 - 08:03:39 PST)
jacob wick
[AMBER] Distance restrain usage for fixing distance between two atoms
(Sat Nov 04 2017 - 06:43:02 PDT)
James Kress
Re: [AMBER] How to extract one frame from a trajectory to use as input file for new MD run?
(Fri Nov 17 2017 - 15:29:14 PST)
[AMBER] How to extract one frame from a trajectory to use as input file for new MD run?
(Thu Nov 16 2017 - 18:25:53 PST)
Jerrano Bowleg
[AMBER] Help Regarding Amber Tools
(Mon Nov 20 2017 - 08:15:41 PST)
Jian Yin
Re: [AMBER] APR error
(Tue Nov 28 2017 - 15:08:56 PST)
Re: [AMBER] APR error
(Tue Nov 28 2017 - 14:57:27 PST)
Joachim Hein
Re: [AMBER] Amber GCC 6.4.0 and MKL 2017.3.196 build failing
(Fri Nov 10 2017 - 08:35:14 PST)
[AMBER] Amber GCC 6.4.0 and MKL 2017.3.196 build failing
(Fri Nov 10 2017 - 08:32:36 PST)
Johannes Löffler
[AMBER] Free Energy GPU
(Mon Nov 06 2017 - 00:57:19 PST)
John Chodera
Re: [AMBER] What forcefield does the DHFR JAC benchmark system use?
(Sun Nov 26 2017 - 10:26:49 PST)
[AMBER] What forcefield does the DHFR JAC benchmark system use?
(Sat Nov 25 2017 - 11:12:55 PST)
Junmei Wang
Re: [AMBER] antechamber: prepgen mainchain file character limit
(Thu Nov 30 2017 - 07:54:48 PST)
junmwang.gmail.com
Re: [AMBER] PF6- octahedral geometry change during equilibration!!
(Thu Nov 30 2017 - 18:20:12 PST)
Kadir Tung
[AMBER] Protein-Ligand Energy Minimization
(Wed Nov 29 2017 - 10:14:58 PST)
Lachele Foley
Re: [AMBER] Query about the Glucose Parameters
(Fri Nov 24 2017 - 21:37:47 PST)
Re: [AMBER] Query about the Glucose Parameters
(Wed Nov 22 2017 - 07:12:12 PST)
Re: [AMBER] Query about the Glucose Parameters
(Tue Nov 21 2017 - 05:56:16 PST)
Re: [AMBER] Regarding Glucose dynamics
(Tue Nov 14 2017 - 08:16:26 PST)
Re: [AMBER] Regarding Glucose dynamics
(Tue Nov 14 2017 - 06:55:38 PST)
Re: [AMBER] 1-4 scaling factors in case of GAFF-GLYCAM mixed dihedral terms ?
(Sun Nov 05 2017 - 02:34:59 PST)
Re: [AMBER] 1-4 scaling factors in case of GAFF-GLYCAM mixed dihedral terms ?
(Sat Nov 04 2017 - 03:02:38 PDT)
Leena Aggarwal
Re: [AMBER] ntxo option in amber
(Sat Nov 11 2017 - 02:45:09 PST)
[AMBER] ntxo option in amber
(Sat Nov 11 2017 - 02:36:59 PST)
Lei Zhao
[AMBER] error of pdb4amber
(Sun Nov 12 2017 - 08:02:59 PST)
Lizelle Lubbe
Re: [AMBER] PCA eigenvalues
(Thu Nov 23 2017 - 10:56:12 PST)
Re: [AMBER] Equilibration
(Wed Nov 22 2017 - 23:23:36 PST)
[AMBER] PCA eigenvalues
(Sat Nov 18 2017 - 07:05:51 PST)
Re: [AMBER] PCA scree plots
(Thu Nov 16 2017 - 02:40:28 PST)
[AMBER] PCA scree plots
(Thu Nov 16 2017 - 02:27:47 PST)
Re: [AMBER] pdb snapshots
(Wed Nov 15 2017 - 04:16:13 PST)
[AMBER] pdb snapshots
(Tue Nov 14 2017 - 04:49:39 PST)
Re: [AMBER] Convert prmtop
(Mon Nov 13 2017 - 07:25:10 PST)
Re: [AMBER] Cpptraj pdb snapshots
(Mon Nov 13 2017 - 05:07:18 PST)
[AMBER] Convert prmtop
(Mon Nov 13 2017 - 04:48:54 PST)
[AMBER] Cpptraj pdb snapshots
(Mon Nov 13 2017 - 04:28:32 PST)
Marcelo Andrade Chagas
Re: [AMBER] structure minimization
(Tue Nov 28 2017 - 03:10:56 PST)
Re: [AMBER] PCA eigenvalues
(Mon Nov 27 2017 - 07:52:09 PST)
Re: [AMBER] Query about the Glucose Parameters
(Sat Nov 25 2017 - 04:21:20 PST)
Marek Havrila
Re: [AMBER] Computer for running MD simulation using Amber
(Thu Nov 09 2017 - 04:15:15 PST)
Marek Maly
Re: [AMBER] 1-4 scaling factors in case of GAFF-GLYCAM mixed dihedral terms ?
(Sun Nov 05 2017 - 16:15:41 PST)
Re: [AMBER] 1-4 scaling factors in case of GAFF-GLYCAM mixed dihedral terms ?
(Sat Nov 04 2017 - 07:07:59 PDT)
[AMBER] 1-4 scaling factors in case of GAFF-GLYCAM mixed dihedral terms ?
(Fri Nov 03 2017 - 15:28:32 PDT)
Markus Schneider
Re: [AMBER] antechamber: prepgen mainchain file character limit
(Thu Nov 30 2017 - 09:10:52 PST)
[AMBER] antechamber: prepgen mainchain file character limit
(Thu Nov 30 2017 - 07:36:02 PST)
Maura Malinska
[AMBER] APR error
(Tue Nov 28 2017 - 03:25:14 PST)
MinYuan
Re: [AMBER] how to generate the force fied file of AsO3H3?
(Wed Nov 29 2017 - 19:37:54 PST)
Re: [AMBER] how to generate the force fied file of AsO3H3?
(Wed Nov 29 2017 - 02:31:04 PST)
[AMBER] Fw: mpirun Error opening unit 5
(Wed Nov 29 2017 - 02:22:44 PST)
[AMBER] mpirun Error opening unit 5
(Wed Nov 29 2017 - 02:00:00 PST)
Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib
(Tue Nov 28 2017 - 22:42:23 PST)
Re: [AMBER] [SPAM] Re: cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib
(Tue Nov 28 2017 - 17:28:40 PST)
[AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib
(Tue Nov 28 2017 - 01:24:11 PST)
Re: [AMBER] STOP PMEMD Terminated Abnormally
(Mon Nov 27 2017 - 16:35:52 PST)
Re: [AMBER] STOP PMEMD Terminated Abnormally
(Mon Nov 27 2017 - 16:17:15 PST)
[AMBER] STOP PMEMD Terminated Abnormally
(Mon Nov 27 2017 - 08:08:08 PST)
[AMBER] any opportunity of using the pmemd.cuda if one cannot afford the fee
(Sun Nov 26 2017 - 22:08:15 PST)
minyuan.mail.ustc.edu.cn
Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib
(Wed Nov 29 2017 - 06:23:04 PST)
Re: [AMBER] how to generate the force fied file of AsO3H3?
(Wed Nov 29 2017 - 06:20:50 PST)
[AMBER] how to generate the force fied file of AsO3H3?
(Tue Nov 28 2017 - 23:50:58 PST)
Re: [AMBER] Does amber16 support gaussian16?
(Wed Nov 22 2017 - 01:59:20 PST)
[AMBER] Does amber16 support gaussian16?
(Tue Nov 21 2017 - 00:39:27 PST)
Re: [AMBER] [SPAM] Re: Can't find pad4amber module.
(Mon Nov 20 2017 - 23:01:24 PST)
[AMBER] Can't find pad4amber module.
(Mon Nov 20 2017 - 17:37:58 PST)
mirzo
Re: [AMBER] Query about the Glucose Parameters
(Fri Nov 24 2017 - 23:11:55 PST)
Re: [AMBER] Confusion in urea Model
(Wed Nov 15 2017 - 06:27:05 PST)
Mo Rahman
[AMBER] Unknown flag error - sander
(Mon Nov 06 2017 - 05:55:00 PST)
Mustafa Alhaji Isa
[AMBER] H-bond analysis
(Wed Nov 08 2017 - 04:17:45 PST)
Neha Gandhi
Re: [AMBER] change in density on multiple gpus
(Fri Nov 10 2017 - 17:26:51 PST)
Re: [AMBER] change in density on multiple gpus
(Wed Nov 08 2017 - 16:22:48 PST)
Re: [AMBER] change in density on multiple gpus
(Wed Nov 08 2017 - 13:24:48 PST)
[AMBER] change in density on multiple gpus
(Tue Nov 07 2017 - 22:15:27 PST)
Niel Henriksen
Re: [AMBER] MC barostat
(Tue Nov 14 2017 - 10:17:16 PST)
Nisha Amarnath Jonniya
Re: [AMBER] PCA eigenvalues
(Wed Nov 29 2017 - 03:24:50 PST)
Re: [AMBER] PCA eigenvalues
(Tue Nov 28 2017 - 00:40:59 PST)
Re: [AMBER] PCA eigenvalues
(Mon Nov 27 2017 - 04:20:46 PST)
Re: [AMBER] PCA eigenvalues
(Mon Nov 27 2017 - 00:45:38 PST)
Re: [AMBER] PCA eigenvalues
(Fri Nov 24 2017 - 03:39:01 PST)
Osman, Roman
[AMBER] force field for xylose
(Sun Nov 12 2017 - 11:58:34 PST)
Pablo Galaz-Davison
[AMBER] About position restrains
(Wed Nov 22 2017 - 12:25:20 PST)
Pacheco, Sayuri
Re: [AMBER] Running Explicit pH MD
(Thu Nov 16 2017 - 14:48:26 PST)
Re: [AMBER] Running Explicit pH MD
(Fri Nov 10 2017 - 13:06:04 PST)
Re: [AMBER] Running Explicit pH MD
(Fri Nov 10 2017 - 10:56:28 PST)
Re: [AMBER] Running Explicit pH MD
(Thu Nov 09 2017 - 22:56:59 PST)
Paul Mortenson
Re: [AMBER] imin=5 not working in AMBER16?
(Wed Nov 29 2017 - 23:52:08 PST)
Re: [AMBER] imin=5 not working in AMBER16?
(Wed Nov 29 2017 - 07:51:25 PST)
[AMBER] imin=5 not working in AMBER16?
(Wed Nov 29 2017 - 07:19:37 PST)
Pengfei Li
Re: [AMBER] how to generate the force fied file of AsO3H3?
(Wed Nov 29 2017 - 20:14:10 PST)
Re: [AMBER] Does amber16 support gaussian16?
(Tue Nov 28 2017 - 18:10:38 PST)
Re: [AMBER] Does amber16 support gaussian16?
(Tue Nov 21 2017 - 15:44:21 PST)
Re: [AMBER] Does amber16 support gaussian16?
(Tue Nov 21 2017 - 07:15:17 PST)
Re: [AMBER] restrain charge during MCPB.py parametrization
(Tue Nov 14 2017 - 12:43:26 PST)
Re: [AMBER] Regarding MCPB.py error
(Mon Nov 13 2017 - 08:08:46 PST)
Re: [AMBER] Regarding MCPB.py error
(Mon Nov 13 2017 - 08:07:21 PST)
Re: [AMBER] MCPB.py step 1 help please
(Wed Nov 08 2017 - 06:51:26 PST)
Re: [AMBER] No Cartesian force constants found
(Wed Nov 08 2017 - 06:46:11 PST)
Prithvi Raj Pandey
[AMBER] MMPBSA.py calculations on protein domain
(Thu Nov 16 2017 - 01:05:35 PST)
Prunotto Alessio
[AMBER] Parameterizing cardiolipins in Lipid17 force field
(Thu Nov 16 2017 - 03:35:52 PST)
Qinghua Liao
Re: [AMBER] Fwd: simulations of enzyme with ligand
(Mon Nov 20 2017 - 08:09:25 PST)
[AMBER] Fwd: simulations of enzyme with ligand
(Sun Nov 19 2017 - 06:58:47 PST)
[AMBER] simulations of enzyme with ligand
(Thu Nov 16 2017 - 08:51:19 PST)
Re: [AMBER] protein && DNA in implicit solvents
(Wed Nov 01 2017 - 14:19:45 PDT)
[AMBER] protein && DNA in implicit solvents
(Wed Nov 01 2017 - 05:15:26 PDT)
[AMBER] pulling along RMSD
(Wed Nov 01 2017 - 05:07:06 PDT)
Rana Rehan Khalid
[AMBER] MCPB.py how to insert the heteroatom heme in the one domain of macromolecule
(Thu Nov 30 2017 - 06:44:54 PST)
Re: [AMBER] structure minimization
(Tue Nov 28 2017 - 06:05:59 PST)
Re: [AMBER] structure minimization
(Tue Nov 28 2017 - 03:28:51 PST)
Re: [AMBER] structure minimization
(Tue Nov 28 2017 - 03:13:23 PST)
[AMBER] structure minimization
(Tue Nov 28 2017 - 03:01:12 PST)
[AMBER] Multidomain protein Simulation
(Mon Nov 27 2017 - 14:50:11 PST)
Re: [AMBER] Hydrogen bond analysis Through CPPTRAJ
(Mon Nov 27 2017 - 08:58:22 PST)
[AMBER] Hydrogen bond analysis Through CPPTRAJ
(Sun Nov 26 2017 - 06:03:15 PST)
Re: [AMBER] Can we study the bond breaking event through Md simulation
(Sat Nov 25 2017 - 04:38:15 PST)
Re: [AMBER] Can we study the bond breaking event through Md simulation
(Fri Nov 24 2017 - 01:14:01 PST)
Re: [AMBER] Can we study the bond breaking event through Md simulation
(Thu Nov 23 2017 - 23:46:32 PST)
Re: [AMBER] Can we study the bond breaking event through Md simulation
(Thu Nov 23 2017 - 22:59:35 PST)
[AMBER] Can we study the bond breaking event through Md simulation
(Thu Nov 23 2017 - 21:51:39 PST)
[AMBER] how to set hetrodimer for MD Simulation
(Wed Nov 22 2017 - 13:13:49 PST)
[AMBER] Cpptraj
(Tue Nov 14 2017 - 23:51:46 PST)
[AMBER] Domain domain interaction study
(Mon Nov 13 2017 - 09:42:37 PST)
Re: [AMBER] cpptraj error
(Mon Nov 13 2017 - 05:03:25 PST)
Re: [AMBER] cpptraj error
(Mon Nov 13 2017 - 04:41:25 PST)
Re: [AMBER] cpptraj error
(Mon Nov 13 2017 - 04:36:08 PST)
Re: [AMBER] cpptraj error
(Mon Nov 13 2017 - 04:32:24 PST)
Re: [AMBER] cpptraj error
(Mon Nov 13 2017 - 04:30:24 PST)
Re: [AMBER] cpptraj error
(Mon Nov 13 2017 - 04:22:31 PST)
Re: [AMBER] cpptraj error
(Mon Nov 13 2017 - 03:32:00 PST)
[AMBER] cpptraj error
(Mon Nov 13 2017 - 03:24:22 PST)
Ray Luo
Re: [AMBER] mmpbsa.py
(Thu Nov 09 2017 - 13:29:41 PST)
Re: [AMBER] mmpbsa.py
(Thu Nov 09 2017 - 05:40:47 PST)
Re: [AMBER] mmpbsa.py error
(Fri Nov 03 2017 - 10:30:36 PDT)
Rinsha Chk
[AMBER] What does "NRF ne Abs NRFX" error (Gaussian 09) mean?
(Thu Nov 16 2017 - 21:41:47 PST)
Robin Betz
Re: [AMBER] The strange way of paramfit working process
(Thu Nov 16 2017 - 16:26:07 PST)
Rodrigo Galindo-Murillo
Re: [AMBER] problem with TUTORAL C5: Hydrogen Bond Analysis with CPPTRAJ
(Fri Nov 03 2017 - 15:53:23 PDT)
Ross Walker
Re: [AMBER] lipid 14 compatibility with FF14SB
(Wed Nov 29 2017 - 11:36:33 PST)
Re: [AMBER] What forcefield does the DHFR JAC benchmark system use?
(Sat Nov 25 2017 - 12:42:52 PST)
Re: [AMBER] cudaGetDeviceCount failed unknown error
(Sat Nov 25 2017 - 12:33:16 PST)
Re: [AMBER] cudaGetDeviceCount failed unknown error
(Thu Nov 23 2017 - 08:08:13 PST)
Re: [AMBER] SCEE/SCNB zeros
(Wed Nov 22 2017 - 05:29:00 PST)
Re: [AMBER] suggestion for a GTX 1080
(Mon Nov 13 2017 - 04:40:03 PST)
Re: [AMBER] suggestion for a GTX 1080
(Sun Nov 12 2017 - 16:06:38 PST)
Re: [AMBER] change in density on multiple gpus
(Fri Nov 10 2017 - 03:08:30 PST)
Re: [AMBER] change in density on multiple gpus
(Wed Nov 08 2017 - 13:33:15 PST)
Re: [AMBER] change in density on multiple gpus
(Wed Nov 08 2017 - 06:21:19 PST)
Re: [AMBER] Free Energy GPU
(Mon Nov 06 2017 - 05:13:50 PST)
Ruchika Bhat
[AMBER] All interactions fraction analysis
(Thu Nov 16 2017 - 03:14:21 PST)
Saikat Pal
[AMBER] Is GAFF polarizable forcefield ??
(Fri Nov 17 2017 - 02:16:22 PST)
[AMBER] Confusion in urea Model
(Tue Nov 14 2017 - 22:47:53 PST)
Re: [AMBER] UREA PDB file from xleap
(Fri Nov 10 2017 - 21:18:31 PST)
[AMBER] UREA PDB file from xleap
(Fri Nov 10 2017 - 02:46:59 PST)
[AMBER] Need information regarding frcmod.urea
(Mon Nov 06 2017 - 23:14:12 PST)
Sanaa ALAbbad
[AMBER] PF6- octahedral geometry change during equilibration!!
(Thu Nov 30 2017 - 16:00:48 PST)
sangita kachhap
Re: [AMBER] Centriod in clustering
(Tue Nov 28 2017 - 08:28:46 PST)
[AMBER] Centriod in clustering
(Tue Nov 28 2017 - 07:09:41 PST)
[AMBER] SHAKEH problem in GPU calculation
(Tue Nov 21 2017 - 02:30:25 PST)
[AMBER] SHAKEH problem in GPU calculation
(Tue Nov 21 2017 - 02:08:32 PST)
[AMBER] Hydrogen atom SHAKEH problem
(Mon Nov 06 2017 - 08:18:15 PST)
sara.iti.lk
Re: [AMBER] Equiliibration
(Thu Nov 23 2017 - 21:20:15 PST)
Re: [AMBER] Equiliibration
(Thu Nov 23 2017 - 21:13:10 PST)
Re: [AMBER] Equilibration
(Wed Nov 22 2017 - 22:30:54 PST)
Re: [AMBER] Equilibration
(Tue Nov 21 2017 - 23:03:07 PST)
[AMBER] Equilibration
(Sun Nov 19 2017 - 22:20:22 PST)
Scott Le Grand
Re: [AMBER] suggestion for a GTX 1080
(Sun Nov 12 2017 - 17:34:41 PST)
Setyanto Md
Re: [AMBER] problem with TUTORAL C5: Hydrogen Bond Analysis with CPPTRAJ
(Fri Nov 03 2017 - 16:17:07 PDT)
Shilpa Gupta
[AMBER] solvation box
(Thu Nov 09 2017 - 01:32:13 PST)
[AMBER] error: Atom does not have type
(Tue Nov 07 2017 - 23:32:57 PST)
Re: [AMBER] chloride as anion
(Fri Nov 03 2017 - 03:38:34 PDT)
[AMBER] chloride as anion
(Fri Nov 03 2017 - 03:16:28 PDT)
Re: [AMBER] Acetate ion using xleap
(Thu Nov 02 2017 - 22:11:52 PDT)
Re: [AMBER] Acetate ion using xleap
(Thu Nov 02 2017 - 21:48:50 PDT)
[AMBER] Acetate ion using xleap
(Thu Nov 02 2017 - 21:19:00 PDT)
[AMBER] the best APS is not zero, bonds involved by this atom are frozen
(Wed Nov 01 2017 - 07:40:59 PDT)
Sowmya Indrakumar
Re: [AMBER] Post processing of trajectory
(Wed Nov 29 2017 - 05:39:31 PST)
[AMBER] Post processing of trajectory
(Wed Nov 29 2017 - 05:04:42 PST)
Stefan Doerr
Re: [AMBER] SCEE/SCNB zeros
(Wed Nov 22 2017 - 07:17:04 PST)
[AMBER] SCEE/SCNB zeros
(Wed Nov 22 2017 - 02:11:00 PST)
sudipta.mml
[AMBER] Fw(4): sudipta.mml.gmail.com
(Thu Nov 16 2017 - 08:55:47 PST)
Sushi Shilpa
[AMBER] No Cartesian force constants found
(Mon Nov 06 2017 - 21:20:32 PST)
sylvester kisembo
[AMBER] Energy Calculations by cpptraj
(Thu Nov 09 2017 - 05:56:01 PST)
Szymon Żaczek
Re: [AMBER] Can we study the bond breaking event through Md simulation
(Fri Nov 24 2017 - 02:50:08 PST)
Taisung Lee
Re: [AMBER] cudaGetDeviceCount failed unknown error
(Thu Nov 23 2017 - 14:18:12 PST)
Re: [AMBER] Free Energy GPU
(Mon Nov 06 2017 - 04:36:50 PST)
Taylor, Miles
[AMBER] New ligand [antechamber->prepgen->parmchk2->xLeap]
(Tue Nov 07 2017 - 13:53:42 PST)
Thakur, Abhishek
[AMBER] aMD- alphaD- what does solute residues mean?
(Tue Nov 28 2017 - 12:36:51 PST)
Thomas Cheatham
Re: [AMBER] About position restrains
(Wed Nov 22 2017 - 14:22:09 PST)
Re: [AMBER] REMD jobs slowing down unexpectedly
(Fri Nov 10 2017 - 12:41:05 PST)
Thomas Evangelidis
Re: [AMBER] cpptraj: partial charges missing from mol2 file
(Wed Nov 22 2017 - 17:04:37 PST)
[AMBER] cpptraj: partial charges missing from mol2 file
(Wed Nov 22 2017 - 08:04:07 PST)
Re: [AMBER] energy minimum vs binding pose for charge calculation
(Wed Nov 01 2017 - 15:16:07 PDT)
Re: [AMBER] energy minimum vs binding pose for charge calculation
(Wed Nov 01 2017 - 11:20:50 PDT)
[AMBER] energy minimum vs binding pose for charge calculation
(Wed Nov 01 2017 - 07:45:32 PDT)
Urszula Uciechowska
Re: [AMBER] mmpbsa.py
(Thu Nov 09 2017 - 07:06:35 PST)
[AMBER] mmpbsa.py
(Thu Nov 09 2017 - 01:22:30 PST)
[AMBER] mmpbsa.py error
(Fri Nov 03 2017 - 00:22:15 PDT)
[AMBER] PB Bomb in pb_aaradi() while running mmpbsa.py
(Wed Nov 01 2017 - 03:39:04 PDT)
viktor drobot
Re: [AMBER] The strange way of paramfit working process
(Fri Nov 17 2017 - 12:25:29 PST)
Re: [AMBER] The strange way of paramfit working process
(Wed Nov 15 2017 - 07:19:14 PST)
Re: [AMBER] The strange way of paramfit working process
(Wed Nov 15 2017 - 04:14:55 PST)
[AMBER] The strange way of paramfit working process
(Tue Nov 14 2017 - 13:32:33 PST)
Wenbo Zhang
[AMBER] How to generate a cis-isomoerization of PRO?
(Tue Nov 21 2017 - 01:05:37 PST)
Wesley Michael Botello-Smith
Re: [AMBER] Analysis of percentage contact in residue-ligand interaction with CPPTRAJ
(Mon Nov 20 2017 - 17:25:44 PST)
Yang Jinpeng
[AMBER] Using soft-core potentials to run TI simulations
(Wed Nov 29 2017 - 02:50:12 PST)
Yuliia Varenyk
[AMBER] Help
(Tue Nov 14 2017 - 07:16:36 PST)
张姝姝
[AMBER] Is accelerated MD suitable for DFG-flip simulation in kinase?
(Fri Nov 10 2017 - 07:51:06 PST)
杨满意
Re: [AMBER] How to generate inpcrd and prmtop files for A and B mixed solution
(Thu Nov 02 2017 - 18:13:53 PDT)
Re: [AMBER] How to generate inpcrd and prmtop files for A and B mixed solution
(Thu Nov 02 2017 - 05:52:03 PDT)
[AMBER] How to generate inpcrd and prmtop files for A and B mixed solution
(Wed Nov 01 2017 - 18:52:38 PDT)
闵媛
[AMBER] 回复: Re: Does amber16 support gaussian16?
(Tue Nov 21 2017 - 07:37:37 PST)
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