Amber Archive Sep 2016 by author
474 messages
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Starting
Wed Aug 31 2016 - 19:00:02 PDT,
Ending
Fri Sep 30 2016 - 20:00:02 PDT
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ABEL Stephane 175950
Re: [AMBER] "ATTN, need revision" in frcmod file / Could not find bond parameter & Could not find angle parameter
(Fri Sep 16 2016 - 12:12:10 PDT)
Abhi Acharya
[AMBER] Problem with MCPB.py workflow after calculation of force constants.
(Wed Sep 07 2016 - 02:15:49 PDT)
ABHIJEET CHOWDHURY
Re: [AMBER] Unstable SHAKE
(Thu Sep 22 2016 - 08:53:49 PDT)
[AMBER] Unstable SHAKE
(Thu Sep 22 2016 - 08:49:51 PDT)
Abhilash J
Re: [AMBER] Speed issue with Accelerated molecular dynamics.
(Sun Sep 11 2016 - 01:54:44 PDT)
[AMBER] Speed issue with Accelerated molecular dynamics.
(Sun Sep 11 2016 - 00:35:47 PDT)
Adrian Roitberg
Re: [AMBER] MM-PBSA calculation in different temprature
(Fri Sep 23 2016 - 05:45:58 PDT)
Re: [AMBER] SCC-DFTB
(Mon Sep 12 2016 - 09:09:22 PDT)
Re: [AMBER] MMPBSA with different external Dielectric Constant
(Mon Sep 12 2016 - 08:29:04 PDT)
Re: [AMBER] Switching from PM3-PDDG to SCC-DFT method
(Wed Sep 07 2016 - 15:29:56 PDT)
Re: [AMBER] changepot
(Wed Sep 07 2016 - 11:53:17 PDT)
Re: [AMBER] [Amber] Periodic Box Issue
(Tue Sep 06 2016 - 09:07:34 PDT)
Re: [AMBER] Question about QM/MM
(Tue Sep 06 2016 - 08:36:18 PDT)
Re: [AMBER] Question about QM/MM
(Tue Sep 06 2016 - 07:44:25 PDT)
Re: [AMBER] Question about QM/MM
(Fri Sep 02 2016 - 10:59:31 PDT)
Re: [AMBER] Question about QM/MM
(Fri Sep 02 2016 - 10:54:07 PDT)
Re: [AMBER] Question about QM/MM
(Fri Sep 02 2016 - 10:37:53 PDT)
Re: [AMBER] Question about QM/MM
(Fri Sep 02 2016 - 10:09:35 PDT)
Re: [AMBER] Question about QM/MM
(Fri Sep 02 2016 - 08:27:46 PDT)
amitosh gautam
[AMBER] Problem regarding sccdftb not converging
(Thu Sep 29 2016 - 22:36:34 PDT)
Ana Bergues
[AMBER] Implicit solvent with GPU AMBER and Pulling direction in SMD
(Thu Sep 22 2016 - 00:38:16 PDT)
Anasuya Dighe
[AMBER] RMS-fit during PCA
(Fri Sep 02 2016 - 02:38:31 PDT)
Andrew Bostick
Re: [AMBER] netcdf trajectory
(Sun Sep 25 2016 - 01:20:29 PDT)
[AMBER] netcdf trajectory
(Sun Sep 25 2016 - 00:09:01 PDT)
[AMBER] netcdf trajectory
(Sat Sep 24 2016 - 13:39:38 PDT)
[AMBER] netcdf trajectory
(Fri Sep 23 2016 - 01:28:50 PDT)
Andrew Schaub
[AMBER] 2 ns heating in constant pH tutorial inquiry
(Sun Sep 25 2016 - 08:56:29 PDT)
Anna Cebrian Prats
Re: [AMBER] Force field ff14SB
(Wed Sep 14 2016 - 09:11:16 PDT)
[AMBER] Force field ff14SB
(Wed Sep 14 2016 - 04:06:44 PDT)
Re: [AMBER] Question about QM/MM
(Wed Sep 07 2016 - 07:48:00 PDT)
Re: [AMBER] How to assign frame range for cpptraj analysis?
(Wed Sep 07 2016 - 02:21:06 PDT)
Re: [AMBER] Question about QM/MM
(Tue Sep 06 2016 - 08:26:29 PDT)
Re: [AMBER] Question about QM/MM
(Tue Sep 06 2016 - 05:57:54 PDT)
Re: [AMBER] Question about QM/MM
(Mon Sep 05 2016 - 09:14:31 PDT)
[AMBER] Select a snapshot
(Mon Sep 05 2016 - 02:42:24 PDT)
[AMBER] Trajectory analysis
(Fri Sep 02 2016 - 08:05:39 PDT)
Re: [AMBER] Question about QM/MM
(Fri Sep 02 2016 - 02:01:06 PDT)
Anton Perera
[AMBER] Upgrade AMBER 14 to 16
(Thu Sep 08 2016 - 01:44:52 PDT)
Aronica, Pietro
[AMBER] Parmed.py, deleteBond and setBond
(Sun Sep 04 2016 - 21:18:05 PDT)
Ashutosh Shandilya
Re: [AMBER] Unable to find mopac charges in mopac.out
(Thu Sep 01 2016 - 23:46:15 PDT)
Atila Petrosian
Re: [AMBER] Hydrophobic interactions in MM-GBSA
(Sun Sep 04 2016 - 14:14:37 PDT)
[AMBER] Hydrophobic interactions in MM-GBSA
(Sun Sep 04 2016 - 13:37:01 PDT)
ATUL KUMAR
[AMBER] Restrain in Umbrella Sampling
(Sun Sep 25 2016 - 07:12:10 PDT)
Batuhan Kav
[AMBER] changeLJPair/pmemd.cuda
(Thu Sep 15 2016 - 13:32:23 PDT)
Beale, John
[AMBER] cpptraj
(Mon Sep 12 2016 - 02:16:14 PDT)
Bence Hégely
Re: [AMBER] Checking AmberTools16 installation
(Tue Sep 06 2016 - 05:24:34 PDT)
Bilal Nizami
Re: [AMBER] Continue a simulation run
(Thu Sep 15 2016 - 10:13:58 PDT)
Bill Ross
Re: [AMBER] FMN parameters
(Thu Sep 29 2016 - 00:48:34 PDT)
Re: [AMBER] FMN parameters
(Wed Sep 28 2016 - 23:47:46 PDT)
Re: [AMBER] Can amber handle carbon -- nitrogen double and single bond?
(Wed Sep 28 2016 - 02:38:18 PDT)
Re: [AMBER] netcdf trajectory
(Sun Sep 25 2016 - 09:45:24 PDT)
Re: [AMBER] netcdf trajectory
(Sun Sep 25 2016 - 09:31:08 PDT)
Re: [AMBER] netcdf trajectory
(Sun Sep 25 2016 - 00:44:48 PDT)
Re: [AMBER] netcdf trajectory
(Sun Sep 25 2016 - 00:30:14 PDT)
Re: [AMBER] netcdf trajectory
(Sat Sep 24 2016 - 13:53:48 PDT)
Re: [AMBER] dihedral PCA amber
(Thu Sep 22 2016 - 19:14:46 PDT)
Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file.
(Wed Sep 21 2016 - 19:44:36 PDT)
Re: [AMBER] Segmentation fault in tleap when using "sequence" command
(Wed Sep 21 2016 - 17:34:26 PDT)
Re: [AMBER] delete residue in tleap
(Sun Sep 18 2016 - 17:24:58 PDT)
Re: [AMBER] delete residue in tleap
(Sun Sep 18 2016 - 16:33:20 PDT)
Re: [AMBER] Installing amber tools on ubuntu
(Sat Sep 17 2016 - 13:20:31 PDT)
Re: [AMBER] AMBER installation help
(Sat Sep 17 2016 - 13:19:09 PDT)
Re: [AMBER] DNA residue atom names.
(Fri Sep 16 2016 - 13:14:43 PDT)
Re: [AMBER] aromatic ring plane distorted
(Fri Sep 16 2016 - 10:26:40 PDT)
Re: [AMBER] Fwd: query with amber
(Wed Sep 14 2016 - 23:26:03 PDT)
Re: [AMBER] Fwd: query with amber
(Wed Sep 14 2016 - 01:27:07 PDT)
Re: [AMBER] Fwd: query with amber
(Tue Sep 13 2016 - 23:39:41 PDT)
Re: [AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type. Failed to generate parameters Parameter file was not saved.
(Tue Sep 13 2016 - 23:32:36 PDT)
Re: [AMBER] cpptraj
(Mon Sep 12 2016 - 02:28:11 PDT)
Re: [AMBER] Problems about creating ligand leap input files
(Sun Sep 11 2016 - 21:14:47 PDT)
Re: [AMBER] PME calculation for Vacuum?
(Fri Sep 09 2016 - 14:35:24 PDT)
Re: [AMBER] PME calculation for Vacuum?
(Fri Sep 09 2016 - 14:19:10 PDT)
Re: [AMBER] PME calculation for Vacuum?
(Fri Sep 09 2016 - 11:49:06 PDT)
Re: [AMBER] Fwd: File redirection commands with targeted MD
(Thu Sep 08 2016 - 10:03:56 PDT)
Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16
(Mon Sep 05 2016 - 18:20:12 PDT)
Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16
(Mon Sep 05 2016 - 10:11:01 PDT)
Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16
(Sun Sep 04 2016 - 21:44:16 PDT)
Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16
(Sun Sep 04 2016 - 17:53:08 PDT)
Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16
(Sun Sep 04 2016 - 02:22:56 PDT)
BLEY Michael
[AMBER] Temperature connected to the dipole convergence in the output
(Mon Sep 05 2016 - 07:39:57 PDT)
Bruno Falcone
Re: [AMBER] How to "not" strip an ion (say Mg) in MMPBSA
(Wed Sep 14 2016 - 08:13:52 PDT)
Carlos Simmerling
[AMBER] ACS COMP award deadline for Spring 2017
(Wed Sep 28 2016 - 03:48:05 PDT)
Re: [AMBER] Unstable SHAKE
(Thu Sep 22 2016 - 08:52:35 PDT)
Re: [AMBER] Segmentation fault in tleap when using "sequence" command
(Thu Sep 22 2016 - 08:17:20 PDT)
Re: [AMBER] fixing concentration in implicit solvent simulation
(Tue Sep 20 2016 - 08:42:49 PDT)
Re: [AMBER] Amber16: COM's in GPU version
(Tue Sep 20 2016 - 07:53:13 PDT)
Re: [AMBER] aromatic ring plane distorted
(Fri Sep 16 2016 - 04:41:00 PDT)
Re: [AMBER] Force field ff14SB
(Wed Sep 14 2016 - 09:05:33 PDT)
Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations
(Wed Sep 14 2016 - 03:02:12 PDT)
Re: [AMBER] Add Molecule symmetry to sander
(Sun Sep 11 2016 - 04:39:29 PDT)
Re: [AMBER] Fwd: File redirection commands with targeted MD
(Thu Sep 08 2016 - 06:26:31 PDT)
Re: [AMBER] historical changes to LYN charges in amber03
(Mon Sep 05 2016 - 09:41:43 PDT)
Re: [AMBER] historical changes to LYN charges in amber03
(Mon Sep 05 2016 - 08:56:47 PDT)
Re: [AMBER] Hydrophobic interactions in MM-GBSA
(Sun Sep 04 2016 - 16:37:44 PDT)
Re: [AMBER] Hydrophobic interactions in MM-GBSA
(Sun Sep 04 2016 - 14:02:44 PDT)
Casalini Tommaso
[AMBER] On the simulation of phosphate ions in water solution
(Thu Sep 08 2016 - 01:49:56 PDT)
chandan patel
Re: [AMBER] Installing amber tools on ubuntu
(Sat Sep 17 2016 - 15:30:22 PDT)
Charles Lin
Re: [AMBER] PME calculation for Vacuum?
(Fri Sep 09 2016 - 11:51:12 PDT)
Chase Zagorec-Marks
Re: [AMBER] [Amber] Periodic Box Issue
(Tue Sep 06 2016 - 09:31:14 PDT)
[AMBER] [Amber] Periodic Box Issue
(Tue Sep 06 2016 - 09:04:41 PDT)
Chitrak Gupta
Re: [AMBER] fixing concentration in implicit solvent simulation
(Wed Sep 21 2016 - 13:11:51 PDT)
[AMBER] fixing concentration in implicit solvent simulation
(Tue Sep 20 2016 - 08:12:48 PDT)
[AMBER] generating topology file for non-standard amino acid
(Fri Sep 09 2016 - 15:17:06 PDT)
Christian Schafmeister
Re: [AMBER] How aggressively should bond, angle, torsion parameters be coalesced?
(Sat Sep 24 2016 - 13:03:34 PDT)
[AMBER] How aggressively should bond, angle, torsion parameters be coalesced?
(Sat Sep 24 2016 - 06:58:11 PDT)
Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file.
(Wed Sep 21 2016 - 13:13:07 PDT)
[AMBER] A refresher on how non-bonding terms are represented in a topology file.
(Wed Sep 21 2016 - 10:10:42 PDT)
[AMBER] DNA residue atom names.
(Thu Sep 15 2016 - 17:57:41 PDT)
Christina Bergonzo
Re: [AMBER] tleap cannot solvate unit in amber16
(Tue Sep 27 2016 - 06:25:26 PDT)
Daniel Mermelstein
Re: [AMBER] setup time with pmemd.cuda
(Sat Sep 24 2016 - 10:54:43 PDT)
Daniel Roe
Re: [AMBER] netcdf trajectory
(Fri Sep 30 2016 - 05:28:58 PDT)
Re: [AMBER] using boundary information from previous run
(Fri Sep 30 2016 - 05:25:10 PDT)
Re: [AMBER] using boundary information from previous run
(Thu Sep 29 2016 - 06:38:42 PDT)
Re: [AMBER] Pressure of the system during equilibration
(Thu Sep 29 2016 - 06:28:17 PDT)
Re: [AMBER] Disparities in H-bond lifetimes calculated through different approaches
(Thu Sep 29 2016 - 06:22:42 PDT)
Re: [AMBER] autoimage bug?
(Wed Sep 28 2016 - 06:53:45 PDT)
Re: [AMBER] dihedral PCA amber
(Tue Sep 27 2016 - 05:42:11 PDT)
Re: [AMBER] strip waters using distance criteria
(Fri Sep 23 2016 - 12:45:09 PDT)
Re: [AMBER] cpptraj gist core dumped
(Fri Sep 23 2016 - 05:22:11 PDT)
Re: [AMBER] netcdf trajectory
(Fri Sep 23 2016 - 05:17:38 PDT)
Re: [AMBER] dihedral PCA amber
(Fri Sep 23 2016 - 05:11:42 PDT)
Re: [AMBER] dihedral PCA amber
(Thu Sep 22 2016 - 12:16:11 PDT)
Re: [AMBER] Unstable SHAKE
(Thu Sep 22 2016 - 08:52:17 PDT)
Re: [AMBER] Segmentation fault in tleap when using "sequence" command
(Thu Sep 22 2016 - 08:51:36 PDT)
Re: [AMBER] Segmentation fault in tleap when using "sequence" command
(Wed Sep 21 2016 - 17:12:34 PDT)
Re: [AMBER] Segmentation fault in tleap when using "sequence" command
(Wed Sep 21 2016 - 17:11:17 PDT)
Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file.
(Wed Sep 21 2016 - 13:09:14 PDT)
Re: [AMBER] Problem with CRD files
(Tue Sep 20 2016 - 08:24:35 PDT)
Re: [AMBER] Problem with atommap function in cpptraj (v16)
(Tue Sep 20 2016 - 08:11:15 PDT)
Re: [AMBER] Problem with atommap function in cpptraj (v16)
(Tue Sep 20 2016 - 07:06:49 PDT)
Re: [AMBER] autoimage bug?
(Mon Sep 19 2016 - 07:20:50 PDT)
Re: [AMBER] Problem with CRD files
(Mon Sep 19 2016 - 07:12:24 PDT)
Re: [AMBER] hbond and autoimage
(Fri Sep 16 2016 - 06:17:11 PDT)
Re: [AMBER] comparing pytraj vs. sander output
(Tue Sep 13 2016 - 08:29:42 PDT)
Re: [AMBER] comparing pytraj vs. sander output
(Tue Sep 13 2016 - 07:53:19 PDT)
Re: [AMBER] cpptraj
(Mon Sep 12 2016 - 10:43:31 PDT)
Re: [AMBER] distance based mask
(Wed Sep 07 2016 - 12:26:07 PDT)
Re: [AMBER] query regarding radial distribution function plot.
(Tue Sep 06 2016 - 18:26:53 PDT)
Re: [AMBER] Select a snapshot
(Mon Sep 05 2016 - 18:41:40 PDT)
David A Case
Re: [AMBER] using boundary information from previous run
(Fri Sep 30 2016 - 07:17:45 PDT)
Re: [AMBER] LEaP and PARMSETs
(Fri Sep 30 2016 - 04:57:06 PDT)
Re: [AMBER] using boundary information from previous run
(Fri Sep 30 2016 - 04:22:09 PDT)
Re: [AMBER] using boundary information from previous run
(Thu Sep 29 2016 - 12:05:29 PDT)
Re: [AMBER] 答复: Amber NaN error
(Thu Sep 29 2016 - 11:57:18 PDT)
Re: [AMBER] on periodic conditions and unspecified launch failure
(Thu Sep 29 2016 - 11:53:59 PDT)
Re: [AMBER] Signal: Segmentation fault (11)
(Wed Sep 28 2016 - 11:53:28 PDT)
Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes.
(Wed Sep 28 2016 - 11:53:52 PDT)
Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes.
(Wed Sep 28 2016 - 06:09:46 PDT)
Re: [AMBER] Amber NaN error
(Wed Sep 28 2016 - 06:04:45 PDT)
Re: [AMBER] Issue regarding parametrization
(Tue Sep 27 2016 - 05:11:46 PDT)
Re: [AMBER] Signal: Segmentation fault (11)
(Mon Sep 26 2016 - 18:04:26 PDT)
Re: [AMBER] create a cubic box of 4.5 nm
(Mon Sep 26 2016 - 05:17:59 PDT)
Re: [AMBER] Signal: Segmentation fault (11)
(Sun Sep 25 2016 - 13:38:58 PDT)
Re: [AMBER] netcdf trajectory
(Fri Sep 23 2016 - 05:23:52 PDT)
Re: [AMBER] Parmchk - missing improper parameter for nitro group
(Thu Sep 22 2016 - 06:34:00 PDT)
Re: [AMBER] fixing concentration in implicit solvent simulation
(Thu Sep 22 2016 - 06:10:20 PDT)
Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file.
(Wed Sep 21 2016 - 19:29:18 PDT)
Re: [AMBER] positive electrostatic energy MM-PBSA
(Wed Sep 21 2016 - 04:38:36 PDT)
Re: [AMBER] DNA residue atom names.
(Fri Sep 16 2016 - 02:19:51 PDT)
Re: [AMBER] Follow up
(Fri Sep 16 2016 - 02:13:40 PDT)
Re: [AMBER] changeLJPair/pmemd.cuda
(Fri Sep 16 2016 - 02:10:27 PDT)
Re: [AMBER] WARNING: The unperturbed charge of the unit: -0.99 is not zero.
(Fri Sep 16 2016 - 02:08:28 PDT)
Re: [AMBER] Continue a simulation run
(Fri Sep 16 2016 - 02:05:49 PDT)
Re: [AMBER] Fwd: query with amber
(Wed Sep 14 2016 - 06:54:41 PDT)
Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations
(Wed Sep 14 2016 - 06:49:43 PDT)
Re: [AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type. Failed to generate parameters Parameter file was not saved.
(Wed Sep 14 2016 - 06:40:52 PDT)
Re: [AMBER] Fullerene RESP charges derivation
(Wed Sep 14 2016 - 06:36:42 PDT)
Re: [AMBER] generating topology file for non-standard amino acid
(Sat Sep 10 2016 - 09:40:36 PDT)
Re: [AMBER] PME calculation for Vacuum?
(Sat Sep 10 2016 - 09:19:07 PDT)
Re: [AMBER] Radial Distribution Function
(Thu Sep 08 2016 - 05:04:40 PDT)
Re: [AMBER] question on the reference data of GIST
(Thu Sep 08 2016 - 05:02:01 PDT)
Re: [AMBER] Upgrade AMBER 14 to 16
(Thu Sep 08 2016 - 04:58:06 PDT)
Re: [AMBER] MMPBSA analysis for a heme protein
(Wed Sep 07 2016 - 04:50:03 PDT)
Re: [AMBER] Temperature connected to the dipole convergence in the output
(Tue Sep 06 2016 - 06:57:15 PDT)
Re: [AMBER] Which is the best thermostat for cMD?
(Tue Sep 06 2016 - 06:41:37 PDT)
Re: [AMBER] Checking AmberTools16 installation
(Tue Sep 06 2016 - 05:52:56 PDT)
Re: [AMBER] How to fixed residues in amber?
(Tue Sep 06 2016 - 04:20:40 PDT)
Re: [AMBER] Question about QM/MM
(Tue Sep 06 2016 - 04:17:09 PDT)
Re: [AMBER] historical changes to LYN charges in amber03
(Mon Sep 05 2016 - 17:45:05 PDT)
Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16
(Sun Sep 04 2016 - 15:01:02 PDT)
Re: [AMBER] how to center a polipeptide inside a solvent box
(Fri Sep 02 2016 - 05:37:57 PDT)
Re: [AMBER] Unable to find mopac charges in mopac.out
(Fri Sep 02 2016 - 05:31:07 PDT)
Re: [AMBER] Unable to find mopac charges in mopac.out
(Thu Sep 01 2016 - 11:49:57 PDT)
Re: [AMBER] error in sander minimization
(Thu Sep 01 2016 - 09:41:54 PDT)
Re: [AMBER] autocorr of hydrogen bonds
(Thu Sep 01 2016 - 09:46:22 PDT)
Re: [AMBER] Fwd: MD stop at different time period without giving any error
(Thu Sep 01 2016 - 04:35:05 PDT)
Re: [AMBER] Regarding the use of sed command to replace water
(Thu Sep 01 2016 - 04:30:01 PDT)
David Cerutti
[AMBER] Any idea about this Amber compile bug?
(Thu Sep 01 2016 - 13:45:35 PDT)
Dd H
[AMBER] How to get GppNHp parameters.
(Fri Sep 16 2016 - 19:44:46 PDT)
[AMBER] Parameters for GppNHp ligand.
(Wed Sep 14 2016 - 07:31:29 PDT)
Re: [AMBER] Which is the best thermostat for cMD?
(Tue Sep 06 2016 - 19:11:46 PDT)
[AMBER] Which is the best thermostat for cMD?
(Fri Sep 02 2016 - 01:15:21 PDT)
Debodyuti Dutta
[AMBER] Pressure of the system during equilibration
(Thu Sep 29 2016 - 06:01:20 PDT)
dhanasekar.mbu.iisc.ernet.in
Re: [AMBER] Problem with CRD files
(Fri Sep 16 2016 - 02:55:38 PDT)
[AMBER] Problem with CRD files
(Wed Sep 14 2016 - 23:24:10 PDT)
[AMBER] Problem with CRD files
(Thu Sep 08 2016 - 08:05:38 PDT)
DIAO Jianxiong
[AMBER] 答复: Amber NaN error
(Wed Sep 28 2016 - 14:24:12 PDT)
[AMBER] Amber NaN error
(Tue Sep 27 2016 - 15:53:13 PDT)
Dickson, Callum J
Re: [AMBER] resp charges in LIPID14
(Tue Sep 06 2016 - 06:43:36 PDT)
Dr. Andreas W. Goetz
Re: [AMBER] SCC-DFTB
(Mon Sep 19 2016 - 20:53:29 PDT)
Re: [AMBER] adaptive qm/mm NVT, number of quantum atoms outside the legal range
(Mon Sep 19 2016 - 20:46:27 PDT)
Dwight McGee
Re: [AMBER] MMPBSA.py error Your ligand residues must be sequential in your complex
(Wed Sep 28 2016 - 07:19:12 PDT)
Elisa Pieri
Re: [AMBER] on periodic conditions and unspecified launch failure
(Fri Sep 30 2016 - 04:42:21 PDT)
[AMBER] on periodic conditions and unspecified launch failure
(Wed Sep 28 2016 - 13:46:26 PDT)
Re: [AMBER] Tcl problem
(Wed Sep 28 2016 - 00:58:19 PDT)
Re: [AMBER] Tcl problem
(Tue Sep 27 2016 - 07:40:19 PDT)
[AMBER] Tcl problem
(Tue Sep 27 2016 - 06:59:02 PDT)
Re: [AMBER] cpinutil.py describe flag
(Mon Sep 12 2016 - 08:44:48 PDT)
[AMBER] cpinutil.py describe flag
(Mon Sep 12 2016 - 07:47:03 PDT)
Re: [AMBER] how to center a polipeptide inside a solvent box
(Fri Sep 02 2016 - 03:01:02 PDT)
[AMBER] how to center a polipeptide inside a solvent box
(Thu Sep 01 2016 - 05:27:59 PDT)
Elvis Martis
Re: [AMBER] MMPBSA with different external Dielectric Constant
(Mon Sep 12 2016 - 20:12:03 PDT)
[AMBER] MMPBSA with different external Dielectric Constant
(Mon Sep 12 2016 - 03:15:25 PDT)
Fabio Bologna
[AMBER] R: Fullerene RESP charges derivation
(Wed Sep 14 2016 - 07:18:52 PDT)
[AMBER] Fullerene RESP charges derivation
(Tue Sep 13 2016 - 06:04:41 PDT)
Fabrício Bracht
Re: [AMBER] Question about QM/MM
(Fri Sep 02 2016 - 10:57:31 PDT)
Re: [AMBER] Question about QM/MM
(Fri Sep 02 2016 - 10:46:06 PDT)
Re: [AMBER] Question about QM/MM
(Fri Sep 02 2016 - 10:34:20 PDT)
Re: [AMBER] Question about QM/MM
(Fri Sep 02 2016 - 10:03:30 PDT)
[AMBER] noshakemask and qmshake
(Thu Sep 01 2016 - 11:34:47 PDT)
Fatema Al-Haddad [fy14fmah]
[AMBER] Radial Distribution Function
(Thu Sep 08 2016 - 02:27:02 PDT)
Filip Persson
Re: [AMBER] autoimage bug?
(Tue Sep 27 2016 - 23:48:13 PDT)
Re: [AMBER] autoimage bug?
(Thu Sep 08 2016 - 05:34:09 PDT)
Re: [AMBER] autoimage bug?
(Thu Sep 08 2016 - 05:32:36 PDT)
Florent Barbault
Re: [AMBER] Fwd: File redirection commands with targeted MD
(Thu Sep 08 2016 - 07:24:02 PDT)
Francesco Gentile
[AMBER] hbond and autoimage
(Thu Sep 15 2016 - 23:24:29 PDT)
FyD
Re: [AMBER] Glaycam04 version for q4md-CD FF
(Tue Sep 20 2016 - 05:43:19 PDT)
Re: [AMBER] Fullerene RESP charges derivation
(Tue Sep 20 2016 - 02:01:13 PDT)
Re: [AMBER] Glaycam04 version for q4md-CD FF
(Tue Sep 20 2016 - 01:57:00 PDT)
Garima Singh
[AMBER] Fwd: MD stop at different time period without giving any error
(Thu Sep 01 2016 - 01:39:30 PDT)
Gustavo Seabra
Re: [AMBER] Question about QM/MM
(Fri Sep 02 2016 - 09:17:30 PDT)
Hai Nguyen
Re: [AMBER] Save the average structure from two pdb files
(Fri Sep 30 2016 - 15:47:01 PDT)
Re: [AMBER] Tcl problem
(Tue Sep 27 2016 - 08:37:47 PDT)
Re: [AMBER] netcdf trajectory
(Mon Sep 26 2016 - 10:31:39 PDT)
Re: [AMBER] strip waters using distance criteria
(Sat Sep 24 2016 - 23:13:04 PDT)
Re: [AMBER] AMBER installation help
(Sat Sep 17 2016 - 15:37:02 PDT)
Re: [AMBER] Continue a simulation run
(Fri Sep 16 2016 - 10:51:20 PDT)
Re: [AMBER] Problem with CRD files
(Thu Sep 15 2016 - 07:22:15 PDT)
Re: [AMBER] comparing pytraj vs. sander output
(Tue Sep 13 2016 - 09:52:49 PDT)
Re: [AMBER] comparing pytraj vs. sander output
(Tue Sep 13 2016 - 09:41:44 PDT)
Re: [AMBER] comparing pytraj vs. sander output
(Tue Sep 13 2016 - 09:39:52 PDT)
Re: [AMBER] comparing pytraj vs. sander output
(Tue Sep 13 2016 - 09:06:56 PDT)
Re: [AMBER] comparing pytraj vs. sander output
(Mon Sep 12 2016 - 22:52:13 PDT)
Re: [AMBER] Trajectory analysis
(Fri Sep 02 2016 - 09:45:57 PDT)
Re: [AMBER] RMS-fit during PCA
(Fri Sep 02 2016 - 08:42:03 PDT)
Hannes Loeffler
[AMBER] pmemd.cuda: multiple bonds illegal for SHAKEH
(Mon Sep 26 2016 - 07:57:31 PDT)
Re: [AMBER] setup time with pmemd.cuda
(Sat Sep 24 2016 - 02:05:46 PDT)
Re: [AMBER] setup time with pmemd.cuda
(Thu Sep 22 2016 - 03:10:34 PDT)
Re: [AMBER] setup time with pmemd.cuda
(Wed Sep 21 2016 - 13:17:38 PDT)
Re: [AMBER] setup time with pmemd.cuda
(Wed Sep 21 2016 - 13:01:38 PDT)
[AMBER] setup time with pmemd.cuda
(Wed Sep 21 2016 - 11:06:34 PDT)
Re: [AMBER] "ATTN, need revision" in frcmod file / Could not find bond parameter & Could not find angle parameter
(Fri Sep 16 2016 - 12:16:22 PDT)
Re: [AMBER] Unable to find mopac charges in mopac.out
(Thu Sep 01 2016 - 11:01:23 PDT)
hari krishna
Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations
(Wed Sep 14 2016 - 10:54:13 PDT)
[AMBER] MM-PBSA, Protein-nucleic acids free energy calculations
(Tue Sep 13 2016 - 22:30:10 PDT)
Hector A. Baldoni
[AMBER] mdin for LIO interface
(Wed Sep 28 2016 - 04:03:53 PDT)
Re: [AMBER] PGI Fortran/C/C++ workstation
(Mon Sep 26 2016 - 05:51:34 PDT)
[AMBER] PGI Fortran/C/C++ workstation
(Mon Sep 26 2016 - 05:29:32 PDT)
Helen Lvy
[AMBER] Glaycam04 version for q4md-CD FF
(Thu Sep 15 2016 - 07:20:41 PDT)
Hirdesh Kumar
Re: [AMBER] using boundary information from previous run
(Fri Sep 30 2016 - 05:54:46 PDT)
Re: [AMBER] using boundary information from previous run
(Fri Sep 30 2016 - 05:19:48 PDT)
Re: [AMBER] using boundary information from previous run
(Fri Sep 30 2016 - 01:53:31 PDT)
[AMBER] using boundary information from previous run
(Thu Sep 29 2016 - 04:45:46 PDT)
Re: [AMBER] netcdf trajectory
(Sat Sep 24 2016 - 23:06:38 PDT)
Re: [AMBER] frame wise MMPBSA energy difference
(Wed Sep 21 2016 - 07:12:39 PDT)
[AMBER] frame wise MMPBSA energy difference
(Wed Sep 21 2016 - 02:15:07 PDT)
[AMBER] How to "not" strip an ion (say Mg) in MMPBSA
(Wed Sep 14 2016 - 03:06:57 PDT)
Huma Tahir
Re: [AMBER] AMBER installation help
(Sun Sep 18 2016 - 02:49:14 PDT)
[AMBER] AMBER installation help
(Sat Sep 17 2016 - 12:58:22 PDT)
Iqbal, Muhammad Sajid
[AMBER] Save the average structure from two pdb files
(Fri Sep 30 2016 - 15:22:11 PDT)
Irina Ivanova
[AMBER] How by residue decomposition in MMPBSA.py is performed?
(Mon Sep 12 2016 - 21:53:48 PDT)
Jacopo Sgrignani
Re: [AMBER] changing atom type
(Thu Sep 01 2016 - 01:43:19 PDT)
Jag Silwal
[AMBER] Simulation of protein complex with four protein chains
(Sat Sep 17 2016 - 12:30:01 PDT)
James Starlight
[AMBER] Calculations of dG for protein-ions
(Sat Sep 10 2016 - 13:57:36 PDT)
Jason Swails
Re: [AMBER] How to read prmtop file flag pointer section
(Fri Sep 30 2016 - 12:35:02 PDT)
Re: [AMBER] on periodic conditions and unspecified launch failure
(Fri Sep 30 2016 - 05:06:03 PDT)
Re: [AMBER] scaling of mpi version of pmemd.mpi (AMBER14) and that of the MMPBSA.py.MPI
(Thu Sep 29 2016 - 11:26:07 PDT)
Re: [AMBER] on periodic conditions and unspecified launch failure
(Thu Sep 29 2016 - 09:40:28 PDT)
Re: [AMBER] Tcl problem
(Tue Sep 27 2016 - 08:41:47 PDT)
Re: [AMBER] Tcl problem
(Tue Sep 27 2016 - 08:40:12 PDT)
Re: [AMBER] Tcl problem
(Tue Sep 27 2016 - 07:26:59 PDT)
Re: [AMBER] 2 ns heating in constant pH tutorial inquiry
(Mon Sep 26 2016 - 08:45:48 PDT)
Re: [AMBER] pmemd.cuda: multiple bonds illegal for SHAKEH
(Mon Sep 26 2016 - 08:36:55 PDT)
Re: [AMBER] problem about Using ParmEd or xParmEd
(Mon Sep 26 2016 - 08:32:52 PDT)
Re: [AMBER] netcdf trajectory
(Sun Sep 25 2016 - 09:58:10 PDT)
Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file.
(Thu Sep 22 2016 - 07:24:49 PDT)
Re: [AMBER] fixing concentration in implicit solvent simulation
(Wed Sep 21 2016 - 17:58:00 PDT)
Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file.
(Wed Sep 21 2016 - 17:48:31 PDT)
Re: [AMBER] frame wise MMPBSA energy difference
(Wed Sep 21 2016 - 06:46:53 PDT)
Re: [AMBER] chamber in parmed (Amber16)
(Sun Sep 18 2016 - 11:04:32 PDT)
Re: [AMBER] Force field ff14SB
(Wed Sep 14 2016 - 09:00:34 PDT)
Re: [AMBER] How to "not" strip an ion (say Mg) in MMPBSA
(Wed Sep 14 2016 - 08:58:20 PDT)
Re: [AMBER] comparing pytraj vs. sander output
(Tue Sep 13 2016 - 10:36:39 PDT)
Re: [AMBER] comparing pytraj vs. sander output
(Tue Sep 13 2016 - 09:19:18 PDT)
Re: [AMBER] 回复：Re: Add Molecule symmetry to sander
(Tue Sep 13 2016 - 05:30:11 PDT)
Re: [AMBER] How by residue decomposition in MMPBSA.py is performed?
(Tue Sep 13 2016 - 05:28:40 PDT)
Re: [AMBER] comparing pytraj vs. sander output
(Tue Sep 13 2016 - 03:48:01 PDT)
Re: [AMBER] MMPBSA with different external Dielectric Constant
(Mon Sep 12 2016 - 20:41:56 PDT)
Re: [AMBER] cpinutil.py describe flag
(Mon Sep 12 2016 - 12:30:41 PDT)
Re: [AMBER] cpinutil.py describe flag
(Mon Sep 12 2016 - 08:15:32 PDT)
Re: [AMBER] PCA plotting
(Mon Sep 12 2016 - 05:36:11 PDT)
Re: [AMBER] MMPBSA with different external Dielectric Constant
(Mon Sep 12 2016 - 05:28:21 PDT)
Re: [AMBER] about print_res in MMPBSA.py
(Tue Sep 06 2016 - 13:37:58 PDT)
Re: [AMBER] about print_res in MMPBSA.py
(Tue Sep 06 2016 - 09:37:57 PDT)
Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16
(Mon Sep 05 2016 - 18:03:36 PDT)
Re: [AMBER] Any idea about this Amber compile bug?
(Thu Sep 01 2016 - 17:53:07 PDT)
Re: [AMBER] how to center a polipeptide inside a solvent box
(Thu Sep 01 2016 - 17:47:04 PDT)
Jesmita Dhar
[AMBER] create a cubic box of 4.5 nm
(Mon Sep 26 2016 - 01:39:18 PDT)
Jinfeng Huang
[AMBER] Fw:car_to_files.py in AMBER16 is not available.
(Thu Sep 22 2016 - 02:23:43 PDT)
Jingyi Yan
[AMBER] radial distribution function from 1drism calculation
(Thu Sep 01 2016 - 12:21:32 PDT)
Jiri Sponer
Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations
(Wed Sep 14 2016 - 11:27:16 PDT)
jojartb.jgypk.u-szeged.hu
[AMBER] resp charges in LIPID14
(Tue Sep 06 2016 - 04:55:21 PDT)
Kris Feher
[AMBER] scaling of mpi version of pmemd.mpi (AMBER14) and that of the MMPBSA.py.MPI
(Wed Sep 28 2016 - 12:40:37 PDT)
Re: [AMBER] distance based mask
(Wed Sep 07 2016 - 12:52:08 PDT)
[AMBER] distance based mask
(Wed Sep 07 2016 - 12:09:24 PDT)
Kshatresh Dutta Dubey
Re: [AMBER] netcdf trajectory
(Mon Sep 26 2016 - 06:25:19 PDT)
Lachele Foley
Re: [AMBER] Glaycam04 version for q4md-CD FF
(Tue Sep 20 2016 - 02:08:41 PDT)
Lane Votapka
Re: [AMBER] Segmentation fault in tleap when using "sequence" command
(Thu Sep 22 2016 - 09:12:22 PDT)
Re: [AMBER] Segmentation fault in tleap when using "sequence" command
(Thu Sep 22 2016 - 08:21:00 PDT)
Re: [AMBER] Segmentation fault in tleap when using "sequence" command
(Thu Sep 22 2016 - 08:14:07 PDT)
Re: [AMBER] Segmentation fault in tleap when using "sequence" command
(Thu Sep 22 2016 - 08:01:08 PDT)
[AMBER] Segmentation fault in tleap when using "sequence" command
(Wed Sep 21 2016 - 13:31:58 PDT)
liu junjun
Re: [AMBER] pmemd Segmentation fault on Tutorial A27
(Mon Sep 12 2016 - 15:08:19 PDT)
[AMBER] pmemd Segmentation fault on Tutorial A27
(Mon Sep 12 2016 - 09:01:33 PDT)
Mahrukh Imtiaz
[AMBER] Issue regarding parametrization
(Tue Sep 27 2016 - 04:22:41 PDT)
Maksim Mišin
[AMBER] Potential Energy in 3D-RISM
(Wed Sep 14 2016 - 12:16:29 PDT)
Marc van der Kamp
Re: [AMBER] what is DFTB and SCC-DFTB
(Tue Sep 20 2016 - 11:41:08 PDT)
Re: [AMBER] Speed issue with Accelerated molecular dynamics.
(Sun Sep 11 2016 - 01:33:48 PDT)
Re: [AMBER] Question about QM/MM
(Fri Sep 02 2016 - 12:09:18 PDT)
Marcelo Andrade Chagas
Re: [AMBER] Problem with MCPB.py workflow after calculation of force constants.
(Wed Sep 07 2016 - 08:16:23 PDT)
Re: [AMBER] Unable to find mopac charges in mopac.out
(Thu Sep 01 2016 - 11:37:16 PDT)
Re: [AMBER] Unable to find mopac charges in mopac.out
(Thu Sep 01 2016 - 05:42:09 PDT)
Mark Abraham
Re: [AMBER] historical changes to LYN charges in amber03
(Tue Sep 06 2016 - 07:08:24 PDT)
Re: [AMBER] historical changes to LYN charges in amber03
(Mon Sep 05 2016 - 09:05:44 PDT)
[AMBER] historical changes to LYN charges in amber03
(Mon Sep 05 2016 - 08:40:38 PDT)
Re: [AMBER] GROMACS File Conversion Subtlety
(Mon Sep 05 2016 - 08:19:19 PDT)
Markowska
Re: [AMBER] netcdf trajectory
(Fri Sep 30 2016 - 06:08:08 PDT)
Re: [AMBER] netcdf trajectory
(Fri Sep 30 2016 - 01:29:50 PDT)
Markus Kaukonen
[AMBER] DFTB and slater koster files
(Wed Sep 21 2016 - 02:30:58 PDT)
maryam azimzadehirani
[AMBER] MMPBSA.py error Your ligand residues must be sequential in your complex
(Wed Sep 28 2016 - 06:06:42 PDT)
Michael Shokhen
Re: [AMBER] Fwd: File redirection commands with targeted MD
(Fri Sep 09 2016 - 01:36:01 PDT)
Miha Purg
[AMBER] Parmchk - missing improper parameter for nitro group
(Wed Sep 21 2016 - 00:25:45 PDT)
[AMBER] Parmchk - missing nitro improper
(Mon Sep 19 2016 - 11:50:37 PDT)
Ming Tang
[AMBER] Can amber handle carbon -- nitrogen double and single bond?
(Wed Sep 28 2016 - 01:43:52 PDT)
mmaestre
Re: [AMBER] Plot activesite water vs time.
(Wed Sep 21 2016 - 22:15:46 PDT)
Re: [AMBER] Plot activesite water vs time.
(Wed Sep 21 2016 - 21:49:10 PDT)
Mochena, Mogus D.
[AMBER] Follow up
(Thu Sep 15 2016 - 14:15:48 PDT)
Re: [AMBER] PME calculation for Vacuum?
(Sat Sep 10 2016 - 09:30:55 PDT)
Re: [AMBER] PME calculation for Vacuum?
(Fri Sep 09 2016 - 14:10:53 PDT)
[AMBER] PME calculation for Vacuum?
(Fri Sep 09 2016 - 11:36:27 PDT)
MOHD HOMAIDUR RAHMAN
Re: [AMBER] Regarding the use of sed command to replace water
(Wed Aug 31 2016 - 21:29:51 PDT)
neelam wafa
[AMBER] Installing amber tools on ubuntu
(Sat Sep 17 2016 - 13:07:37 PDT)
Neha Gandhi
Re: [AMBER] dihedral PCA amber
(Wed Sep 28 2016 - 03:19:46 PDT)
Re: [AMBER] dihedral PCA amber
(Mon Sep 26 2016 - 21:09:08 PDT)
Re: [AMBER] dihedral PCA amber
(Thu Sep 22 2016 - 19:00:41 PDT)
[AMBER] dihedral PCA amber
(Wed Sep 21 2016 - 20:08:10 PDT)
[AMBER] accelerated MD
(Thu Sep 01 2016 - 14:55:27 PDT)
Nhai
Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes.
(Wed Sep 28 2016 - 08:12:47 PDT)
Re: [AMBER] cpptraj gist core dumped
(Fri Sep 23 2016 - 00:11:21 PDT)
Re: [AMBER] comparing pytraj vs. sander output
(Tue Sep 13 2016 - 07:40:38 PDT)
Re: [AMBER] Problem with CRD files
(Thu Sep 08 2016 - 10:35:36 PDT)
Re: [AMBER] Problem with CRD files
(Thu Sep 08 2016 - 10:25:25 PDT)
Re: [AMBER] Hydrophobic interactions in MM-GBSA
(Sun Sep 04 2016 - 14:56:29 PDT)
Niel Henriksen
Re: [AMBER] comparing pytraj vs. sander output
(Tue Sep 13 2016 - 09:56:36 PDT)
Re: [AMBER] comparing pytraj vs. sander output
(Tue Sep 13 2016 - 09:48:25 PDT)
Re: [AMBER] comparing pytraj vs. sander output
(Tue Sep 13 2016 - 08:10:23 PDT)
Re: [AMBER] comparing pytraj vs. sander output
(Tue Sep 13 2016 - 07:34:19 PDT)
[AMBER] comparing pytraj vs. sander output
(Mon Sep 12 2016 - 22:07:57 PDT)
Re: [AMBER] On the simulation of phosphate ions in water solution
(Thu Sep 08 2016 - 19:08:17 PDT)
Osman, Roman
Re: [AMBER] autocorr of hydrogen bonds
(Thu Sep 01 2016 - 09:06:44 PDT)
Pengfei Li
Re: [AMBER] Error in the second step using MCPB.py
(Fri Sep 30 2016 - 19:49:17 PDT)
Re: [AMBER] Problem with MCPB.py workflow after calculation of force constants.
(Thu Sep 08 2016 - 07:58:24 PDT)
peter.schmidtke.discngine.servier.com
[AMBER] cpptraj gist core dumped
(Thu Sep 22 2016 - 23:40:23 PDT)
Pooja Kesari
Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes.
(Wed Sep 28 2016 - 07:47:42 PDT)
[AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes.
(Wed Sep 28 2016 - 04:38:28 PDT)
Re: [AMBER] Continue a simulation run
(Fri Sep 16 2016 - 03:40:41 PDT)
[AMBER] Continue a simulation run
(Thu Sep 15 2016 - 08:18:47 PDT)
Re: [AMBER] Fwd: query with amber
(Wed Sep 14 2016 - 21:47:20 PDT)
Re: [AMBER] Fwd: query with amber
(Wed Sep 14 2016 - 00:12:40 PDT)
[AMBER] Fwd: query with amber
(Tue Sep 13 2016 - 23:00:50 PDT)
Praneeth Bommisetti
[AMBER] Disparities in H-bond lifetimes calculated through different approaches
(Wed Sep 28 2016 - 23:03:25 PDT)
Prayagraj Fandilolu
Re: [AMBER] error in sander minimization
(Fri Sep 02 2016 - 07:30:45 PDT)
[AMBER] error in sander minimization
(Thu Sep 01 2016 - 04:45:13 PDT)
Roitberg,Adrian E
Re: [AMBER] autocorr of hydrogen bonds
(Thu Sep 01 2016 - 09:27:06 PDT)
Ross Walker
Re: [AMBER] setup time with pmemd.cuda
(Wed Sep 21 2016 - 15:23:39 PDT)
Re: [AMBER] setup time with pmemd.cuda
(Wed Sep 21 2016 - 13:08:11 PDT)
Re: [AMBER] setup time with pmemd.cuda
(Wed Sep 21 2016 - 12:16:40 PDT)
Re: [AMBER] Amber16: COM's in GPU version
(Tue Sep 20 2016 - 08:05:43 PDT)
[AMBER] NVIDIA GTX-970 Class Action Suit $30 settlement link
(Mon Sep 12 2016 - 12:03:23 PDT)
ruqaiya khalil
Re: [AMBER] FMN parameters
(Thu Sep 29 2016 - 02:51:05 PDT)
[AMBER] FMN parameters
(Wed Sep 28 2016 - 22:46:13 PDT)
Saman Yousuf ali
[AMBER] How to 2D-RDF in cpptraj.
(Thu Sep 22 2016 - 01:05:25 PDT)
Re: [AMBER] Plot activesite water vs time.
(Wed Sep 21 2016 - 22:00:29 PDT)
[AMBER] Plot activesite water vs time.
(Wed Sep 21 2016 - 21:24:38 PDT)
[AMBER] query regarding radial distribution function plot.
(Tue Sep 06 2016 - 14:08:46 PDT)
[AMBER] query regaridng unrestarint minimization step
(Fri Sep 02 2016 - 00:29:56 PDT)
Samuel Bowerman
Re: [AMBER] Problem with atommap function in cpptraj (v16)
(Tue Sep 20 2016 - 08:01:29 PDT)
Re: [AMBER] Error: cannot run "/share/apps/amber/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
(Tue Sep 13 2016 - 11:00:05 PDT)
Scott Brozell
Re: [AMBER] setup time with pmemd.cuda
(Thu Sep 22 2016 - 06:17:00 PDT)
Re: [AMBER] Any idea about this Amber compile bug?
(Thu Sep 01 2016 - 20:13:28 PDT)
shahab shariati
Re: [AMBER] Signal: Segmentation fault (11)
(Wed Sep 28 2016 - 05:35:08 PDT)
Re: [AMBER] Signal: Segmentation fault (11)
(Mon Sep 26 2016 - 12:01:40 PDT)
[AMBER] Signal: Segmentation fault (11)
(Sun Sep 25 2016 - 02:10:03 PDT)
Re: [AMBER] MM-PBSA calculation in different temprature
(Fri Sep 23 2016 - 07:03:32 PDT)
[AMBER] MM-PBSA calculation in different temprature
(Fri Sep 23 2016 - 05:07:04 PDT)
[AMBER] "ATTN, need revision" in frcmod file / Could not find bond parameter & Could not find angle parameter
(Fri Sep 16 2016 - 11:25:50 PDT)
[AMBER] WARNING: The unperturbed charge of the unit: -0.99 is not zero.
(Thu Sep 15 2016 - 11:41:22 PDT)
[AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type. Failed to generate parameters Parameter file was not saved.
(Tue Sep 13 2016 - 22:29:57 PDT)
Re: [AMBER] Error: cannot run "/share/apps/amber/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
(Tue Sep 13 2016 - 04:31:45 PDT)
Re: [AMBER] Error: cannot run "/share/apps/amber/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
(Tue Sep 13 2016 - 04:28:03 PDT)
[AMBER] Error: cannot run "/share/apps/amber/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
(Tue Sep 13 2016 - 04:25:41 PDT)
Shunsuke Mizutani
[AMBER] question on the reference data of GIST
(Thu Sep 08 2016 - 01:54:31 PDT)
Smriti Sharma
[AMBER] MMPBSA analysis for a heme protein
(Tue Sep 06 2016 - 22:07:34 PDT)
Sneha Rai
Re: [AMBER] Unable to find mopac charges in mopac.out
(Fri Sep 02 2016 - 00:00:45 PDT)
Re: [AMBER] Unable to find mopac charges in mopac.out
(Thu Sep 01 2016 - 11:31:16 PDT)
Re: [AMBER] Unable to find mopac charges in mopac.out
(Thu Sep 01 2016 - 10:55:58 PDT)
[AMBER] Unable to find mopac charges in mopac.out
(Thu Sep 01 2016 - 05:29:18 PDT)
Sofia Vasilakaki
[AMBER] lipid bilayer
(Sat Sep 10 2016 - 16:17:05 PDT)
Song-Ho Chong
Re: [AMBER] chamber in parmed (Amber16)
(Sun Sep 18 2016 - 17:52:22 PDT)
[AMBER] chamber in parmed (Amber16)
(Sun Sep 18 2016 - 09:21:18 PDT)
Sonia Ziada
Re: [AMBER] Fwd: File redirection commands with targeted MD
(Thu Sep 08 2016 - 07:45:22 PDT)
Re: [AMBER] Fwd: File redirection commands with targeted MD
(Thu Sep 08 2016 - 06:37:39 PDT)
Re: [AMBER] Fwd: File redirection commands with targeted MD
(Thu Sep 08 2016 - 06:11:32 PDT)
[AMBER] Fwd: File redirection commands with targeted MD
(Fri Sep 02 2016 - 00:03:35 PDT)
Steven Ramsey
Re: [AMBER] cpptraj gist core dumped
(Fri Sep 23 2016 - 08:34:48 PDT)
Stregone
[AMBER] adaptive qm/mm NVT, number of quantum atoms outside the legal range
(Mon Sep 19 2016 - 05:12:19 PDT)
sunyeping
Re: [AMBER] How to assign frame range for cpptraj analysis?
(Wed Sep 07 2016 - 02:44:36 PDT)
[AMBER] How to assign frame range for cpptraj analysis?
(Wed Sep 07 2016 - 02:04:30 PDT)
Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16
(Mon Sep 05 2016 - 07:24:23 PDT)
Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16
(Sun Sep 04 2016 - 21:39:21 PDT)
Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16
(Sun Sep 04 2016 - 16:30:20 PDT)
[AMBER] why does my computer cannot access to Internet after Installing ambertool 16
(Sun Sep 04 2016 - 01:35:20 PDT)
tanfei777.sina.cn
[AMBER] 回复： Enforced Symmetry?
(Sun Sep 11 2016 - 18:02:50 PDT)
[AMBER] 回复：Re: Add Molecule symmetry to sander
(Sun Sep 11 2016 - 06:53:00 PDT)
[AMBER] Add Molecule symmetry to sander
(Sat Sep 10 2016 - 17:58:28 PDT)
TERREUX RAPHAEL
Re: [AMBER] netcdf trajectory
(Sun Sep 25 2016 - 01:28:09 PDT)
Thakur, Abhishek
Re: [AMBER] Problem regarding sccdftb not converging
(Fri Sep 30 2016 - 09:07:04 PDT)
Re: [AMBER] what is DFTB and SCC-DFTB
(Tue Sep 20 2016 - 12:29:18 PDT)
[AMBER] what is DFTB and SCC-DFTB
(Tue Sep 20 2016 - 07:55:50 PDT)
[AMBER] SCC-DFTB
(Mon Sep 19 2016 - 07:44:03 PDT)
[AMBER] SCC-DFTB
(Mon Sep 12 2016 - 09:04:01 PDT)
[AMBER] Switching from PM3-PDDG to SCC-DFT method
(Wed Sep 07 2016 - 14:02:20 PDT)
Thomas Evangelidis
Re: [AMBER] strip waters using distance criteria
(Sat Sep 24 2016 - 17:14:13 PDT)
[AMBER] strip waters using distance criteria
(Fri Sep 23 2016 - 06:23:07 PDT)
Re: [AMBER] minimzation & MD in vacuo
(Thu Sep 22 2016 - 16:01:03 PDT)
[AMBER] minimzation & MD in vacuo
(Thu Sep 22 2016 - 09:54:48 PDT)
Re: [AMBER] delete residue in tleap
(Sun Sep 18 2016 - 16:55:35 PDT)
[AMBER] delete residue in tleap
(Sun Sep 18 2016 - 15:46:19 PDT)
Re: [AMBER] aromatic ring plane distorted
(Fri Sep 16 2016 - 09:26:35 PDT)
[AMBER] aromatic ring plane distorted
(Fri Sep 16 2016 - 04:03:03 PDT)
[AMBER] bad atom type: Mn
(Mon Sep 12 2016 - 18:08:07 PDT)
Re: [AMBER] about print_res in MMPBSA.py
(Tue Sep 06 2016 - 10:44:46 PDT)
[AMBER] about print_res in MMPBSA.py
(Tue Sep 06 2016 - 08:37:34 PDT)
Tiffani Rovira
[AMBER] Error in the second step using MCPB.py
(Thu Sep 29 2016 - 02:26:41 PDT)
Tom Kurtzman
Re: [AMBER] question on the reference data of GIST
(Thu Sep 08 2016 - 08:04:18 PDT)
Trang Nguyen
[AMBER] positive electrostatic energy MM-PBSA
(Tue Sep 20 2016 - 22:03:34 PDT)
Tyler Luchko (Lists)
Re: [AMBER] Potential Energy in 3D-RISM
(Wed Sep 14 2016 - 15:07:03 PDT)
Re: [AMBER] radial distribution function from 1drism calculation
(Thu Sep 01 2016 - 13:26:05 PDT)
Vishal Nemaysh
[AMBER] Fwd: lig.frcmod file is not formed
(Mon Sep 05 2016 - 00:08:32 PDT)
[AMBER] lig.frcmod file is not formed
(Sat Sep 03 2016 - 07:37:58 PDT)
Vlad Cojocaru
Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations
(Wed Sep 14 2016 - 07:57:36 PDT)
W. Andeas Svrcek-Seiler
Re: [AMBER] How aggressively should bond, angle, torsion parameters be coalesced?
(Sat Sep 24 2016 - 12:26:07 PDT)
waleed zalloum
[AMBER] PCA plotting
(Sun Sep 11 2016 - 04:00:32 PDT)
windy
Re: [AMBER] tleap cannot solvate unit in amber16
(Tue Sep 27 2016 - 22:33:39 PDT)
[AMBER] tleap cannot solvate unit in amber16
(Tue Sep 27 2016 - 05:53:00 PDT)
[AMBER] How to fixed residues in amber?
(Mon Sep 05 2016 - 19:32:36 PDT)
Re: [AMBER] change the atom charge in a restart simulations
(Wed Aug 31 2016 - 18:53:55 PDT)
Xiaoliu Zhang
[AMBER] changepot
(Wed Sep 07 2016 - 11:49:10 PDT)
Xiaoyu Wang
[AMBER] How to read prmtop file flag pointer section
(Fri Sep 30 2016 - 11:43:05 PDT)
Yeng-Tseng Wang
Re: [AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type. Failed to generate parameters Parameter file was not saved.
(Wed Sep 14 2016 - 15:03:29 PDT)
zycz138.126.com
[AMBER] RESP charge fitting error in MCPB.py
(Mon Sep 26 2016 - 17:54:06 PDT)
[AMBER] QMMM simulation with user-specified basis set in amber
(Thu Sep 01 2016 - 20:31:59 PDT)
康宁
[AMBER] Problems about creating ligand leap input files
(Sun Sep 11 2016 - 20:37:20 PDT)
杨金鹏
[AMBER] problem about Using ParmEd or xParmEd
(Mon Sep 26 2016 - 04:06:02 PDT)
Last message date
:
Fri Sep 30 2016 - 20:00:02 PDT
Archived on
: Fri Nov 15 2024 - 05:55:28 PST
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