Amber Archive Sep 2019 by author
371 messages
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Starting
Sun Sep 01 2019 - 11:00:01 PDT,
Ending
Mon Sep 30 2019 - 11:00:02 PDT
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174026008.iitb.ac.in
[AMBER] sqm error
(Sat Sep 14 2019 - 04:51:44 PDT)
[AMBER] AmberTools19 installation error
(Thu Sep 12 2019 - 22:10:18 PDT)
[AMBER] Fwd: AmberTools19 installation error
(Wed Sep 11 2019 - 22:57:00 PDT)
2018808152.njau.edu.cn
[AMBER] EstJ6_DBP_bound_sus
(Tue Sep 24 2019 - 01:34:36 PDT)
[AMBER] EstJ6_DBP_bound_sus
(Fri Sep 20 2019 - 02:18:46 PDT)
[AMBER] ANTECHAMBER_AC
(Thu Sep 19 2019 - 05:38:07 PDT)
aa
Re: [AMBER] AMBER18 installation error
(Tue Sep 03 2019 - 08:31:25 PDT)
Aashish Bhatt
[AMBER] Hybrid topology for mutating residue
(Mon Sep 16 2019 - 08:37:37 PDT)
Re: [AMBER] PCA calculation projection
(Wed Sep 11 2019 - 22:15:26 PDT)
Re: [AMBER] error regarding MCPB.py
(Wed Sep 11 2019 - 21:50:41 PDT)
[AMBER] PCA calculation projection
(Wed Sep 11 2019 - 03:22:35 PDT)
ABEL Stephane
Re: [AMBER] problem installing miniconda
(Thu Sep 26 2019 - 08:41:20 PDT)
Adrian Roitberg
Re: [AMBER] How can I change the default unit of density?
(Thu Sep 26 2019 - 01:02:58 PDT)
Re: [AMBER] restraintmask (Cannot match namelist object name :1-294)
(Mon Sep 02 2019 - 09:29:21 PDT)
Ahmed Elrashedy
Re: [AMBER] seek for how to calculate the binding free energy of a covalent inhibitor
(Tue Sep 17 2019 - 05:46:57 PDT)
Re: [AMBER] Coordinate resetting (SHAKE) can not be accomplished
(Tue Sep 17 2019 - 00:30:29 PDT)
Airy Sanjeev
[AMBER] Problem in calculating MMPBSA-GBSA
(Tue Sep 24 2019 - 22:53:46 PDT)
[AMBER] Query regarding plot
(Tue Sep 10 2019 - 04:44:19 PDT)
Alaa Abdelrahman
[AMBER] Small Molecules parameters
(Tue Sep 10 2019 - 08:51:10 PDT)
Amit Kumar
Re: [AMBER] Question about unusual RMSD behaviour
(Tue Sep 17 2019 - 06:14:18 PDT)
Re: [AMBER] Question about unusual RMSD behaviour
(Tue Sep 17 2019 - 02:14:25 PDT)
[AMBER] Question about unusual RMSD behaviour
(Mon Sep 16 2019 - 06:19:48 PDT)
Anthony Bogetti
[AMBER] PNEB--"vlimit exceeded" error
(Wed Sep 11 2019 - 08:03:46 PDT)
Aswin Hanagal
[AMBER] PCA reweighting
(Thu Sep 26 2019 - 23:51:37 PDT)
Avirup Ghosh
[AMBER] Amber_Cpptraj
(Tue Sep 10 2019 - 09:12:24 PDT)
Bharat Manna
[AMBER] Helix Structures Lost during Heating and Equilibrium Steps
(Wed Sep 11 2019 - 03:43:38 PDT)
Bill Ross
Re: [AMBER] ambpdb error while conversion
(Wed Sep 25 2019 - 05:15:53 PDT)
Re: [AMBER] ambpdb error while conversion
(Wed Sep 25 2019 - 03:11:41 PDT)
Re: [AMBER] ambpdb error while conversion
(Wed Sep 25 2019 - 01:16:43 PDT)
Re: [AMBER] ambpdb error while conversion
(Tue Sep 24 2019 - 04:25:00 PDT)
Re: [AMBER] md distorted
(Mon Sep 23 2019 - 04:27:42 PDT)
Re: [AMBER] MD distorted
(Mon Sep 23 2019 - 02:51:28 PDT)
Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered
(Fri Sep 20 2019 - 02:53:26 PDT)
Re: [AMBER] EstJ6_DBP_bound_sus
(Fri Sep 20 2019 - 02:50:34 PDT)
Re: [AMBER] AMBER: Segmentation fault
(Mon Sep 16 2019 - 01:26:22 PDT)
Re: [AMBER] tMD and free energy calculation
(Mon Sep 09 2019 - 02:03:58 PDT)
Carlos Simmerling
Re: [AMBER] MMGBSA energy calculation problem for RNA
(Wed Sep 25 2019 - 09:06:16 PDT)
Re: [AMBER] ambpdb error while conversion
(Tue Sep 24 2019 - 04:26:47 PDT)
Re: [AMBER] problem with random seed
(Tue Sep 17 2019 - 09:17:22 PDT)
Re: [AMBER] seek for how to calculate the binding free energy of a covalent inhibitor
(Tue Sep 17 2019 - 08:46:21 PDT)
Re: [AMBER] Question about unusual RMSD behaviour
(Tue Sep 17 2019 - 08:45:39 PDT)
Re: [AMBER] Question about unusual RMSD behaviour
(Tue Sep 17 2019 - 03:58:13 PDT)
Re: [AMBER] Question about unusual RMSD behaviour
(Mon Sep 16 2019 - 06:26:55 PDT)
Re: [AMBER] GBSA
(Fri Sep 13 2019 - 06:13:48 PDT)
Re: [AMBER] problem with random seed
(Wed Sep 11 2019 - 07:56:36 PDT)
Re: [AMBER] Helix Structures Lost during Heating and Equilibrium Steps
(Wed Sep 11 2019 - 03:56:51 PDT)
Re: [AMBER] Force field for aMD
(Tue Sep 10 2019 - 10:01:50 PDT)
Re: [AMBER] Generating the parameters for non-standard amino-acid residue
(Mon Sep 09 2019 - 10:21:49 PDT)
Re: [AMBER] Generating the parameters for non-standard amino-acid residue
(Mon Sep 09 2019 - 08:18:40 PDT)
Re: [AMBER] ff14SB overestimation of helical comformation
(Tue Sep 03 2019 - 11:17:14 PDT)
Casalini Tommaso
Re: [AMBER] imin=5 fails to produce output
(Thu Sep 26 2019 - 11:52:53 PDT)
Re: [AMBER] imin=5 fails to produce output
(Thu Sep 26 2019 - 08:41:14 PDT)
charalamm.cheng.auth.gr
[AMBER] MMPBSA.py -> FATAL: NATOM mismatch in coord and topology files
(Tue Sep 24 2019 - 09:50:57 PDT)
Re: [AMBER] Amber not working after installation - Help from github
(Sun Sep 15 2019 - 01:24:38 PDT)
Re: [AMBER] Amber not working after installation - Help from github
(Sat Sep 14 2019 - 01:36:17 PDT)
Re: [AMBER] Amber not working after installation - Help from github
(Fri Sep 13 2019 - 09:56:04 PDT)
Re: [AMBER] Amber not working after installation - Help from github
(Fri Sep 13 2019 - 06:05:08 PDT)
[AMBER] Amber not working after installation - Help from github
(Fri Sep 13 2019 - 02:59:24 PDT)
Re: [AMBER] Error creating topology and coordinates file
(Mon Sep 02 2019 - 02:58:21 PDT)
[AMBER] Error creating topology and coordinates file
(Mon Sep 02 2019 - 02:42:20 PDT)
Chetna Tyagi
Re: [AMBER] How to incorporate new lipid molecules through packmol-memgen
(Mon Sep 30 2019 - 04:33:30 PDT)
[AMBER] How to incorporate new lipid molecules through packmol-memgen
(Fri Sep 27 2019 - 09:00:32 PDT)
Christian Schafmeister
[AMBER-Developers] Job opening for AMBER developer.
(Tue Sep 03 2019 - 10:30:03 PDT)
Christos Deligkaris
[AMBER] optimizing GAFF2 torsional parameters
(Wed Sep 11 2019 - 11:22:38 PDT)
cpimenta
[AMBER] Modified variables in cphstats
(Mon Sep 16 2019 - 05:36:33 PDT)
[AMBER] Force field for aMD
(Tue Sep 10 2019 - 09:56:25 PDT)
Daniel Roe
Re: [AMBER] Compilation of Amber on Cray
(Mon Sep 30 2019 - 04:48:00 PDT)
Re: [AMBER] imin=5 fails to produce output
(Sat Sep 28 2019 - 05:46:19 PDT)
Re: [AMBER] imin=5 fails to produce output
(Fri Sep 27 2019 - 11:39:33 PDT)
Re: [AMBER] Restart file format.
(Fri Sep 27 2019 - 11:09:23 PDT)
Re: [AMBER] cpptraj rms with different pdb
(Thu Sep 26 2019 - 10:58:30 PDT)
Re: [AMBER] ambpdb error while conversion
(Mon Sep 23 2019 - 06:21:45 PDT)
Re: [AMBER] cpptraj rms with different pdb
(Mon Sep 23 2019 - 06:16:48 PDT)
Re: [AMBER] Cpptraj extracting coordinate data of a projectile
(Thu Sep 19 2019 - 11:08:43 PDT)
Re: [AMBER] trajectory coordinate out of box
(Thu Sep 19 2019 - 10:49:36 PDT)
Re: [AMBER] Cpptraj extracting coordinate data of a projectile
(Thu Sep 19 2019 - 03:55:12 PDT)
Re: [AMBER] Trouble installing Amber 18
(Wed Sep 18 2019 - 08:22:15 PDT)
Re: [AMBER] lipid order per leaflet
(Mon Sep 16 2019 - 10:08:05 PDT)
Re: [AMBER] Amber 18 installation
(Mon Sep 16 2019 - 07:39:28 PDT)
Re: [AMBER] Modified variables in cphstats
(Mon Sep 16 2019 - 06:33:17 PDT)
Re: [AMBER] Amber_Cpptraj
(Fri Sep 13 2019 - 09:26:42 PDT)
Re: [AMBER] lipid order per leaflet
(Fri Sep 13 2019 - 09:22:40 PDT)
[AMBER] Recent Enhancements to secstruct/dssp in Cpptraj
(Fri Sep 06 2019 - 12:47:12 PDT)
Re: [AMBER] Calculating RMSF
(Thu Sep 05 2019 - 08:34:52 PDT)
Re: [AMBER] Lateral diffusion of lipid head groups
(Tue Sep 03 2019 - 10:46:56 PDT)
Re: [AMBER] Preparation of trajectory for stfc diffusion calculations
(Tue Sep 03 2019 - 10:42:46 PDT)
Re: [AMBER] Problem with CPPTRAJ (RMSD)
(Tue Sep 03 2019 - 10:05:59 PDT)
Re: [AMBER] Cpptraj watershell CUDA
(Tue Sep 03 2019 - 07:00:29 PDT)
Re: [AMBER] Problem with CPPTRAJ (RMSD)
(Tue Sep 03 2019 - 05:38:40 PDT)
Re: [AMBER] AMBER18 installation error
(Tue Sep 03 2019 - 05:31:01 PDT)
David A Case
Re: [AMBER] avoiding protein residue renumbering during tleap processing
(Fri Sep 27 2019 - 13:15:22 PDT)
Re: [AMBER] trajectory coordinate out of box
(Thu Sep 19 2019 - 12:48:42 PDT)
Re: [AMBER] ANTECHAMBER_AC
(Thu Sep 19 2019 - 07:08:07 PDT)
Re: [AMBER] How big a molecule can antechamber (sqm) put charges on?
(Thu Sep 19 2019 - 06:57:43 PDT)
Re: [AMBER] Small ligand activators molecule
(Wed Sep 18 2019 - 06:31:07 PDT)
Re: [AMBER] seek for how to calculate the binding free energy of a covalent inhibitor
(Tue Sep 17 2019 - 12:20:30 PDT)
Re: [AMBER] Error installing Amber on Centos 7
(Tue Sep 17 2019 - 12:18:56 PDT)
Re: [AMBER] Hybrid topology for mutating residue
(Tue Sep 17 2019 - 05:43:11 PDT)
Re: [AMBER] Amber 18 installation
(Tue Sep 17 2019 - 05:36:46 PDT)
Re: [AMBER] AMBER: Segmentation fault
(Mon Sep 16 2019 - 05:31:45 PDT)
Re: [AMBER] AMBER: error in reading namelist cntrl
(Mon Sep 16 2019 - 05:29:13 PDT)
Re: [AMBER] How can I make the initial configuration and topology with polarizable force field?
(Mon Sep 16 2019 - 05:24:57 PDT)
Re: [AMBER] sander.MPI gives segfault if compiled with Intel compilers
(Mon Sep 16 2019 - 05:21:16 PDT)
Re: [AMBER] Implicit solvent simulation.
(Tue Sep 10 2019 - 05:35:55 PDT)
Re: [AMBER] Energy minimization in Implicit solvent for Langevin dynamics simulation
(Mon Sep 09 2019 - 05:58:23 PDT)
Re: [AMBER] Force conversion
(Mon Sep 09 2019 - 05:57:07 PDT)
Re: [AMBER] Generating the parameters for non-standard amino-acid residue
(Mon Sep 09 2019 - 05:50:53 PDT)
[AMBER] Recent updates to how Amber carries out softcore free energy calculations
(Thu Sep 05 2019 - 06:40:38 PDT)
Re: [AMBER] how to read the outup file of QMMM MD simulation with Amber combined with Gaussian (Geng Dong)
(Thu Sep 05 2019 - 05:40:28 PDT)
Re: [AMBER] Ligand parameterization
(Tue Sep 03 2019 - 09:51:31 PDT)
Re: [AMBER] AMBER18 installation error
(Tue Sep 03 2019 - 06:29:50 PDT)
David Case
Re: [AMBER] Amber18 installation
(Mon Sep 30 2019 - 05:14:25 PDT)
Re: [AMBER] Free energy calculation
(Mon Sep 30 2019 - 05:12:11 PDT)
Re: [AMBER] Compilation of Amber on Cray
(Sun Sep 29 2019 - 05:21:48 PDT)
Re: [AMBER] Small Molecules parameters
(Sat Sep 28 2019 - 05:52:08 PDT)
Re: [AMBER] DNA methylation parameters
(Sat Sep 28 2019 - 05:49:17 PDT)
Re: [AMBER] Please how to solve the unfilled valence problem in antechamber
(Sat Sep 28 2019 - 05:46:49 PDT)
Re: [AMBER] -Antechamber error for modified residues
(Sat Sep 28 2019 - 05:44:55 PDT)
Re: [AMBER] Query regarding mmgbsa
(Sat Sep 28 2019 - 05:35:24 PDT)
Re: [AMBER] free energy calculation
(Thu Sep 26 2019 - 13:04:16 PDT)
Re: [AMBER] Compilation of Amber on Cray
(Thu Sep 26 2019 - 12:41:30 PDT)
Re: [AMBER] not able to install python...using cygwin
(Thu Sep 26 2019 - 07:13:26 PDT)
Re: [AMBER] not able to install python...using cygwin
(Thu Sep 26 2019 - 07:11:23 PDT)
Re: [AMBER] BORON parameters
(Thu Sep 26 2019 - 07:09:29 PDT)
Re: [AMBER] Compilation of Amber on Cray
(Thu Sep 26 2019 - 07:07:00 PDT)
Re: [AMBER] MMGBSA energy calculation problem for RNA
(Wed Sep 25 2019 - 06:54:17 PDT)
Re: [AMBER] Question regarding ntx and irest
(Wed Sep 25 2019 - 06:43:35 PDT)
Re: [AMBER] installation error
(Wed Sep 25 2019 - 06:08:43 PDT)
Re: [AMBER] Packmol and Amber
(Wed Sep 25 2019 - 06:03:09 PDT)
Re: [AMBER] ambpdb error while conversion
(Wed Sep 25 2019 - 05:59:07 PDT)
Re: [AMBER] restraints error
(Tue Sep 24 2019 - 05:03:45 PDT)
Re: [AMBER] EstJ6_DBP_bound_sus
(Tue Sep 24 2019 - 04:55:54 PDT)
Re: [AMBER] Unable to generate parameters of modified amino acids using LEAP
(Mon Sep 23 2019 - 08:31:24 PDT)
Re: [AMBER] ambpdb error while conversion
(Fri Sep 20 2019 - 06:13:57 PDT)
Re: [AMBER] TI residue mutation with pmemd on GPU
(Fri Sep 20 2019 - 05:56:16 PDT)
Re: [AMBER] EstJ6_DBP_bound_sus
(Fri Sep 20 2019 - 05:43:41 PDT)
Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered
(Fri Sep 20 2019 - 05:40:26 PDT)
Re: [AMBER] Amber17 to Amber18 considerations and archive?
(Wed Sep 18 2019 - 18:12:59 PDT)
Re: [AMBER] sander.MPI gives segfault if compiled with Intel compilers
(Wed Sep 18 2019 - 18:06:45 PDT)
Re: [AMBER] sqm error
(Sat Sep 14 2019 - 09:28:55 PDT)
Re: [AMBER] Fwd: tutorial for finding binding free energies
(Fri Sep 13 2019 - 14:39:00 PDT)
Re: [AMBER] Fwd: AmberTools19 installation error
(Thu Sep 12 2019 - 06:30:37 PDT)
Re: [AMBER] How to generate parameter files of modified terminal amino acid residue using Antechamber
(Fri Sep 06 2019 - 05:19:47 PDT)
Re: [AMBER] GBSA
(Tue Sep 03 2019 - 18:18:46 PDT)
Re: [AMBER] issue during TI minimisation
(Mon Sep 02 2019 - 09:02:26 PDT)
Re: [AMBER] running NAMD with AMBER inputs
(Sun Sep 01 2019 - 13:02:37 PDT)
Re: [AMBER] running NAMD with AMBER inputs
(Sun Sep 01 2019 - 13:00:43 PDT)
David Cerutti
Re: [AMBER] Explicit understanding the force computed from U(CMAP) term
(Mon Sep 09 2019 - 10:13:06 PDT)
Re: [AMBER] Explicit understanding the force computed from U(CMAP) term
(Fri Sep 06 2019 - 01:28:58 PDT)
Re: [AMBER] Print non bonded pair list
(Tue Sep 03 2019 - 15:36:52 PDT)
Re: [AMBER] Print non bonded pair list
(Tue Sep 03 2019 - 14:08:05 PDT)
David Mathog
Re: [AMBER] installation error
(Tue Sep 24 2019 - 09:34:58 PDT)
Re: [AMBER] many failures on "make test"
(Mon Sep 23 2019 - 16:46:46 PDT)
Re: [AMBER] many failures on "make test"
(Mon Sep 23 2019 - 13:57:17 PDT)
[AMBER] many failures on "make test"
(Mon Sep 23 2019 - 13:18:45 PDT)
David Ricardo Figueroa Blanco
[AMBER] PARAMFIT
(Mon Sep 23 2019 - 08:28:15 PDT)
diane lynch
Re: [AMBER] problem with random seed
(Wed Sep 11 2019 - 08:08:22 PDT)
Elena Gomez
[AMBER] tMD and free energy calculation
(Mon Sep 09 2019 - 01:38:22 PDT)
Elvis Martis
Re: [AMBER] Restart file format.
(Fri Sep 27 2019 - 10:52:33 PDT)
Re: [AMBER] problem with heavy atom (Cl atom) of ligand in tleap
(Fri Sep 27 2019 - 05:27:35 PDT)
Re: [AMBER] problem with heavy atom (Cl atom) of ligand in tleap
(Fri Sep 27 2019 - 04:51:50 PDT)
Re: [AMBER] ambpdb error while conversion
(Wed Sep 25 2019 - 01:42:53 PDT)
Re: [AMBER] ambpdb error while conversion
(Tue Sep 24 2019 - 04:58:21 PDT)
Re: [AMBER] ambpdb error while conversion
(Tue Sep 24 2019 - 04:42:42 PDT)
Re: [AMBER] EstJ6_DBP_bound_sus
(Tue Sep 24 2019 - 01:48:43 PDT)
Re: [AMBER] cpptraj rms with different pdb
(Sat Sep 21 2019 - 21:31:43 PDT)
Re: [AMBER] cpptraj rms with different pdb
(Fri Sep 20 2019 - 22:29:43 PDT)
Re: [AMBER] ambpdb error while conversion
(Thu Sep 19 2019 - 04:41:07 PDT)
Re: [AMBER] Cpptraj RDF onlyframes
(Wed Sep 18 2019 - 06:15:22 PDT)
Re: [AMBER] AMBER: error in reading namelist cntrl
(Mon Sep 16 2019 - 00:46:31 PDT)
Re: [AMBER] AMBER: error in reading namelist cntrl
(Mon Sep 16 2019 - 00:24:43 PDT)
Re: [AMBER] Amber not working after installation - Help from github
(Sun Sep 15 2019 - 05:02:29 PDT)
Re: [AMBER] Amber not working after installation - Help from github
(Fri Sep 13 2019 - 10:12:20 PDT)
Re: [AMBER] Amber not working after installation - Help from github
(Fri Sep 13 2019 - 06:49:31 PDT)
Re: [AMBER] Amber not working after installation - Help from github
(Fri Sep 13 2019 - 04:11:39 PDT)
Re: [AMBER] bad atom type i
(Sun Sep 08 2019 - 22:53:37 PDT)
Re: [AMBER] how to load amber rst file in vmd for observing box size
(Wed Sep 04 2019 - 10:07:17 PDT)
Re: [AMBER] how to load amber rst file in vmd for observing box size
(Wed Sep 04 2019 - 09:22:50 PDT)
Re: [AMBER] how to load amber rst file in vmd for observing box size
(Wed Sep 04 2019 - 08:21:15 PDT)
Re: [AMBER] Cpptraj watershell CUDA
(Mon Sep 02 2019 - 03:50:46 PDT)
Re: [AMBER] MMGBSA.py lignad
(Mon Sep 02 2019 - 00:01:15 PDT)
Re: [AMBER] MMGBSA.py lignad
(Sun Sep 01 2019 - 23:59:21 PDT)
Re: [AMBER] MMGBSA.py lignad
(Sun Sep 01 2019 - 23:42:05 PDT)
emanuele falbo
[AMBER] Packmol and Amber
(Tue Sep 24 2019 - 06:33:12 PDT)
Fabian Glaser
[AMBER] angles analysis
(Sun Sep 22 2019 - 05:15:44 PDT)
Re: [AMBER] cloud vs purchase
(Thu Sep 05 2019 - 07:32:54 PDT)
[AMBER] cloud vs purchase
(Thu Sep 05 2019 - 00:25:38 PDT)
Re: [AMBER] how to load amber rst file in vmd for observing box size
(Wed Sep 04 2019 - 09:09:41 PDT)
Gerald Monard
Re: [AMBER] Ligand parameterization
(Tue Sep 03 2019 - 06:17:16 PDT)
Groner, Rob
[AMBER] Trouble installing Amber 18
(Wed Sep 18 2019 - 06:43:47 PDT)
Gustaf Olsson
Re: [AMBER] Rotational/torsion energy
(Thu Sep 26 2019 - 03:13:36 PDT)
[AMBER] Rotational/torsion energy
(Wed Sep 25 2019 - 23:30:31 PDT)
Re: [AMBER] Question regarding ntx and irest
(Wed Sep 25 2019 - 13:01:19 PDT)
[AMBER] Question regarding ntx and irest
(Wed Sep 25 2019 - 03:09:58 PDT)
Re: [AMBER] Cpptraj RDF onlyframes
(Wed Sep 18 2019 - 06:15:12 PDT)
Re: [AMBER] Protein-ligand simulation and help w.r.t files for carrying out simulation
(Wed Sep 11 2019 - 22:38:18 PDT)
Re: [AMBER] how to load amber rst file in vmd for observing box size
(Mon Sep 09 2019 - 06:29:44 PDT)
Re: [AMBER] how to load amber rst file in vmd for observing box size
(Sat Sep 07 2019 - 01:14:22 PDT)
Re: [AMBER] cloud vs purchase
(Thu Sep 05 2019 - 02:16:01 PDT)
Re: [AMBER] how to load amber rst file in vmd for observing box size
(Wed Sep 04 2019 - 23:06:12 PDT)
Re: [AMBER] H - bond calculations
(Mon Sep 02 2019 - 06:47:04 PDT)
[AMBER] Installing on Mac - Back at it
(Mon Sep 02 2019 - 06:43:55 PDT)
Hadi Rahmaninejad
Re: [AMBER] trajectory coordinate out of box
(Thu Sep 19 2019 - 11:40:09 PDT)
[AMBER] trajectory coordinate out of box
(Thu Sep 19 2019 - 09:47:31 PDT)
Re: [AMBER] Cpptraj extracting coordinate data of a projectile
(Thu Sep 19 2019 - 07:14:36 PDT)
[AMBER] Cpptraj extracting coordinate data of a projectile
(Wed Sep 18 2019 - 21:04:44 PDT)
Hai Nguyen
Re: [AMBER] Compilation of Amber on Cray
(Thu Sep 26 2019 - 07:52:57 PDT)
Re: [AMBER] MMGBSA energy calculation problem for RNA
(Wed Sep 25 2019 - 09:13:00 PDT)
Re: [AMBER] many failures on "make test"
(Mon Sep 23 2019 - 15:03:26 PDT)
Re: [AMBER] many failures on "make test"
(Mon Sep 23 2019 - 13:47:51 PDT)
Re: [AMBER] Amber not working after installation - Help from github
(Sun Sep 15 2019 - 12:27:13 PDT)
Re: [AMBER] Amber not working after installation - Help from github
(Sat Sep 14 2019 - 11:37:08 PDT)
Re: [AMBER] Amber not working after installation - Help from github
(Fri Sep 13 2019 - 12:45:03 PDT)
Re: [AMBER] Amber not working after installation - Help from github
(Fri Sep 13 2019 - 12:44:04 PDT)
Hemant Kisan
[AMBER] error regarding MCPB.py
(Wed Sep 11 2019 - 08:59:16 PDT)
Hira Jabeen
Re: [AMBER] Ligand parameterization
(Tue Sep 03 2019 - 08:49:01 PDT)
[AMBER] Ligand parameterization
(Tue Sep 03 2019 - 03:56:42 PDT)
HOCHEOL LIM
[AMBER] About Thermodynamic Integration tutorial (A9) with pmemd.cuda (GPU)
(Mon Sep 23 2019 - 18:35:20 PDT)
Hosein Geraili Daronkola
Re: [AMBER] TI residue mutation with pmemd on GPU
(Thu Sep 26 2019 - 07:33:59 PDT)
Re: [AMBER] About Thermodynamic Integration tutorial (A9) with pmemd.cuda (GPU)
(Mon Sep 23 2019 - 23:37:03 PDT)
[AMBER] TI residue mutation with pmemd on GPU
(Fri Sep 20 2019 - 03:18:11 PDT)
ilhan.yavuz
[AMBER] installation error
(Tue Sep 24 2019 - 07:13:08 PDT)
Jason Swails
Re: [AMBER] Compilation of Amber on Cray
(Sun Sep 29 2019 - 19:27:50 PDT)
Re: [AMBER] GROMACS to AMBER .top and .pdb conversion using gromber
(Mon Sep 09 2019 - 08:57:50 PDT)
Re: [AMBER] Difference in velocity values between parmed and pytraj
(Mon Sep 09 2019 - 08:56:34 PDT)
Jinfeng Huang
[AMBER] problem with random seed
(Tue Sep 17 2019 - 06:57:30 PDT)
[AMBER] problem with random seed
(Wed Sep 11 2019 - 07:44:17 PDT)
Johnny Guevara
[AMBER] bad atom type i
(Sun Sep 08 2019 - 12:49:15 PDT)
Jon Uranga
[AMBER] Replica Exchange pH simulations with explicit solvent
(Fri Sep 20 2019 - 03:07:55 PDT)
Juan Etchart
[AMBER] Error installing Amber on Centos 7
(Tue Sep 17 2019 - 05:19:53 PDT)
Karl Kirschner
Re: [AMBER] Rotational/torsion energy
(Thu Sep 26 2019 - 00:48:13 PDT)
Re: [AMBER] optimizing GAFF2 torsional parameters
(Thu Sep 12 2019 - 00:06:56 PDT)
Kolattukudy P. Santo
Re: [AMBER] GBSA
(Fri Sep 13 2019 - 07:40:40 PDT)
Re: [AMBER] GBSA
(Tue Sep 03 2019 - 18:45:42 PDT)
[AMBER] GBSA
(Tue Sep 03 2019 - 13:13:35 PDT)
Re: [AMBER] Constant PH simulations for non-proteins and nonstandard residues
(Tue Sep 03 2019 - 13:08:05 PDT)
koushik kasavajhala
Re: [AMBER] Error in calculation of per residue decomposition
(Mon Sep 09 2019 - 08:39:05 PDT)
Lenka
Re: [AMBER] cpptraj rms with different pdb
(Mon Sep 23 2019 - 07:49:02 PDT)
Re: [AMBER] cpptraj rms with different pdb
(Sun Sep 22 2019 - 05:15:24 PDT)
Re: [AMBER] cpptraj rms with different pdb
(Sat Sep 21 2019 - 05:59:23 PDT)
[AMBER] cpptraj rms with different pdb
(Fri Sep 20 2019 - 12:24:59 PDT)
Liao
Re: [AMBER] MMGBSA energy calculation problem for RNA
(Wed Sep 25 2019 - 19:13:53 PDT)
Re: [AMBER] Please how to solve the unfilled valence problem in antechamber
(Wed Sep 25 2019 - 19:10:46 PDT)
Re: [AMBER] MMGBSA energy calculation problem for RNA
(Wed Sep 25 2019 - 08:18:38 PDT)
[AMBER] Self-update: MMGBSA energy calculation problem for RNA
(Wed Sep 25 2019 - 08:12:55 PDT)
[AMBER] MMGBSA energy calculation problem for RNA
(Wed Sep 25 2019 - 03:49:23 PDT)
[AMBER] How big a molecule can antechamber (sqm) put charges on?
(Wed Sep 18 2019 - 18:29:24 PDT)
Lod King
Re: [AMBER] Explicit understanding the force computed from U(CMAP) term
(Mon Sep 09 2019 - 10:53:56 PDT)
Re: [AMBER] Explicit understanding the force computed from U(CMAP) term
(Fri Sep 06 2019 - 17:20:48 PDT)
Re: [AMBER] Explicit understanding the force computed from U(CMAP) term
(Fri Sep 06 2019 - 02:03:58 PDT)
[AMBER] Explicit understanding the force computed from U(CMAP) term
(Thu Sep 05 2019 - 15:34:34 PDT)
Re: [AMBER] ff14SB overestimation of helical comformation
(Tue Sep 03 2019 - 11:46:14 PDT)
[AMBER] ff14SB overestimation of helical comformation
(Tue Sep 03 2019 - 10:49:41 PDT)
M. Pyrka
[AMBER] titratable residues cuda
(Wed Sep 11 2019 - 00:27:35 PDT)
Martín Pettinati
[AMBER] Calculating RMSF
(Thu Sep 05 2019 - 08:20:40 PDT)
maryam azimzadehirani
[AMBER] aMD on a protein-protein complex
(Wed Sep 25 2019 - 01:27:05 PDT)
Re: [AMBER] MMGBSA.py lignad
(Mon Sep 02 2019 - 00:09:37 PDT)
Re: [AMBER] MMGBSA.py lignad
(Sun Sep 01 2019 - 23:56:17 PDT)
[AMBER] MMGBSA.py lignad
(Sun Sep 01 2019 - 22:49:40 PDT)
Matias Machado
Re: [AMBER] Packmol and Amber
(Wed Sep 25 2019 - 07:01:40 PDT)
Re: [AMBER] ANTECHAMBER_AC
(Thu Sep 19 2019 - 07:36:48 PDT)
Re: [AMBER] ANTECHAMBER_AC
(Thu Sep 19 2019 - 06:51:27 PDT)
Re: [AMBER] GBSA
(Thu Sep 12 2019 - 07:37:47 PDT)
Re: [AMBER] Error creating topology and coordinates file
(Thu Sep 12 2019 - 07:16:19 PDT)
Re: [AMBER] Error creating topology and coordinates file
(Thu Sep 12 2019 - 07:01:46 PDT)
Max Knicker
[AMBER] Cpptraj watershell CUDA
(Mon Sep 02 2019 - 02:29:54 PDT)
Ming Tang
[AMBER] which force field should be used for proteins when phosaa10 is used for phosphorylated serine?
(Wed Sep 25 2019 - 01:36:14 PDT)
Monika Choudhary
[AMBER] BORON parameters
(Thu Sep 26 2019 - 02:41:29 PDT)
MYRIAN TORRES RICO
Re: [AMBER] restraints error
(Tue Sep 24 2019 - 06:39:33 PDT)
[AMBER] restraints error
(Tue Sep 24 2019 - 01:36:50 PDT)
[AMBER] md distorted
(Mon Sep 23 2019 - 03:54:20 PDT)
[AMBER] MD distorted
(Mon Sep 23 2019 - 02:41:40 PDT)
neha rana
[AMBER] On AWS instance, MD stops running after sometime without producing any error
(Tue Sep 24 2019 - 13:28:32 PDT)
Nikolay N. Kuzmich
Re: [AMBER] Cpptraj RDF onlyframes
(Thu Sep 19 2019 - 09:02:17 PDT)
[AMBER] Cpptraj RDF onlyframes
(Wed Sep 18 2019 - 05:07:41 PDT)
Nisha Amarnath Jonniya
[AMBER] ASMD iat define
(Thu Sep 12 2019 - 05:46:17 PDT)
Núbia Prates
Re: [AMBER] issue during TI minimisation
(Tue Sep 03 2019 - 03:23:04 PDT)
[AMBER] issue during TI minimisation
(Mon Sep 02 2019 - 07:02:42 PDT)
Parviz Seifpanahi Shabane
[AMBER] Restart file format.
(Fri Sep 27 2019 - 10:45:33 PDT)
[AMBER] Implicit solvent simulation.
(Mon Sep 09 2019 - 15:13:39 PDT)
[AMBER] restraintmask (Cannot match namelist object name :1-294)
(Mon Sep 02 2019 - 09:22:06 PDT)
Patil Pranita Uttamrao
[AMBER] -Antechamber error for modified residues
(Wed Sep 25 2019 - 23:16:49 PDT)
Pengfei Li
Re: [AMBER] Generating parameters for iron-sulfur protein
(Sat Sep 07 2019 - 15:03:05 PDT)
Pierre Leprovost
[AMBER] Force field problem : Acyl tail fragments parameters
(Thu Sep 19 2019 - 05:46:03 PDT)
Pratul Agarwal
Re: [AMBER] PCA calculation projection
(Thu Sep 12 2019 - 05:52:24 PDT)
Re: [AMBER] PCA calculation projection
(Wed Sep 11 2019 - 05:59:51 PDT)
Premila Samuel Mohan Dass
Re: [AMBER] TI residue mutation with pmemd on GPU
(Fri Sep 20 2019 - 06:15:19 PDT)
Ray Luo
Re: [AMBER] Problem in calculating MMPBSA-GBSA
(Wed Sep 25 2019 - 08:30:52 PDT)
Renato Araujo
[AMBER] Please how to solve the unfilled valence problem in antechamber
(Wed Sep 25 2019 - 10:27:40 PDT)
[AMBER] Protein-ligand simulation and help w.r.t files for carrying out simulation
(Wed Sep 11 2019 - 15:06:04 PDT)
RITUPARNA ROY
Re: [AMBER] Generating the parameters for non-standard amino-acid residue
(Mon Sep 09 2019 - 09:25:58 PDT)
Re: [AMBER] Generating the parameters for non-standard amino-acid residue
(Mon Sep 09 2019 - 07:01:53 PDT)
[AMBER] Generating the parameters for non-standard amino-acid residue
(Sat Sep 07 2019 - 00:37:24 PDT)
Robin Betz
Re: [AMBER] PARAMFIT
(Mon Sep 23 2019 - 16:05:18 PDT)
Ross Walker
Re: [AMBER] up to date CUDA versions?
(Wed Sep 25 2019 - 03:25:52 PDT)
Re: [AMBER] cloud vs purchase
(Thu Sep 05 2019 - 06:13:13 PDT)
Rui Chen
Re: [AMBER] Problem with CPPTRAJ (RMSD)
(Tue Sep 03 2019 - 10:10:11 PDT)
Re: [AMBER] Problem with CPPTRAJ (RMSD)
(Tue Sep 03 2019 - 08:18:57 PDT)
[AMBER] Problem with CPPTRAJ (RMSD)
(Mon Sep 02 2019 - 22:21:47 PDT)
[AMBER] running NAMD with AMBER inputs
(Sun Sep 01 2019 - 10:29:28 PDT)
Ruxi Qi
Re: [AMBER] Recent updates to how Amber carries out softcore free energy calculations
(Wed Sep 11 2019 - 23:36:21 PDT)
Ryoichi Utsumi
Re: [AMBER] Installaiton of pmemd for Amber16
(Wed Sep 25 2019 - 06:16:40 PDT)
Sadaf Rani
[AMBER] Free energy calculation
(Mon Sep 30 2019 - 03:56:07 PDT)
[AMBER] free energy calculation
(Thu Sep 26 2019 - 07:25:56 PDT)
[AMBER] Fwd: tutorial for finding binding free energies
(Fri Sep 13 2019 - 08:45:07 PDT)
Re: [AMBER] how to load amber rst file in vmd for observing box size
(Fri Sep 06 2019 - 12:55:30 PDT)
Re: [AMBER] Regarding setting up FEP calculations in AMBER18
(Fri Sep 06 2019 - 04:42:48 PDT)
Re: [AMBER] how to load amber rst file in vmd for observing box size
(Wed Sep 04 2019 - 10:25:38 PDT)
Re: [AMBER] how to load amber rst file in vmd for observing box size
(Wed Sep 04 2019 - 10:21:25 PDT)
Re: [AMBER] how to load amber rst file in vmd for observing box size
(Wed Sep 04 2019 - 09:45:55 PDT)
Re: [AMBER] how to load amber rst file in vmd for observing box size
(Wed Sep 04 2019 - 09:03:12 PDT)
[AMBER] how to load amber rst file in vmd for observing box size
(Wed Sep 04 2019 - 08:04:52 PDT)
Saeed Izadi
Re: [AMBER] Implicit solvent simulation.
(Tue Sep 10 2019 - 12:16:51 PDT)
Saikat Pal
[AMBER] Query regarding mmgbsa
(Fri Sep 27 2019 - 21:52:22 PDT)
SATYAJIT KHATUA
[AMBER] unit conversion during umbrella sampling and then PMF calculation
(Wed Sep 18 2019 - 01:06:34 PDT)
Scott Brozell
Re: [AMBER] sander.MPI gives segfault if compiled with Intel compilers
(Wed Sep 18 2019 - 13:16:37 PDT)
Re: [AMBER] Trouble installing Amber 18
(Wed Sep 18 2019 - 12:48:00 PDT)
Seketoulie Keretsu
[AMBER] avoiding protein residue renumbering during tleap processing
(Fri Sep 27 2019 - 07:04:38 PDT)
Re: [AMBER] problem with heavy atom (Cl atom) of ligand in tleap
(Fri Sep 27 2019 - 05:34:57 PDT)
[AMBER] problem with heavy atom (Cl atom) of ligand in tleap
(Fri Sep 27 2019 - 04:52:02 PDT)
Shankha Banerjee
[AMBER] Unable to generate parameters of modified amino acids using LEAP
(Mon Sep 23 2019 - 07:04:07 PDT)
[AMBER] How to generate parameter files of N-terminal modified amino acid residue?
(Thu Sep 12 2019 - 00:56:30 PDT)
Re: [AMBER] How to generate parameter files of modified terminal amino acid residue using Antechamber
(Fri Sep 06 2019 - 23:00:26 PDT)
[AMBER] How to generate parameter files of modified terminal amino acid residue using Antechamber
(Thu Sep 05 2019 - 11:19:51 PDT)
Shayna Hilburg
[AMBER] up to date CUDA versions?
(Tue Sep 24 2019 - 13:07:28 PDT)
[AMBER] Amber17 to Amber18 considerations and archive?
(Tue Sep 17 2019 - 13:59:18 PDT)
shivangi agarwal
[AMBER] Small ligand activators molecule
(Tue Sep 17 2019 - 05:15:14 PDT)
Re: [AMBER] Error in calculation of per residue decomposition
(Mon Sep 09 2019 - 08:13:24 PDT)
[AMBER] Error in calculation of per residue decomposition
(Sat Sep 07 2019 - 12:42:35 PDT)
Re: [AMBER] H - bond calculations
(Mon Sep 02 2019 - 06:16:25 PDT)
Song, Lin
Re: [AMBER] unit conversion during umbrella sampling and then PMF calculation
(Wed Sep 18 2019 - 09:27:28 PDT)
Re: [AMBER] Print non bonded pair list
(Tue Sep 03 2019 - 14:26:01 PDT)
Re: [AMBER] Print non bonded pair list
(Tue Sep 03 2019 - 12:09:06 PDT)
Stephan Schott
Re: [AMBER] How to incorporate new lipid molecules through packmol-memgen
(Mon Sep 30 2019 - 06:05:22 PDT)
Re: [AMBER] How to incorporate new lipid molecules through packmol-memgen
(Mon Sep 30 2019 - 01:44:13 PDT)
Suman Chakrabarty
Re: [AMBER] Compilation of Amber on Cray
(Mon Sep 30 2019 - 10:42:13 PDT)
Re: [AMBER] Compilation of Amber on Cray
(Mon Sep 30 2019 - 04:05:40 PDT)
Re: [AMBER] Compilation of Amber on Cray
(Sun Sep 29 2019 - 01:07:32 PDT)
Re: [AMBER] Compilation of Amber on Cray
(Thu Sep 26 2019 - 09:30:22 PDT)
[AMBER] Compilation of Amber on Cray
(Thu Sep 26 2019 - 01:53:28 PDT)
Sunita Patel
Re: [AMBER] Amber18 installation
(Mon Sep 30 2019 - 04:27:42 PDT)
Re: [AMBER] ambpdb error while conversion
(Wed Sep 25 2019 - 04:35:20 PDT)
Re: [AMBER] ambpdb error while conversion
(Wed Sep 25 2019 - 01:29:15 PDT)
Re: [AMBER] ambpdb error while conversion
(Wed Sep 25 2019 - 01:06:22 PDT)
Re: [AMBER] ambpdb error while conversion
(Tue Sep 24 2019 - 04:45:51 PDT)
Re: [AMBER] ambpdb error while conversion
(Tue Sep 24 2019 - 04:23:10 PDT)
Re: [AMBER] ambpdb error while conversion
(Tue Sep 24 2019 - 04:12:54 PDT)
[AMBER] ambpdb error while conversion
(Thu Sep 19 2019 - 04:25:29 PDT)
[AMBER] Coordinate resetting (SHAKE) can not be accomplished
(Mon Sep 16 2019 - 23:30:26 PDT)
[AMBER] Amber 18 installation
(Wed Sep 04 2019 - 02:51:58 PDT)
Thomas Cheatham
Re: [AMBER] cloud vs purchase
(Wed Sep 18 2019 - 14:22:29 PDT)
Tyler Luchko (Lists)
Re: [AMBER] AmberTools19 installation error
(Fri Sep 13 2019 - 09:47:17 PDT)
viktor drobot
Re: [AMBER] sander.MPI gives segfault if compiled with Intel compilers
(Wed Sep 18 2019 - 14:45:32 PDT)
Re: [AMBER] sander.MPI gives segfault if compiled with Intel compilers
(Mon Sep 16 2019 - 05:32:25 PDT)
[AMBER] sander.MPI gives segfault if compiled with Intel compilers
(Sun Sep 15 2019 - 06:34:55 PDT)
Violeta Burns Casamayor
Re: [AMBER] lipid order per leaflet
(Mon Sep 16 2019 - 09:36:21 PDT)
[AMBER] lipid order per leaflet
(Tue Sep 03 2019 - 10:49:08 PDT)
Vishal Singh
[AMBER] Energy minimization in Implicit solvent for Langevin dynamics simulation
(Mon Sep 09 2019 - 00:21:04 PDT)
xmgign.126.com
[AMBER] AMBER18 installation error
(Tue Sep 03 2019 - 00:33:15 PDT)
Åsmund Røhr Kjendseth
[AMBER] Bug in Amber-Orca communication ?
(Fri Sep 13 2019 - 02:59:56 PDT)
东庚
[AMBER] how to read the outup file of QMMM MD simulation with Amber combined with Gaussian (Geng Dong)
(Thu Sep 05 2019 - 02:50:36 PDT)
冷灿
[AMBER] the structure of cellulose II in Glycam-06h force field
(Thu Sep 12 2019 - 18:00:44 PDT)
崔佳文
[AMBER] Generating parameters for iron-sulfur protein
(Mon Sep 02 2019 - 21:11:10 PDT)
李振东
[AMBER] DNA methylation parameters
(Mon Sep 23 2019 - 06:10:17 PDT)
石娜
[AMBER] Error: an illegal memory access was encountered launching kernel kClearForces cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered
(Fri Sep 20 2019 - 00:27:20 PDT)
[AMBER] seek for how to calculate the binding free energy of a covalent inhibitor
(Tue Sep 17 2019 - 05:24:50 PDT)
조준범
[AMBER] How can I change the default unit of density?
(Wed Sep 25 2019 - 22:13:02 PDT)
[AMBER] AMBER: Segmentation fault
(Mon Sep 16 2019 - 01:19:35 PDT)
Re: [AMBER] AMBER: error in reading namelist cntrl
(Mon Sep 16 2019 - 00:40:20 PDT)
[AMBER] AMBER: error in reading namelist cntrl
(Mon Sep 16 2019 - 00:14:05 PDT)
[AMBER] How can I make the initial configuration and topology with polarizable force field?
(Sun Sep 15 2019 - 20:25:18 PDT)
Last message date
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Mon Sep 30 2019 - 11:00:02 PDT
Archived on
: Fri Dec 20 2024 - 05:55:53 PST
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