Amber Archive Feb 2018 by author
311 messages
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Starting
Wed Jan 31 2018 - 15:30:02 PST,
Ending
Wed Feb 28 2018 - 21:00:03 PST
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Aashish Bhatt
Re: [AMBER] Regarding error in frcmod file
(Tue Feb 13 2018 - 07:30:23 PST)
[AMBER] Regarding error in frcmod file
(Mon Feb 12 2018 - 05:46:53 PST)
Abhilash J
Re: [AMBER] Simulation does not restart from restart file written in previous step.
(Sat Feb 24 2018 - 05:52:52 PST)
[AMBER] Simulation does not restart from restart file written in previous step.
(Fri Feb 23 2018 - 04:49:29 PST)
accuratefreeenergy.gmail.com
Re: [AMBER] setbox for octahedral
(Fri Feb 02 2018 - 14:08:53 PST)
Adrian Roitberg
[AMBER] EULA/NVIDIA
(Mon Feb 05 2018 - 14:31:20 PST)
Ahmed Mashaly
Re: [AMBER] solvatebox iso error
(Fri Feb 09 2018 - 08:23:48 PST)
Re: [AMBER] solvatebox iso error
(Thu Feb 08 2018 - 08:32:58 PST)
Re: [AMBER] solvatebox iso error
(Thu Feb 08 2018 - 05:16:17 PST)
[AMBER] solvatebox iso error
(Wed Feb 07 2018 - 10:10:21 PST)
Ahsan Mohd
[AMBER] MPI error in running a multi-sander job for TI calculation
(Sat Feb 10 2018 - 11:27:42 PST)
Andreas Tosstorff
Re: [AMBER] Problem with using Monte Carlo Barostat algorithm in pmemd cuda
(Sat Feb 17 2018 - 00:09:17 PST)
Andrew Schaub
[AMBER] setbox for octahedral
(Fri Feb 02 2018 - 10:07:57 PST)
Armin Hodaei
Re: [AMBER] "refc" file
(Tue Feb 27 2018 - 05:43:39 PST)
[AMBER] "refc" file
(Tue Feb 27 2018 - 02:45:29 PST)
Re: [AMBER] distance restrain for group of residues
(Mon Feb 26 2018 - 02:01:08 PST)
Re: [AMBER] distance restrain for group of residues
(Thu Feb 01 2018 - 04:39:22 PST)
[AMBER] distance restrain for group of residues
(Wed Jan 31 2018 - 15:19:56 PST)
Baker D.J.
[AMBER] Amber16/AmberTools17 CUDA version
(Wed Feb 21 2018 - 12:53:42 PST)
[AMBER] Amber16/AmberTools17 CUDA version
(Wed Feb 21 2018 - 08:28:09 PST)
CA gmail
[AMBER] Paramfit WRITE_ENERGY
(Wed Feb 07 2018 - 05:35:25 PST)
Carlos Simmerling
Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
(Tue Feb 27 2018 - 10:54:33 PST)
Re: [AMBER] amber coordinates in VMD
(Thu Feb 22 2018 - 06:42:23 PST)
Re: [AMBER] RMSD with cpptraj
(Fri Feb 09 2018 - 11:40:48 PST)
Re: [AMBER] Strong Na+-ASP interactions
(Fri Feb 09 2018 - 07:00:43 PST)
Re: [AMBER] Units used in ff14sb
(Mon Feb 05 2018 - 08:30:37 PST)
Re: [AMBER] Units used in ff14sb
(Mon Feb 05 2018 - 08:06:47 PST)
Chetna Tyagi
Re: [AMBER] Quasi-harmonic analysis
(Fri Feb 09 2018 - 07:12:39 PST)
[AMBER] Quasi-harmonic analysis
(Tue Feb 06 2018 - 06:50:52 PST)
Chitrak Gupta
Re: [AMBER] lipidorder in cpptraj
(Fri Feb 09 2018 - 11:27:17 PST)
[AMBER] lipidorder in cpptraj
(Wed Feb 07 2018 - 16:13:59 PST)
Chris Neale
Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
(Sun Feb 25 2018 - 11:05:54 PST)
Re: [AMBER] Enquiry on ntt
(Fri Feb 23 2018 - 15:00:25 PST)
Re: [AMBER] EULA/NVIDIA
(Wed Feb 07 2018 - 19:27:40 PST)
Christina Bergonzo
Re: [AMBER] Adding divalent ions in LEaP
(Thu Feb 08 2018 - 06:42:41 PST)
Cruzeiro,Vinicius Wilian D
Re: [AMBER] 3 GPUs and replica exchange MD
(Fri Feb 16 2018 - 16:49:46 PST)
Re: [AMBER] MD simulation of a protein at pH 3.0
(Fri Feb 16 2018 - 06:01:48 PST)
Re: [AMBER] 3 GPUs and replica exchange MD
(Fri Feb 16 2018 - 03:37:33 PST)
Daniel Mermelstein
Re: [AMBER] Thermodynamic Integration query
(Tue Feb 13 2018 - 22:03:47 PST)
Daniel Roe
Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
(Thu Feb 22 2018 - 12:19:59 PST)
Re: [AMBER] Question about how to compute kinetic energy from velocity trajectory
(Tue Feb 20 2018 - 12:36:38 PST)
Re: [AMBER] "Issue" with hbond
(Tue Feb 20 2018 - 09:18:31 PST)
Re: [AMBER] add vertical lines for initial and final angle
(Tue Feb 20 2018 - 09:13:02 PST)
Re: [AMBER] Problem with Atomtype of ligand in protein-ligand complex
(Tue Feb 13 2018 - 05:47:23 PST)
Re: [AMBER] PatchingError: No changes made from this patch
(Tue Feb 13 2018 - 05:46:01 PST)
Re: [AMBER] RMSD with cpptraj
(Fri Feb 09 2018 - 13:36:20 PST)
Re: [AMBER] lipidorder in cpptraj
(Fri Feb 09 2018 - 12:48:03 PST)
Re: [AMBER] solvatebox iso error
(Fri Feb 09 2018 - 08:38:40 PST)
Re: [AMBER] solvatebox iso error
(Fri Feb 09 2018 - 08:10:46 PST)
Re: [AMBER] solvatebox iso error
(Fri Feb 09 2018 - 06:02:16 PST)
Re: [AMBER] B-factor Values
(Fri Feb 09 2018 - 05:50:18 PST)
Re: [AMBER] Trajectory processing
(Fri Feb 09 2018 - 05:48:13 PST)
Re: [AMBER] Certain statistics from the trajectory
(Fri Feb 09 2018 - 05:40:49 PST)
Re: [AMBER] Quasi-harmonic analysis
(Fri Feb 09 2018 - 04:35:09 PST)
Re: [AMBER] Extracting lowest energy snapshot from trajectory
(Fri Feb 09 2018 - 04:27:38 PST)
Re: [AMBER] setbox for octahedral
(Fri Feb 09 2018 - 04:21:42 PST)
Re: [AMBER] solvatebox iso error
(Thu Feb 08 2018 - 04:14:37 PST)
Re: [AMBER] Problem in installing Amber16
(Thu Feb 08 2018 - 04:03:36 PST)
Re: [AMBER] lipidorder in cpptraj
(Thu Feb 08 2018 - 03:55:16 PST)
Re: [AMBER] adding ions
(Tue Feb 06 2018 - 06:37:06 PST)
Re: [AMBER] PCA scree plots
(Thu Feb 01 2018 - 06:26:10 PST)
Re: [AMBER] CPPTRAJ: How to project trajectories of one simulation onto principal components (PCs) of another simulation?
(Thu Feb 01 2018 - 06:20:05 PST)
Re: [AMBER] Compressing trajectory file
(Thu Feb 01 2018 - 06:10:06 PST)
Re: [AMBER] Use amber output velocity for different system
(Thu Feb 01 2018 - 06:06:48 PST)
Re: [AMBER] hbond analysis on DNA-protein complex
(Thu Feb 01 2018 - 06:05:41 PST)
Re: [AMBER] Extract Velocity (and Force) from Gromacs .trr trajectory using cpptraj
(Thu Feb 01 2018 - 06:03:48 PST)
Re: [AMBER] Reorienting the protein during simulation
(Thu Feb 01 2018 - 05:59:19 PST)
Re: [AMBER] CPPTRAJ HBond analysis Segmentation fault (core dumped)
(Thu Feb 01 2018 - 05:58:10 PST)
Re: [AMBER] CPPTRAJ ERROR-Reg.
(Thu Feb 01 2018 - 05:50:28 PST)
David A Case
Re: [AMBER] Has anyone determined a fix for QM_CHECK_PERIODIC or inability to include solvent in qmmask error
(Tue Feb 27 2018 - 17:50:13 PST)
Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
(Tue Feb 27 2018 - 17:33:59 PST)
Re: [AMBER] "refc" file
(Tue Feb 27 2018 - 04:36:47 PST)
Re: [AMBER] Problem with parallel install
(Mon Feb 26 2018 - 18:30:05 PST)
Re: [AMBER] How to generate parameters for two MG 2+ ions ---GTP
(Mon Feb 26 2018 - 14:55:31 PST)
Re: [AMBER] trouble with pdb4amber
(Mon Feb 26 2018 - 14:50:57 PST)
Re: [AMBER] Placing ions within a maximum distance from the solute
(Mon Feb 26 2018 - 04:47:18 PST)
Re: [AMBER] trouble with pdb4amber
(Sun Feb 25 2018 - 09:52:45 PST)
Re: [AMBER] Enquiry on ntt
(Fri Feb 23 2018 - 18:56:35 PST)
Re: [AMBER] Simulation does not restart from restart file written in previous step.
(Fri Feb 23 2018 - 10:29:25 PST)
Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large NITTER, NIT, LL and J are 0 1 151
(Fri Feb 23 2018 - 05:18:05 PST)
Re: [AMBER] selection of the type of box in molecular dynamics in AMBER
(Fri Feb 23 2018 - 05:14:54 PST)
Re: [AMBER] Using solvatebox with a SO2 molecule - difficulties in adding duplicate oxygen atoms in .pdb
(Thu Feb 22 2018 - 09:36:45 PST)
Re: [AMBER] The unperturbed charge of the unit is not integral": really nothing to care about?
(Thu Feb 22 2018 - 09:33:36 PST)
Re: [AMBER] "The unperturbed charge of the unit is not integral": really nothing to care about?
(Wed Feb 21 2018 - 04:48:24 PST)
Re: [AMBER] "The unperturbed charge of the unit is not integral": really nothing to care about?
(Mon Feb 19 2018 - 18:22:01 PST)
Re: [AMBER] Problem with using Monte Carlo Barostat algorithm in pmemd cuda
(Sun Feb 18 2018 - 17:22:16 PST)
Re: [AMBER] Question about proper usage of pysander
(Tue Feb 13 2018 - 09:53:54 PST)
Re: [AMBER] Problem with Atomtype of ligand in protein-ligand complex
(Tue Feb 13 2018 - 09:40:19 PST)
Re: [AMBER] Regarding error in frcmod file
(Tue Feb 13 2018 - 09:34:11 PST)
Re: [AMBER] some programs do not appear
(Tue Feb 13 2018 - 07:13:09 PST)
Re: [AMBER] Information required about the potential of Amber software.
(Mon Feb 12 2018 - 04:57:41 PST)
Re: [AMBER] Strong Na+-ASP interactions
(Mon Feb 12 2018 - 04:50:46 PST)
Re: [AMBER] SMD using Orca for QM region unknown atom specifier
(Mon Feb 12 2018 - 04:44:22 PST)
Re: [AMBER] Ion dissociation computed by umbrella sampling
(Mon Feb 12 2018 - 04:30:17 PST)
Re: [AMBER] MPI error in running a multi-sander job for TI calculation
(Sun Feb 11 2018 - 05:30:12 PST)
Re: [AMBER] Adding divalent ions in LEaP
(Fri Feb 09 2018 - 04:46:51 PST)
Re: [AMBER] Adding divalent ions in LEaP
(Thu Feb 08 2018 - 12:36:43 PST)
Re: [AMBER] how to run/install leap
(Tue Feb 06 2018 - 10:59:23 PST)
Re: [AMBER] adding ions
(Mon Feb 05 2018 - 06:08:23 PST)
Re: [AMBER] setbox for octahedral
(Sun Feb 04 2018 - 05:29:15 PST)
Re: [AMBER] distance restrain for group of residues
(Thu Feb 01 2018 - 10:17:05 PST)
Re: [AMBER] distance restrain for group of residues
(Thu Feb 01 2018 - 04:31:00 PST)
Re: [AMBER] Query on thermodynamic integration of complexes involving metal ions
(Thu Feb 01 2018 - 04:25:28 PST)
Re: [AMBER] AMBER16 and intel 2017, possible to compile?
(Thu Feb 01 2018 - 04:24:40 PST)
David Cerutti
Re: [AMBER] Problem with using Monte Carlo Barostat algorithm in pmemd cuda
(Sun Feb 18 2018 - 21:25:16 PST)
Re: [AMBER] Problem with using Monte Carlo Barostat algorithm in pmemd cuda
(Sun Feb 18 2018 - 17:48:36 PST)
Re: [AMBER] sander API does not support EP with igb 6
(Fri Feb 16 2018 - 07:01:08 PST)
Re: [AMBER] ff15ipq and divalent ions
(Mon Feb 12 2018 - 23:04:59 PST)
David Sáez
[AMBER] path_mode variable in SMD
(Fri Feb 02 2018 - 06:29:46 PST)
[AMBER] printcharges not working when imin=5 and maxcyc=0
(Thu Feb 01 2018 - 05:48:36 PST)
Elisa Pieri
Re: [AMBER] Make install Error
(Tue Feb 13 2018 - 06:57:28 PST)
Re: [AMBER] PatchingError: No changes made from this patch
(Tue Feb 13 2018 - 06:32:19 PST)
Re: [AMBER] Make install Error
(Tue Feb 13 2018 - 06:03:00 PST)
Re: [AMBER] Make install Error
(Tue Feb 13 2018 - 05:11:03 PST)
[AMBER] Make install Error
(Tue Feb 13 2018 - 01:46:05 PST)
[AMBER] PatchingError: No changes made from this patch
(Tue Feb 13 2018 - 01:27:26 PST)
Elvis Martis
Re: [AMBER] visualization of long simulation data with out downloading .mdcrd file
(Wed Feb 21 2018 - 05:43:37 PST)
Re: [AMBER] Problem in installing Amber16
(Wed Feb 07 2018 - 19:26:33 PST)
Fabian Glaser
[AMBER] workshop amber Technion Israel
(Mon Feb 19 2018 - 23:41:38 PST)
[AMBER] amber workshop reminder
(Mon Feb 05 2018 - 02:02:59 PST)
Feng Pan
Re: [AMBER] ABMD write error to MDOUT
(Wed Feb 28 2018 - 20:45:24 PST)
Re: [AMBER] STSM sample files
(Mon Feb 12 2018 - 11:26:01 PST)
Re: [AMBER] path_mode variable in SMD
(Sat Feb 03 2018 - 16:52:15 PST)
Garima Singh
[AMBER] Regarding vdW (or other) parameters for type: Pb
(Thu Feb 01 2018 - 02:03:48 PST)
George M. Giambasu
Re: [AMBER] Dendrogram from cpptraj clustering?
(Thu Feb 15 2018 - 16:37:45 PST)
Goetz, Andreas
Re: [AMBER] Has anyone determined a fix for QM_CHECK_PERIODIC or inability to include solvent in qmmask error
(Tue Feb 27 2018 - 23:59:18 PST)
Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
(Tue Feb 27 2018 - 17:43:23 PST)
Re: [AMBER] AMBER/ORCA for QM/MM
(Mon Feb 26 2018 - 17:56:12 PST)
Re: [AMBER] AMBER/ORCA for QM/MM
(Mon Feb 26 2018 - 13:04:01 PST)
Re: [AMBER] Scaling QM energy/forces
(Tue Feb 20 2018 - 12:29:34 PST)
Re: [AMBER] SMD using Orca for QM region unknown atom specifier
(Thu Feb 08 2018 - 13:52:56 PST)
Gustavo Seabra
Re: [AMBER] Question about using cpptraj - Script
(Wed Feb 28 2018 - 12:59:51 PST)
Re: [AMBER] Has anyone determined a fix for QM_CHECK_PERIODIC or inability to include solvent in qmmask error
(Tue Feb 27 2018 - 12:13:51 PST)
Re: [AMBER] RDF
(Fri Feb 23 2018 - 11:13:46 PST)
Re: [AMBER] Dendrogram from cpptraj clustering?
(Fri Feb 16 2018 - 05:15:07 PST)
[AMBER] Dendrogram from cpptraj clustering?
(Thu Feb 15 2018 - 06:51:00 PST)
Hai Nguyen
Re: [AMBER] trouble with pdb4amber
(Mon Feb 26 2018 - 07:45:03 PST)
Re: [AMBER] trouble with pdb4amber
(Sun Feb 25 2018 - 10:38:50 PST)
Re: [AMBER] Question about proper usage of pysander
(Tue Feb 13 2018 - 09:34:07 PST)
Re: [AMBER] Question about proper usage of pysander
(Tue Feb 13 2018 - 09:32:59 PST)
Re: [AMBER] Make install Error
(Tue Feb 13 2018 - 05:27:41 PST)
Re: [AMBER] Make install Error
(Tue Feb 13 2018 - 05:22:57 PST)
Re: [AMBER] Make install Error
(Tue Feb 13 2018 - 04:30:55 PST)
Re: [AMBER] some programs do not appear
(Mon Feb 12 2018 - 14:55:23 PST)
Hector A. Baldoni
Re: [AMBER] Adding divalent ions in LEaP
(Fri Feb 09 2018 - 04:28:58 PST)
Henrik Hariman
[AMBER] Adding a new atom type - ATTN, no polarizability parameter
(Tue Feb 27 2018 - 12:21:59 PST)
Holger Kruse
Re: [AMBER] Interface with DFTB+
(Tue Feb 27 2018 - 06:11:53 PST)
Ibrahim Said
[AMBER] some programs do not appear
(Mon Feb 12 2018 - 14:50:09 PST)
Jag Silwal
[AMBER] Combining coordinate files + Renumbering residues
(Wed Feb 21 2018 - 12:07:05 PST)
James Kress
Re: [AMBER] Has anyone determined a fix for QM_CHECK_PERIODIC or inability to include solvent in qmmask error
(Tue Feb 27 2018 - 19:26:53 PST)
Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
(Tue Feb 27 2018 - 19:06:03 PST)
[AMBER] Has anyone determined a fix for QM_CHECK_PERIODIC or inability to include solvent in qmmask error
(Tue Feb 27 2018 - 12:02:30 PST)
Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
(Tue Feb 27 2018 - 12:01:37 PST)
Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
(Tue Feb 27 2018 - 10:48:51 PST)
Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
(Sun Feb 25 2018 - 12:55:27 PST)
Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
(Sun Feb 25 2018 - 11:03:06 PST)
Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
(Thu Feb 22 2018 - 14:10:31 PST)
[AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
(Thu Feb 22 2018 - 11:58:54 PST)
[AMBER] Is there a bug in how Amber16 handles qmmask and WAT?
(Wed Feb 21 2018 - 13:25:25 PST)
[AMBER] Mask building problems
(Tue Feb 20 2018 - 16:14:44 PST)
Re: [AMBER] 3 GPUs and replica exchange MD
(Fri Feb 16 2018 - 10:27:51 PST)
[AMBER] Updated Website
(Mon Feb 05 2018 - 11:47:42 PST)
Jan Brezovsky
[AMBER] Ph.D. and Post-doc positions in molecular simulations and structural bioinformatics
(Thu Feb 08 2018 - 05:16:42 PST)
Jason Swails
Re: [AMBER] Question about proper usage of pysander
(Tue Feb 13 2018 - 13:05:30 PST)
Re: [AMBER] Problem calculating energies using cpptraj and sander API
(Mon Feb 12 2018 - 19:31:23 PST)
Re: [AMBER] amb2gmx
(Mon Feb 05 2018 - 07:54:07 PST)
Re: [AMBER] amb2gmx
(Mon Feb 05 2018 - 06:23:22 PST)
Re: [AMBER] amb2gmx
(Mon Feb 05 2018 - 06:10:16 PST)
Re: [AMBER] amb2gmx
(Sat Feb 03 2018 - 21:55:18 PST)
Jennifer L. Muzyka
Re: [AMBER] trouble with pdb4amber
(Mon Feb 26 2018 - 06:49:42 PST)
Re: [AMBER] trouble with pdb4amber
(Mon Feb 26 2018 - 06:44:25 PST)
Re: [AMBER] trouble with pdb4amber
(Mon Feb 26 2018 - 06:20:01 PST)
Re: [AMBER] trouble with pdb4amber
(Mon Feb 26 2018 - 06:18:52 PST)
[AMBER] trouble with pdb4amber
(Sun Feb 25 2018 - 09:18:12 PST)
Jie Zhu
[AMBER] Can I include Mg ions in receptor mask when using MMPBSA.py
(Tue Feb 27 2018 - 14:19:04 PST)
John Chodera
Re: [AMBER] Units used in ff14sb
(Tue Feb 06 2018 - 15:18:47 PST)
Jumin Lee
[AMBER] Jobs and Evens in CHARMM-GUI
(Mon Feb 05 2018 - 14:00:04 PST)
Junmei Wang
Re: [AMBER] Forcefield for methylated and acetylated amino acids
(Thu Feb 08 2018 - 08:12:20 PST)
Kellon Belfon
Re: [AMBER] leap (UNKNOWN ATOM TYPE: O3)
(Wed Feb 28 2018 - 09:59:52 PST)
Kevin Keane
Re: [AMBER] Problem with parallel install
(Mon Feb 26 2018 - 17:04:20 PST)
KRIPI TOMAR
[AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large NITTER, NIT, LL and J are 0 1 151
(Thu Feb 22 2018 - 23:24:35 PST)
Krystyna Zakrzewska
Re: [AMBER] adding ions
(Tue Feb 06 2018 - 07:33:14 PST)
Re: [AMBER] adding ions
(Mon Feb 05 2018 - 06:46:54 PST)
[AMBER] adding ions
(Mon Feb 05 2018 - 02:15:38 PST)
Lee-Ping Wang
Re: [AMBER] Question about how to compute kinetic energy from velocity trajectory
(Tue Feb 20 2018 - 15:38:46 PST)
[AMBER] sander API does not support EP with igb 6
(Fri Feb 16 2018 - 05:44:16 PST)
Re: [AMBER] Question about proper usage of pysander
(Tue Feb 13 2018 - 10:49:54 PST)
Re: [AMBER] Question about proper usage of pysander
(Tue Feb 13 2018 - 10:47:13 PST)
[AMBER] Question about proper usage of pysander
(Tue Feb 13 2018 - 07:31:06 PST)
Re: [AMBER] Problem calculating energies using cpptraj and sander API
(Mon Feb 12 2018 - 19:40:36 PST)
[AMBER] Problem calculating energies using cpptraj and sander API
(Mon Feb 12 2018 - 14:16:27 PST)
[AMBER] Question about how to compute kinetic energy from velocity trajectory
(Mon Feb 12 2018 - 12:04:21 PST)
Leena Aggarwal
Re: [AMBER] BASIC information for AMBER
(Thu Feb 01 2018 - 21:09:50 PST)
Lenz, Stefan
Re: [AMBER] AMBER disk usage on CPU or GPU nodes
(Wed Feb 14 2018 - 08:11:06 PST)
[AMBER] AMBER disk usage on CPU or GPU nodes
(Tue Feb 13 2018 - 09:27:53 PST)
Lizelle Lubbe
[AMBER] Torsion angle frequency
(Thu Feb 15 2018 - 23:56:30 PST)
Lorenzo Gontrani
Re: [AMBER] Regarding vdW (or other) parameters for type: Pb
(Thu Feb 01 2018 - 02:19:42 PST)
M Conte
[AMBER] Using solvatebox with a SO2 molecule - difficulties in adding duplicate oxygen atoms in .pdb
(Thu Feb 22 2018 - 08:52:48 PST)
Mac Kevin Braza
[AMBER] Fwd: B-factor Values
(Thu Feb 08 2018 - 23:13:44 PST)
[AMBER] B-factor Values
(Thu Feb 08 2018 - 23:12:34 PST)
Manjula Saravanan
[AMBER] CPPTRAJ ERROR-Reg.
(Thu Feb 01 2018 - 02:26:52 PST)
Marcelo Andrade Chagas
[AMBER] Question about using cpptraj - Script
(Wed Feb 28 2018 - 11:28:02 PST)
[AMBER] RDF
(Fri Feb 23 2018 - 10:39:06 PST)
Maria Clelia Milletti
Re: [AMBER] Problem with parallel install
(Mon Feb 26 2018 - 14:04:25 PST)
Markowska
Re: [AMBER] leap (UNKNOWN ATOM TYPE: O3)
(Wed Feb 28 2018 - 04:55:15 PST)
Michael Shokhen
[AMBER] by MM-PBSA binding energy at 310K?
(Thu Feb 01 2018 - 00:00:16 PST)
Mike Mazanetz
[AMBER] AMBER on AWS - Beta testers wanted.
(Thu Feb 08 2018 - 17:10:36 PST)
Re: [AMBER] how to run/install leap - solved
(Tue Feb 06 2018 - 12:04:30 PST)
Re: [AMBER] how to run/install leap - help needed
(Tue Feb 06 2018 - 11:04:12 PST)
Re: [AMBER] how to run/install leap
(Tue Feb 06 2018 - 10:00:22 PST)
[AMBER] how to run/install leap
(Tue Feb 06 2018 - 08:39:54 PST)
Ming Tang
Re: [AMBER] Enquiry on ntt
(Fri Feb 23 2018 - 19:28:40 PST)
Re: [AMBER] Enquiry on ntt
(Fri Feb 23 2018 - 14:50:13 PST)
Re: [AMBER] Enquiry on ntt
(Thu Feb 22 2018 - 14:40:41 PST)
[AMBER] Enquiry on ntt
(Thu Feb 22 2018 - 03:22:08 PST)
[AMBER] Trajectory processing
(Thu Feb 08 2018 - 16:39:51 PST)
MinYuan
Re: [AMBER] AMBER/ORCA for QM/MM
(Wed Feb 28 2018 - 04:26:38 PST)
minyuan.mail.ustc.edu.cn
Re: [AMBER] AMBER/ORCA for QM/MM
(Mon Feb 26 2018 - 17:13:21 PST)
[AMBER] AMBER/ORCA for QM/MM
(Mon Feb 26 2018 - 06:24:29 PST)
MOHD HOMAIDUR RAHMAN
[AMBER] Extracting lowest energy snapshot from trajectory
(Mon Feb 05 2018 - 08:28:04 PST)
Morrow,John Kenneth
Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C
(Sun Feb 11 2018 - 14:08:57 PST)
muthu kumaran
Re: [AMBER] Query on thermodynamic integration of complexes involving metal ions
(Thu Feb 01 2018 - 20:32:53 PST)
[AMBER] Query on thermodynamic integration of complexes involving metal ions
(Wed Jan 31 2018 - 21:33:20 PST)
Neha Gandhi
[AMBER] ff15ipq and divalent ions
(Mon Feb 12 2018 - 22:05:15 PST)
Nikolay N. Kuzmich
[AMBER] Placing ions within a maximum distance from the solute
(Mon Feb 26 2018 - 00:14:24 PST)
Re: [AMBER] The unperturbed charge of the unit is not integral: really nothing to care about?
(Fri Feb 23 2018 - 09:33:07 PST)
Re: [AMBER] The unperturbed charge of the unit is not integral": really nothing to care about?
(Thu Feb 22 2018 - 08:18:49 PST)
Re: [AMBER] "The unperturbed charge of the unit is not integral": really nothing to care about?
(Wed Feb 21 2018 - 01:23:13 PST)
[AMBER] "The unperturbed charge of the unit is not integral": really nothing to care about?
(Mon Feb 19 2018 - 01:09:32 PST)
[AMBER] 3 GPUs and replica exchange MD
(Fri Feb 16 2018 - 01:27:01 PST)
Re: [AMBER] Adding divalent ions in LEaP
(Thu Feb 15 2018 - 06:45:24 PST)
Re: [AMBER] Certain statistics from the trajectory
(Mon Feb 12 2018 - 01:10:47 PST)
Re: [AMBER] Adding divalent ions in LEaP
(Fri Feb 09 2018 - 03:04:02 PST)
[AMBER] Adding divalent ions in LEaP
(Thu Feb 08 2018 - 06:19:36 PST)
[AMBER] Certain statistics from the trajectory
(Wed Feb 07 2018 - 03:54:56 PST)
Núbia Prates
Re: [AMBER] "Issue" with hbond
(Tue Feb 20 2018 - 10:00:51 PST)
[AMBER] "Issue" with hbond
(Fri Feb 16 2018 - 13:57:29 PST)
pancham lal Gupta
Re: [AMBER] amber coordinates in VMD
(Thu Feb 22 2018 - 06:30:28 PST)
Parviz Seifpanahi Shabane
[AMBER] is that possible to change the size of the box in one direction in simulation?
(Thu Feb 01 2018 - 08:55:23 PST)
Patrice Peterson
Re: [AMBER] AMBER16 and intel 2017, possible to compile?
(Thu Feb 01 2018 - 04:51:26 PST)
Pengfei Li
Re: [AMBER] Regarding vdW (or other) parameters for type: Pb
(Thu Feb 01 2018 - 08:27:59 PST)
Raimon Fabregat
[AMBER] Interface with DFTB+
(Tue Feb 27 2018 - 02:26:55 PST)
[AMBER] Scaling QM energy/forces
(Mon Feb 19 2018 - 06:50:16 PST)
Rajarshi Roy
[AMBER] Regarding termination of pmemd.cuda
(Thu Feb 08 2018 - 00:41:25 PST)
Rakesh Srivastava
Re: [AMBER] 3D-RISM calculation at pH 3.0
(Mon Feb 19 2018 - 19:59:13 PST)
[AMBER] 3D-RISM calculation at pH 3.0
(Sun Feb 18 2018 - 21:55:12 PST)
Re: [AMBER] MD simulation of a protein at pH 3.0
(Fri Feb 16 2018 - 20:46:16 PST)
[AMBER] MD simulation of a protein at pH 3.0
(Fri Feb 16 2018 - 04:15:48 PST)
Rana Rehan Khalid
[AMBER] How to generate parameters for two MG 2+ ions ---GTP
(Mon Feb 26 2018 - 08:02:02 PST)
[AMBER] visualization of long simulation data with out downloading .mdcrd file
(Wed Feb 21 2018 - 05:23:27 PST)
Ray Luo
Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C
(Sun Feb 11 2018 - 17:40:18 PST)
Richard Smith
[AMBER] Amber16 pmemd.cuda on Tesla M2075
(Fri Feb 16 2018 - 08:46:59 PST)
Roitberg,Adrian E
Re: [AMBER] Torsion angle frequency
(Fri Feb 16 2018 - 11:45:45 PST)
Re: [AMBER] Constant Redox potential MD simulations
(Tue Feb 06 2018 - 16:43:35 PST)
Roja
Re: [AMBER] amb2gmx
(Mon Feb 05 2018 - 08:51:39 PST)
Re: [AMBER] amb2gmx
(Mon Feb 05 2018 - 05:55:24 PST)
roja rahmani
Re: [AMBER] amb2gmx
(Mon Feb 05 2018 - 07:34:31 PST)
Re: [AMBER] amb2gmx
(Mon Feb 05 2018 - 06:58:54 PST)
Re: [AMBER] amb2gmx
(Mon Feb 05 2018 - 06:14:52 PST)
[AMBER] amb2gmx
(Fri Feb 02 2018 - 23:15:46 PST)
Roma Mukhopadhyay
Re: [AMBER] Problem with using Monte Carlo Barostat algorithm in pmemd cuda
(Sun Feb 18 2018 - 20:31:40 PST)
Re: [AMBER] Problem with using Monte Carlo Barostat algorithm in pmemd cuda
(Sat Feb 17 2018 - 08:53:55 PST)
[AMBER] Problem with using Monte Carlo Barostat algorithm in pmemd cuda
(Fri Feb 16 2018 - 20:07:06 PST)
Rosellen, Martin
[AMBER] add vertical lines for initial and final angle
(Mon Feb 19 2018 - 04:41:27 PST)
Ross Walker
Re: [AMBER] AMBER disk usage on CPU or GPU nodes
(Wed Feb 14 2018 - 06:58:43 PST)
Re: [AMBER] EULA/NVIDIA
(Fri Feb 09 2018 - 04:50:35 PST)
Rui, Huan
Re: [AMBER] Strong Na+-ASP interactions
(Mon Feb 12 2018 - 06:33:29 PST)
Re: [AMBER] RMSD with cpptraj
(Fri Feb 09 2018 - 13:54:37 PST)
Re: [AMBER] RMSD with cpptraj
(Fri Feb 09 2018 - 13:29:17 PST)
Re: [AMBER] RMSD with cpptraj
(Fri Feb 09 2018 - 11:50:37 PST)
Re: [AMBER] RMSD with cpptraj
(Fri Feb 09 2018 - 11:46:21 PST)
[AMBER] RMSD with cpptraj
(Fri Feb 09 2018 - 11:38:32 PST)
Re: [AMBER] Strong Na+-ASP interactions
(Fri Feb 09 2018 - 08:39:06 PST)
[AMBER] Strong Na+-ASP interactions
(Fri Feb 09 2018 - 06:57:14 PST)
Ruth Helena Tichauer
Re: [AMBER] leap (UNKNOWN ATOM TYPE: O3)
(Wed Feb 28 2018 - 11:18:45 PST)
Re: [AMBER] leap (UNKNOWN ATOM TYPE: O3)
(Wed Feb 28 2018 - 05:01:08 PST)
[AMBER] leap (UNKNOWN ATOM TYPE: O3)
(Wed Feb 28 2018 - 04:46:59 PST)
Re: [AMBER] SMD using Orca for QM region unknown atom specifier
(Mon Feb 12 2018 - 06:10:51 PST)
Re: [AMBER] SMD using Orca for QM region unknown atom specifier
(Mon Feb 12 2018 - 05:57:23 PST)
Re: [AMBER] SMD using Orca for QM region unknown atom specifier
(Fri Feb 09 2018 - 02:03:57 PST)
[AMBER] SMD using Orca for QM region unknown atom specifier
(Thu Feb 08 2018 - 12:37:28 PST)
Saikat Pal
Re: [AMBER] OL15 (leaprc.DNA.OL15) vs bsc1 (leaprc.DNA.bsc1).
(Tue Feb 20 2018 - 09:23:52 PST)
[AMBER] OL15 (leaprc.DNA.OL15) vs bsc1 (leaprc.DNA.bsc1).
(Tue Feb 20 2018 - 04:41:06 PST)
Shahryar Alavi
[AMBER] Forcefield for methylated and acetylated amino acids
(Thu Feb 08 2018 - 07:55:27 PST)
Siddhartha Jain
Re: [AMBER] Units used in ff14sb
(Mon Feb 05 2018 - 08:40:50 PST)
Re: [AMBER] Units used in ff14sb
(Mon Feb 05 2018 - 08:15:35 PST)
[AMBER] Units used in ff14sb
(Sun Feb 04 2018 - 14:16:41 PST)
Sivasudhan R
Re: [AMBER] Problem with Atomtype of ligand in protein-ligand complex
(Tue Feb 13 2018 - 06:43:52 PST)
[AMBER] Problem with Atomtype of ligand in protein-ligand complex
(Mon Feb 12 2018 - 23:22:33 PST)
Sofia Vasilakaki
[AMBER] gist analysis
(Tue Feb 06 2018 - 16:14:58 PST)
Soumendranath Bhakat
Re: [AMBER] amb2gmx
(Mon Feb 05 2018 - 06:01:58 PST)
Sowmya Indrakumar
Re: [AMBER] Thermodynamic Integration query
(Wed Feb 14 2018 - 01:19:53 PST)
[AMBER] Thermodynamic Integration query
(Fri Feb 02 2018 - 02:15:48 PST)
Stefano Guglielmo
Re: [AMBER] amber coordinates in VMD
(Mon Feb 26 2018 - 17:06:41 PST)
[AMBER] amber coordinates in VMD
(Wed Feb 21 2018 - 16:17:54 PST)
Steven Ramsey
Re: [AMBER] gist analysis
(Tue Feb 06 2018 - 17:47:52 PST)
Szymon Żaczek
[AMBER] STSM sample files
(Mon Feb 12 2018 - 00:48:31 PST)
Tarsis
[AMBER] Constant Redox potential MD simulations
(Tue Feb 06 2018 - 16:19:00 PST)
Tasneem Kausar
Re: [AMBER] Problem in installing Amber16
(Fri Feb 09 2018 - 02:18:41 PST)
Re: [AMBER] Problem in installing Amber16
(Wed Feb 07 2018 - 19:42:18 PST)
Re: [AMBER] Problem in installing Amber16
(Wed Feb 07 2018 - 19:14:29 PST)
[AMBER] Problem in installing Amber16
(Wed Feb 07 2018 - 00:43:25 PST)
Thomas Exner
[AMBER] eChemInfo 2018 workshop on drug design in Milano
(Sat Feb 17 2018 - 02:51:15 PST)
Tom Kurtzman
Re: [AMBER] Enquiry on ntt
(Thu Feb 22 2018 - 04:52:11 PST)
Tyler Luchko (Lists)
Re: [AMBER] 3D-RISM calculation at pH 3.0
(Mon Feb 19 2018 - 14:58:23 PST)
Ubaid Ullah
[AMBER] Information required about the potential of Amber software.
(Fri Feb 09 2018 - 20:10:56 PST)
Veronika Jurásková
[AMBER] Ion dissociation computed by umbrella sampling
(Thu Feb 08 2018 - 02:21:52 PST)
Vikram Dalal
[AMBER] selection of the type of box in molecular dynamics in AMBER
(Thu Feb 22 2018 - 13:22:38 PST)
[AMBER] BASIC information for AMBER
(Thu Feb 01 2018 - 10:35:13 PST)
Vlad Cojocaru
Re: [AMBER] OL15 (leaprc.DNA.OL15) vs bsc1 (leaprc.DNA.bsc1).
(Tue Feb 20 2018 - 05:33:35 PST)
Yuliana Bosken
Re: [AMBER] Torsion angle frequency
(Fri Feb 16 2018 - 11:35:56 PST)
Last message date
:
Wed Feb 28 2018 - 21:00:03 PST
Archived on
: Mon Nov 25 2024 - 05:55:32 PST
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