Amber Archive Aug 2019: by author

A K
- Re: [AMBER] Question about running MMPBSA.py with a mask to exclude certain residues (Fri Aug 23 2019 - 20:03:32 PDT)
- Re: [AMBER] Question about running MMPBSA.py with a mask to exclude certain residues (Fri Aug 23 2019 - 14:03:55 PDT)
- Re: [AMBER] Question about running MMPBSA.py with a mask to exclude certain residues (Fri Aug 23 2019 - 09:22:53 PDT)
- [AMBER] Question about running MMPBSA.py with a mask to exclude certain residues (Fri Aug 16 2019 - 17:05:26 PDT)
- Re: [AMBER] problem with building cpptraj in AmberTools19 (Thu Aug 15 2019 - 13:04:03 PDT)
Airy Sanjeev
- [AMBER] Calculation of ΔG from PMF (Tue Aug 27 2019 - 21:41:06 PDT)
- Re: [AMBER] WaterBox is getting distorted while running PMF (Sun Aug 18 2019 - 23:50:37 PDT)
- [AMBER] WaterBox is getting distorted while running PMF (Thu Aug 15 2019 - 21:17:45 PDT)
Akinpelu Olayinka
- Re: [AMBER] Regarding restarting from RST files using pmemd.cuda (Mon Aug 19 2019 - 06:39:03 PDT)
- [AMBER] Problem Running Antechamber for GTP (Thu Aug 15 2019 - 00:21:48 PDT)
Amen Shamim
- [AMBER] Small molecule break after minimization (Fri Aug 30 2019 - 06:16:46 PDT)
- [AMBER] MD on small molecules, The file contained 8 atoms not in residue templates (Fri Aug 09 2019 - 11:17:52 PDT)
Andrea H. Kasun
- Re: [AMBER] nmropt problems (Thu Aug 29 2019 - 09:02:06 PDT)
- [AMBER] nmropt problems (Wed Aug 28 2019 - 06:50:38 PDT)
Andrew Sugarman
- Re: [AMBER] Error "forrtl: severe (174) : SIGSEGV, segmentation fault" while running MD simulation production run (Tue Aug 27 2019 - 08:13:16 PDT)
Antonios Kolocouris
- [AMBER] ΑΠ: Transcription factor DNA binding - Gibbs of activation (Thu Aug 08 2019 - 00:41:43 PDT)
ATUL KUMAR
- Re: [AMBER] GaMD Not Running in GPU (Mon Aug 05 2019 - 22:13:49 PDT)
Bellesis, Andrew G
- [AMBER] Specifying size of truncated octahedron box manually (Tue Aug 06 2019 - 07:29:57 PDT)
Bill Ross
- Re: [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true? (Tue Aug 27 2019 - 16:06:55 PDT)
- Re: [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true? (Sat Aug 24 2019 - 04:57:15 PDT)
- Re: [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true? (Sat Aug 24 2019 - 04:44:18 PDT)
- Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 (Mon Aug 19 2019 - 22:49:40 PDT)
- Re: [AMBER] Segmentation Fault (Wed Aug 14 2019 - 14:16:22 PDT)
- Re: [AMBER] Simulations without PME (Mon Aug 05 2019 - 18:43:09 PDT)
Bruno Cramer
- [AMBER] MAWS/Amber and python program adjustment (Tue Aug 27 2019 - 15:53:53 PDT)
- [AMBER] MAWS_Amber/antechamber assistance (Sun Aug 25 2019 - 13:06:23 PDT)
Carlos Simmerling
- Re: [AMBER] Calculation of ΔG from PMF (Wed Aug 28 2019 - 08:19:14 PDT)
- Re: [AMBER] NH-pi interaction using ff14SB forcefield (Tue Aug 13 2019 - 06:56:35 PDT)
- Re: [AMBER] Imaging-rst file error (Wed Aug 07 2019 - 06:19:59 PDT)
- Re: [AMBER] How to generate Free energy landscape for amber trajectory? (Wed Aug 07 2019 - 04:58:07 PDT)
- Re: [AMBER] Lazy Question: File conversion NCRST to RST (Wed Aug 07 2019 - 04:41:58 PDT)
- Re: [AMBER] Imaging-rst file error (Wed Aug 07 2019 - 04:41:27 PDT)
charalamm.cheng.auth.gr
- [AMBER] Transcription factor DNA binding - Gibbs of activation (Wed Aug 07 2019 - 23:58:27 PDT)
Christian Schafmeister
- [AMBER-Developers] AMBER developer job opening and TI/FEP calculation postdoc opening coming up (Thu Aug 08 2019 - 10:17:44 PDT)
Cruzeiro,Vinicius Wilian D
- Re: [AMBER] Constant PH simulations for non-proteins and nonstandard residues (Fri Aug 30 2019 - 11:03:56 PDT)
Daniel Roe
- Re: [AMBER] Fwd: evec.pev file in essential dynamics analysis (Tue Aug 27 2019 - 10:29:50 PDT)
- Re: [AMBER] Not able to load Amber trajectories in VMD (Tue Aug 20 2019 - 10:15:20 PDT)
- Re: [AMBER] problem with building cpptraj in AmberTools19 (Mon Aug 19 2019 - 06:40:34 PDT)
- Re: [AMBER] Amber installation error (Mon Aug 19 2019 - 05:35:33 PDT)
- Re: [AMBER] Regarding restarting from RST files using pmemd.cuda (Mon Aug 19 2019 - 05:22:51 PDT)
- Re: [AMBER] Error searching for compatible GPU in Amber18 (Mon Aug 19 2019 - 05:13:12 PDT)
- Re: [AMBER] Lazy Question: File conversion NCRST to RST (Wed Aug 14 2019 - 04:30:10 PDT)
- Re: [AMBER] Lazy Question: File conversion NCRST to RST (Mon Aug 12 2019 - 11:05:31 PDT)
- Re: [AMBER] How to calculate the tilt angle of TM helix (Sat Aug 10 2019 - 06:25:38 PDT)
- Re: [AMBER] Difference in velocity values between parmed and pytraj (Thu Aug 08 2019 - 12:23:05 PDT)
- Re: [AMBER] Imaging-rst file error (Thu Aug 08 2019 - 10:31:46 PDT)
- Re: [AMBER] Imaging-rst file error (Thu Aug 08 2019 - 05:38:38 PDT)
- Re: [AMBER] How to generate Free energy landscape for amber trajectory? (Thu Aug 08 2019 - 05:00:21 PDT)
- Re: [AMBER] Lazy Question: File conversion NCRST to RST (Wed Aug 07 2019 - 05:06:37 PDT)
- Re: [AMBER] error in Cuda installtion (Thu Aug 01 2019 - 04:57:57 PDT)
David A Case
- Re: [AMBER] equilirbration at constant volume (Fri Aug 30 2019 - 09:30:19 PDT)
- Re: [AMBER] periodic box size (Fri Aug 30 2019 - 04:30:27 PDT)
- Re: [AMBER] Calculation of ΔG from PMF (Wed Aug 28 2019 - 08:35:29 PDT)
- Re: [AMBER] nmropt problems (Wed Aug 28 2019 - 08:15:12 PDT)
- Re: [AMBER] CHARMM 3 extra energy terms in AMBER dynamic engines (SANDER&PMEMD) (Thu Aug 22 2019 - 06:35:19 PDT)
- Re: [AMBER] Regarding heating equilibration (Thu Aug 22 2019 - 06:31:00 PDT)
- Re: [AMBER] Amberff99sb topology for phosphorylated tyrosine residue in GROMACS (Tue Aug 20 2019 - 05:24:42 PDT)
- Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 (Tue Aug 20 2019 - 05:21:19 PDT)
- Re: [AMBER] Imaging-rst file error (Thu Aug 08 2019 - 08:41:50 PDT)
- Re: [AMBER] problems with Miniconda installation (Thu Aug 08 2019 - 08:39:10 PDT)
- Re: [AMBER] T-leap. (Tue Aug 06 2019 - 09:24:16 PDT)
- Re: [AMBER] 1-4 EvdW and 1-4 EEL (Fri Aug 02 2019 - 05:42:17 PDT)
- Re: [AMBER] error in Cuda installtion (Thu Aug 01 2019 - 05:23:48 PDT)
David Case
- Re: [AMBER] PIMD is not compatible with the MC Barostat (Fri Aug 23 2019 - 19:07:28 PDT)
- Re: [AMBER] Question about running MMPBSA.py with a mask to exclude certain residues (Fri Aug 23 2019 - 18:58:53 PDT)
- Re: [AMBER] Specifying size of truncated octahedron box manually (Tue Aug 20 2019 - 19:33:01 PDT)
- Re: [AMBER] MMPBSA.py code Error: unknown keyword or invalid value: --closureorder (Tue Aug 20 2019 - 19:30:46 PDT)
- Re: [AMBER] MD on small molecules, The file contained 8 atoms not in residue templates (Tue Aug 20 2019 - 19:29:47 PDT)
- Re: [AMBER] Problem for the frcmod file from the amber tutorial (Tue Aug 20 2019 - 19:24:16 PDT)
- Re: [AMBER] CHARMM forcefield (Tue Aug 20 2019 - 19:20:00 PDT)
- Re: [AMBER] How does PMEMD handle duplicates in GROUP? (Tue Aug 20 2019 - 19:17:02 PDT)
- Re: [AMBER] vlimit exceeded for step (Tue Aug 20 2019 - 19:12:58 PDT)
- Re: [AMBER] Restraint ramp (Sat Aug 17 2019 - 18:16:40 PDT)
- Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues (Sat Aug 17 2019 - 06:03:37 PDT)
- Re: [AMBER] mmPBSA error in Amber19 suite (Sat Aug 17 2019 - 06:11:31 PDT)
- Re: [AMBER] Amber16 + AmberTools19 (Fri Aug 16 2019 - 13:56:44 PDT)
- Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues (Fri Aug 16 2019 - 13:54:31 PDT)
- Re: [AMBER] Installing Amber parallel option (Thu Aug 15 2019 - 18:05:43 PDT)
- Re: [AMBER] Installaiton of pmemd for Amber16 (Wed Aug 14 2019 - 18:32:57 PDT)
- Re: [AMBER] Segmentation Fault (Wed Aug 14 2019 - 18:20:51 PDT)
- Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues (Wed Aug 14 2019 - 18:12:48 PDT)
- Re: [AMBER] Amber16 + AmberTools19 (Wed Aug 14 2019 - 18:06:57 PDT)
- Re: [AMBER] OpenMPI 4 and pmemd.cuda.MPI (Tue Aug 13 2019 - 06:25:54 PDT)
- Re: [AMBER] T-leap "does not have a type" (Sun Aug 11 2019 - 05:36:06 PDT)
- Re: [AMBER] gaff2 parameters of c3-c3-os-c3 (Mon Aug 05 2019 - 18:27:36 PDT)
- Re: [AMBER] Simulations without PME (Mon Aug 05 2019 - 18:18:50 PDT)
David Cerutti
- Re: [AMBER] Print non bonded pair list (Fri Aug 30 2019 - 09:59:34 PDT)
- Re: [AMBER] mdgx, improper terms and multifit (Thu Aug 22 2019 - 10:45:22 PDT)
- Re: [AMBER] AccelleratedMD production (Mon Aug 19 2019 - 09:59:37 PDT)
- Re: [AMBER] Regarding restarting from RST files using pmemd.cuda (Mon Aug 19 2019 - 09:55:18 PDT)
- Re: [AMBER] WaterBox is getting distorted while running PMF (Fri Aug 16 2019 - 10:10:56 PDT)
- Re: [AMBER] gaff2 parameters of c3-c3-os-c3 (Mon Aug 05 2019 - 13:04:28 PDT)
- Re: [AMBER] 1-4 EvdW and 1-4 EEL (Fri Aug 02 2019 - 11:51:42 PDT)
Debarati DasGupta
- [AMBER] Regarding setting up FEP calculations in AMBER18 (Mon Aug 26 2019 - 11:59:52 PDT)
Deepika Sardana
- [AMBER] Error in running simulation in HPC using AMBER-18 (Thu Aug 22 2019 - 21:48:23 PDT)
- [AMBER] Issues in AMBER-18 Installation (Fri Aug 09 2019 - 00:25:40 PDT)
Dhananjay
- [AMBER] Restraint ramp (Sat Aug 17 2019 - 09:58:03 PDT)
Dickson, Callum
- Re: [AMBER] How to calculate the tilt angle of TM helix (Fri Aug 09 2019 - 13:49:44 PDT)
Elvis Martis
- Re: [AMBER] Error in running simulation in HPC using AMBER-18 (Thu Aug 22 2019 - 23:07:48 PDT)
- Re: [AMBER] AccelleratedMD production (Mon Aug 19 2019 - 10:15:09 PDT)
- Re: [AMBER] Error in MMPBSA calculation (Fri Aug 16 2019 - 05:17:46 PDT)
- Re: [AMBER] Installing Amber parallel option (Thu Aug 15 2019 - 07:48:44 PDT)
- Re: [AMBER] Installing Amber parallel option (Thu Aug 15 2019 - 04:08:38 PDT)
- Re: [AMBER] Problem Running Antechamber for GTP (Thu Aug 15 2019 - 00:47:32 PDT)
- Re: [AMBER] MM-PBSA Alanine scanning issue (Fri Aug 09 2019 - 21:23:18 PDT)
- Re: [AMBER] problems with Miniconda installation (Fri Aug 09 2019 - 03:44:09 PDT)
- Re: [AMBER] problems with Miniconda installation (Thu Aug 08 2019 - 08:50:07 PDT)
- [AMBER] problems with Miniconda installation (Wed Aug 07 2019 - 23:52:40 PDT)
- Re: [AMBER] error during the calculation of MMPBSA (Tue Aug 06 2019 - 22:37:57 PDT)
- Re: [AMBER] error during the calculation of MMPBSA (Tue Aug 06 2019 - 19:33:31 PDT)
- Re: [AMBER] error during the calculation of MMPBSA (Tue Aug 06 2019 - 08:21:33 PDT)
- Re: [AMBER] error during the calculation of MMPBSA (Tue Aug 06 2019 - 06:54:02 PDT)
emanuele falbo
- Re: [AMBER] How can I calculate RDF only in a specific region of my system? (Wed Aug 14 2019 - 10:16:30 PDT)
Erdem Yeler
- Re: [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true? (Thu Aug 29 2019 - 13:42:26 PDT)
- Re: [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true? (Tue Aug 27 2019 - 14:32:59 PDT)
- [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true? (Sat Aug 24 2019 - 04:18:49 PDT)
Gerald Monard
- Re: [AMBER] MAWS_Amber/antechamber assistance (Mon Aug 26 2019 - 06:49:18 PDT)
Giulia Paiardi
- Re: [AMBER] AccelleratedMD production (Mon Aug 19 2019 - 05:55:03 PDT)
- [AMBER] AccelleratedMD production (Mon Aug 19 2019 - 04:01:36 PDT)
Gustaf Olsson
- Re: [AMBER] building amber 16 parallel with MPI (Tue Aug 27 2019 - 22:43:39 PDT)
- Re: [AMBER] Problem Running Antechamber for GTP (Thu Aug 15 2019 - 01:14:40 PDT)
- Re: [AMBER] Lazy Question: File conversion NCRST to RST (Wed Aug 14 2019 - 06:06:35 PDT)
- Re: [AMBER] Lazy Question: File conversion NCRST to RST (Wed Aug 14 2019 - 05:28:44 PDT)
- Re: [AMBER] Lazy Question: File conversion NCRST to RST (Wed Aug 14 2019 - 02:32:32 PDT)
- Re: [AMBER] Lazy Question: File conversion NCRST to RST (Mon Aug 12 2019 - 22:42:01 PDT)
- Re: [AMBER] Lazy Question: File conversion NCRST to RST (Wed Aug 07 2019 - 06:43:41 PDT)
- Re: [AMBER] Lazy Question: File conversion NCRST to RST (Wed Aug 07 2019 - 05:58:53 PDT)
- [AMBER] Lazy Question: File conversion NCRST to RST (Wed Aug 07 2019 - 04:40:51 PDT)
Hai Nguyen
- Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 (Wed Aug 21 2019 - 05:33:39 PDT)
- Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 (Tue Aug 20 2019 - 23:10:51 PDT)
- Re: [AMBER] volume in pytraj? (Mon Aug 19 2019 - 09:06:45 PDT)
- Re: [AMBER] volume in pytraj? (Sun Aug 18 2019 - 21:28:43 PDT)
- Re: [AMBER] MMPBSA using amberTools19 (Sun Aug 18 2019 - 08:27:14 PDT)
- Re: [AMBER] volume in pytraj? (Fri Aug 16 2019 - 15:29:58 PDT)
- Re: [AMBER] atom numbering in cpptraj and pytraj (Mon Aug 12 2019 - 07:49:09 PDT)
- Re: [AMBER] atom numbering in cpptraj and pytraj (Mon Aug 12 2019 - 07:45:44 PDT)
- Re: [AMBER] Difference in velocity values between parmed and pytraj (Thu Aug 08 2019 - 12:14:26 PDT)
- Re: [AMBER] Difference in velocity values between parmed and pytraj (Wed Aug 07 2019 - 08:47:37 PDT)
- Re: [AMBER] $AMBERHOME vs $AMBER_PREFIX (Tue Aug 06 2019 - 04:55:15 PDT)
Hashemi, Mohtadin
- Re: [AMBER] RTX 5000 cards and AMBER 16 compatibility (Fri Aug 02 2019 - 20:38:12 PDT)
Hira Jabeen
- [AMBER] CHARMM forcefield (Mon Aug 19 2019 - 06:59:31 PDT)
- Re: [AMBER] Imaging-rst file error (Wed Aug 07 2019 - 06:51:30 PDT)
- Re: [AMBER] Imaging-rst file error (Wed Aug 07 2019 - 05:56:44 PDT)
- [AMBER] Imaging-rst file error (Wed Aug 07 2019 - 03:34:59 PDT)
Homeo Morphism
- [AMBER] using accelerated MD on membrane proteins? (Wed Aug 28 2019 - 09:09:15 PDT)
Horn, Anselm
- Re: [AMBER] Error "forrtl: severe (174) : SIGSEGV, segmentation fault" while running MD simulation production run (Wed Aug 28 2019 - 01:56:06 PDT)
- Re: [AMBER] Glycolipid Simulation (Tue Aug 27 2019 - 00:28:31 PDT)
Irfan Alibay
- Re: [AMBER] Difference in velocity values between parmed and pytraj (Thu Aug 08 2019 - 12:06:34 PDT)
- [AMBER] Difference in velocity values between parmed and pytraj (Wed Aug 07 2019 - 08:13:12 PDT)
jacky zhao
- Re: [AMBER] mmPBSA error in Amber19 suite (Sat Aug 17 2019 - 22:12:33 PDT)
- Re: [AMBER] Error in MMPBSA calculation (Sat Aug 17 2019 - 04:44:03 PDT)
- Re: [AMBER] mmPBSA error in Amber19 suite (Sat Aug 17 2019 - 04:40:29 PDT)
- [AMBER] mmPBSA error in Amber19 suite (Thu Aug 15 2019 - 10:10:25 PDT)
Jacopo Sgrignani
- Re: [AMBER] AccelleratedMD production (Mon Aug 19 2019 - 04:06:50 PDT)
James Kress
- Re: [AMBER] Error searching for compatible GPU in Amber18 (Sat Aug 17 2019 - 09:16:20 PDT)
Jason Swails
- Re: [AMBER] Constant pH MD + HMR (Fri Aug 02 2019 - 21:50:07 PDT)
Jeyaram R A
- Re: [AMBER] error during the calculation of MMPBSA (Tue Aug 06 2019 - 22:33:25 PDT)
- Re: [AMBER] error during the calculation of MMPBSA (Tue Aug 06 2019 - 09:51:51 PDT)
- Re: [AMBER] error during the calculation of MMPBSA (Tue Aug 06 2019 - 09:50:38 PDT)
- Re: [AMBER] error during the calculation of MMPBSA (Tue Aug 06 2019 - 08:26:31 PDT)
- Re: [AMBER] error during the calculation of MMPBSA (Tue Aug 06 2019 - 08:24:47 PDT)
- Re: [AMBER] error during the calculation of MMPBSA (Tue Aug 06 2019 - 08:14:22 PDT)
- [AMBER] error during the calculation of MMPBSA (Tue Aug 06 2019 - 06:03:44 PDT)
jinfeng liu
- [AMBER] PIMD is not compatible with the MC Barostat (Fri Aug 23 2019 - 17:29:19 PDT)
Jose Christian Flores Canales
- Re: [AMBER] OpenMPI 4 and pmemd.cuda.MPI (Tue Aug 13 2019 - 04:22:58 PDT)
- [AMBER] OpenMPI 4 and pmemd.cuda.MPI (Tue Aug 13 2019 - 04:20:31 PDT)
Jose Javier Muñoz Criollo
- Re: [AMBER] Amber16 + AmberTools19 (Fri Aug 16 2019 - 05:29:05 PDT)
- [AMBER] Amber16 + AmberTools19 (Wed Aug 14 2019 - 08:39:27 PDT)
Junmei Wang
- Re: [AMBER] gaff2 parameters of c3-c3-os-c3 (Fri Aug 09 2019 - 13:03:14 PDT)
Karim Mahnam
- Re: [AMBER] Error searching for compatible GPU in Amber18 (Mon Aug 19 2019 - 06:44:43 PDT)
- Re: [AMBER] Error searching for compatible GPU in Amber18 (Sun Aug 18 2019 - 19:22:38 PDT)
- [AMBER] Error searching for compatible GPU in Amber18 (Sat Aug 17 2019 - 00:47:18 PDT)
- [AMBER] error in Cuda installtion (Thu Aug 01 2019 - 03:41:04 PDT)
Kevin Hauser
- Re: [AMBER] Transcription factor DNA binding - Gibbs of activation (Thu Aug 08 2019 - 07:38:03 PDT)
Kolattukudy P. Santo
- [AMBER] Constant PH simulations for non-proteins and nonstandard residues (Fri Aug 30 2019 - 09:00:26 PDT)
Lachele Foley
- Re: [AMBER] PDB file carbohydrates naming problem (Sat Aug 31 2019 - 02:51:35 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem (Mon Aug 26 2019 - 11:30:22 PDT)
- Re: [AMBER] Glycolipid Simulation (Sat Aug 24 2019 - 13:17:52 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem (Fri Aug 23 2019 - 05:59:04 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem (Thu Aug 22 2019 - 07:24:07 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem (Wed Aug 21 2019 - 18:35:32 PDT)
- Re: [AMBER] Glycan naming problem (Wed Aug 21 2019 - 12:53:42 PDT)
- [AMBER] Did I miss anyone? Sorry I was gone so long (Wed Aug 21 2019 - 12:44:58 PDT)
- Re: [AMBER] Glycan naming problem (Wed Aug 21 2019 - 12:40:17 PDT)
- Re: [AMBER] Non-integer charge problem with tleap using GLYCAM_06EPb but not GLYCAM_06j-1 (Wed Aug 21 2019 - 12:36:10 PDT)
- Re: [AMBER] R . E. D (Wed Aug 21 2019 - 12:34:09 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem (Tue Aug 20 2019 - 22:32:14 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem (Tue Aug 20 2019 - 21:07:18 PDT)
Laura Furge
- [AMBER] RTX 5000 cards and AMBER 16 compatibility (Fri Aug 02 2019 - 14:17:05 PDT)
Leena Aggarwal
- Re: [AMBER] Error "forrtl: severe (174) : SIGSEGV, segmentation fault" while running MD simulation production run (Wed Aug 28 2019 - 04:49:01 PDT)
- Re: [AMBER] Error "forrtl: severe (174) : SIGSEGV, segmentation fault" while running MD simulation production run (Wed Aug 28 2019 - 00:31:31 PDT)
- [AMBER] Error "forrtl: severe (174) : SIGSEGV, segmentation fault" while running MD simulation production run (Tue Aug 27 2019 - 07:02:15 PDT)
Lei Zhao
- Re: [AMBER] Error in MMPBSA calculation (Sat Aug 17 2019 - 19:57:54 PDT)
- Re: [AMBER] mmPBSA error in Amber19 suite (Sat Aug 17 2019 - 19:55:45 PDT)
Lod King
- Re: [AMBER] CHARMM 3 extra energy terms in AMBER dynamic engines (SANDER&PMEMD) (Thu Aug 22 2019 - 08:14:46 PDT)
- [AMBER] CHARMM 3 extra energy terms in AMBER dynamic engines (SANDER&PMEMD) (Wed Aug 21 2019 - 20:52:39 PDT)
- Re: [AMBER] 1-4 EvdW and 1-4 EEL (Fri Aug 02 2019 - 11:54:43 PDT)
- [AMBER] 1-4 EvdW and 1-4 EEL (Thu Aug 01 2019 - 14:24:56 PDT)
Lucas Bandeira
- [AMBER] How can I calculate RDF only in a specific region of my system? (Wed Aug 14 2019 - 09:57:28 PDT)
M RCC
- [AMBER] How to generate Free energy landscape for amber trajectory? (Tue Aug 06 2019 - 22:10:14 PDT)
Maria Bzówka
- [AMBER] Preparation of trajectory for stfc diffusion calculations (Wed Aug 21 2019 - 06:37:34 PDT)
- [AMBER] Lateral diffusion of lipid head groups (Thu Aug 15 2019 - 04:12:21 PDT)
- Re: [AMBER] How to calculate the tilt angle of TM helix (Mon Aug 12 2019 - 04:22:47 PDT)
- Re: [AMBER] How to calculate the tilt angle of TM helix (Mon Aug 12 2019 - 01:57:36 PDT)
- [AMBER] How to calculate the tilt angle of TM helix (Fri Aug 09 2019 - 01:17:53 PDT)
maryam azimzadehirani
- [AMBER] MMPBS.py error: IOError: [Errno 2] No such file or directory (Wed Aug 28 2019 - 00:48:45 PDT)
Matias Machado
- Re: [AMBER] question about bond command in tleap (Wed Aug 28 2019 - 14:33:44 PDT)
- Re: [AMBER] Combining sevaral frcmods into single file (Tue Aug 27 2019 - 08:20:28 PDT)
- Re: [AMBER] Specifying size of truncated octahedron box manually (Fri Aug 23 2019 - 13:32:20 PDT)
- Re: [AMBER] Graphene residue name Tleap (Fri Aug 23 2019 - 10:57:33 PDT)
- Re: [AMBER] T-leap "does not have a type" (Sat Aug 10 2019 - 13:18:17 PDT)
- Re: [AMBER] DNA force field. (Sat Aug 10 2019 - 13:01:51 PDT)
- Re: [AMBER] T-leap "does not have a type" (Sat Aug 10 2019 - 12:39:12 PDT)
Midhun K Madhu
- [AMBER] Regarding heating equilibration (Wed Aug 21 2019 - 16:11:09 PDT)
- [AMBER] Regarding restarting from RST files using pmemd.cuda (Mon Aug 19 2019 - 03:53:03 PDT)
Mohammad Salem
- Re: [AMBER] error with CPPTRAj (Fri Aug 16 2019 - 04:25:01 PDT)
- [AMBER] error with CPPTRAj (Fri Aug 16 2019 - 03:44:50 PDT)
Nathan Guerin
- Re: [AMBER] Bug in ambpdb in anaconda distribution? (Fri Aug 30 2019 - 10:58:25 PDT)
- Re: [AMBER] Bug in ambpdb in anaconda distribution? (Fri Aug 30 2019 - 10:42:22 PDT)
- [AMBER] Bug in ambpdb in anaconda distribution? (Fri Aug 30 2019 - 10:27:17 PDT)
Nisha Amarnath Jonniya
- [AMBER] per residue decompose energy error (Thu Aug 29 2019 - 02:07:09 PDT)
Nora Kremer
- [AMBER] Graphene residue name Tleap (Mon Aug 19 2019 - 01:03:12 PDT)
Parviz Seifpanahi Shabane
- [AMBER] Segmentation Fault (Wed Aug 14 2019 - 13:53:15 PDT)
- [AMBER] DNA force field. (Fri Aug 09 2019 - 09:54:06 PDT)
- [AMBER] T-leap "does not have a type" (Fri Aug 09 2019 - 09:47:14 PDT)
- [AMBER] T-leap. (Tue Aug 06 2019 - 07:01:25 PDT)
Pavlína Pokorná
- Re: [AMBER] Question about DFTB3 method with dispersion correction (Mon Aug 12 2019 - 07:43:40 PDT)
Pengfei Li
- Re: [AMBER] 答复: probelm -- QMMM-MD with ZN（Znic atom）in QM region (Mon Aug 26 2019 - 14:55:58 PDT)
- Re: [AMBER] 答复: probelm -- QMMM-MD with ZN（Znic atom）in QM region (Tue Aug 20 2019 - 12:28:59 PDT)
- Re: [AMBER] probelm -- QMMM-MD with ZN（Znic atom）in QM region (Fri Aug 16 2019 - 20:12:00 PDT)
- Re: [AMBER] Force field for Cecl3, Lacl3 and Prcl3 (Wed Aug 14 2019 - 19:15:07 PDT)
- Re: [AMBER] modelling of a penta coordination around zinc ion (+2) using MCPB.py (Wed Aug 07 2019 - 19:56:47 PDT)
- Re: [AMBER] MCPB.py showing error in the step: MCPB.py -i 1OKL.in -s 2 (Wed Aug 07 2019 - 19:49:23 PDT)
Pete Biggs
- Re: [AMBER] $AMBERHOME vs $AMBER_PREFIX (Tue Aug 06 2019 - 08:40:59 PDT)
- [AMBER] $AMBERHOME vs $AMBER_PREFIX (Tue Aug 06 2019 - 01:23:19 PDT)
Prajwal Nandekar
- Re: [AMBER] How to calculate the tilt angle of TM helix (Fri Aug 09 2019 - 21:56:17 PDT)
Pratul Agarwal
- Re: [AMBER] sander engine problem (Mon Aug 12 2019 - 07:28:24 PDT)
Quynh N. Vo
- [AMBER] How does PMEMD handle duplicates in GROUP? (Mon Aug 19 2019 - 12:04:01 PDT)
Quynh Vo
- [AMBER] mismatch between parm files from CHARMM-GUI and chamber (Fri Aug 16 2019 - 17:13:52 PDT)
Rajarshi Roy
- Re: [AMBER] Glycolipid Simulation (Tue Aug 27 2019 - 04:27:46 PDT)
- [AMBER] Glycolipid Simulation (Fri Aug 23 2019 - 05:07:40 PDT)
Rajiv
- [AMBER] Question about DFTB3 method with dispersion correction (Sun Aug 11 2019 - 09:55:33 PDT)
Ray Luo
- Re: [AMBER] MMPBSA using amberTools19 (Sun Aug 18 2019 - 07:10:58 PDT)
- Re: [AMBER] Error in MMPBSA calculation (Sun Aug 18 2019 - 07:08:27 PDT)
- Re: [AMBER] Error in MMPBSA calculation (Fri Aug 16 2019 - 02:27:20 PDT)
RAY LUO, Ph.D.
- Re: [AMBER] Error in MMPBSA calculation (Fri Aug 16 2019 - 13:29:34 PDT)
rluo.uci.edu
- Re: [AMBER] Error in MMPBSA calculation (Sat Aug 17 2019 - 06:21:04 PDT)
- Re: [AMBER] error during the calculation of MMPBSA (Tue Aug 06 2019 - 06:50:54 PDT)
Robin Betz
- Re: [AMBER] using accelerated MD on membrane proteins? (Wed Aug 28 2019 - 10:39:36 PDT)
Rosellen, Martin
- [AMBER] atom numbering in cpptraj and pytraj (Mon Aug 12 2019 - 07:38:29 PDT)
Ross Walker
- Re: [AMBER] Error searching for compatible GPU in Amber18 (Mon Aug 19 2019 - 19:59:54 PDT)
Roy Ashworth
- Re: [AMBER] Installing Amber parallel option (Thu Aug 15 2019 - 07:45:27 PDT)
- [AMBER] Installing Amber parallel option (Thu Aug 15 2019 - 04:00:40 PDT)
Rui Chen
- Re: [AMBER] PDB file carbohydrates naming problem (Sat Aug 31 2019 - 09:59:27 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem (Fri Aug 30 2019 - 14:37:52 PDT)
- Re: [AMBER] periodic box size (Fri Aug 30 2019 - 08:42:13 PDT)
- [AMBER] periodic box size (Thu Aug 29 2019 - 17:58:54 PDT)
- [AMBER] question about bond command in tleap (Wed Aug 28 2019 - 13:47:11 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem (Mon Aug 26 2019 - 12:23:20 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem (Fri Aug 23 2019 - 21:53:24 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem (Fri Aug 23 2019 - 21:44:51 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem (Thu Aug 22 2019 - 19:21:03 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem (Thu Aug 22 2019 - 08:45:11 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem (Wed Aug 21 2019 - 19:17:53 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem (Wed Aug 21 2019 - 16:02:22 PDT)
- Re: [AMBER] Glycan naming problem (Wed Aug 21 2019 - 12:51:37 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem (Tue Aug 20 2019 - 21:32:14 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem (Tue Aug 20 2019 - 20:49:26 PDT)
- [AMBER] PDB file carbohydrates naming problem (Tue Aug 20 2019 - 20:43:45 PDT)
- [AMBER] sander engine problem (Mon Aug 12 2019 - 07:24:43 PDT)
Ryoichi Utsumi
- [AMBER] Installaiton of pmemd for Amber16 (Sat Aug 10 2019 - 04:18:40 PDT)
Sadaf Rani
- [AMBER] equilirbration at constant volume (Fri Aug 30 2019 - 07:48:24 PDT)
- [AMBER] building amber 16 parallel with MPI (Tue Aug 27 2019 - 09:57:42 PDT)
- Re: [AMBER] vlimit exceeded for step (Wed Aug 21 2019 - 02:02:36 PDT)
- [AMBER] vlimit exceeded for step (Tue Aug 20 2019 - 15:54:12 PDT)
Saikat Pal
- [AMBER] NH-pi interaction using ff14SB forcefield (Tue Aug 13 2019 - 04:44:50 PDT)
Seketoulie Keretsu
- [AMBER] Amberff99sb topology for phosphorylated tyrosine residue in GROMACS (Tue Aug 20 2019 - 02:22:09 PDT)
Shayna Hilburg
- Re: [AMBER] volume in pytraj? (Mon Aug 19 2019 - 06:51:13 PDT)
- Re: [AMBER] volume in pytraj? (Sun Aug 18 2019 - 18:03:44 PDT)
- [AMBER] volume in pytraj? (Fri Aug 16 2019 - 14:56:12 PDT)
Shirin Jamshidi
- Re: [AMBER] evec.pev file in essential dynamics analysis (Thu Aug 29 2019 - 08:14:44 PDT)
- Re: [AMBER] evec.pev file in essential dynamics analysis (Thu Aug 29 2019 - 03:24:49 PDT)
- [AMBER] Fwd: evec.pev file in essential dynamics analysis (Tue Aug 27 2019 - 08:39:24 PDT)
shivangi agarwal
- [AMBER] H - bond calculations (Fri Aug 30 2019 - 10:20:31 PDT)
- [AMBER] Not able to load Amber trajectories in VMD (Tue Aug 20 2019 - 09:50:35 PDT)
- [AMBER] MMPBSA using amberTools19 (Sun Aug 18 2019 - 00:39:28 PDT)
- Re: [AMBER] Error in MMPBSA calculation (Fri Aug 16 2019 - 05:40:39 PDT)
- Re: [AMBER] Error in MMPBSA calculation (Fri Aug 16 2019 - 04:52:13 PDT)
- [AMBER] Error in MMPBSA calculation (Fri Aug 16 2019 - 01:14:43 PDT)
- [AMBER] Error iin running mmpbsa (Sat Aug 10 2019 - 09:36:39 PDT)
Song, Lin
- [AMBER] Print non bonded pair list (Fri Aug 30 2019 - 09:39:54 PDT)
- Re: [AMBER] gaff2 parameters of c3-c3-os-c3 (Fri Aug 09 2019 - 08:30:28 PDT)
- Re: [AMBER] gaff2 parameters of c3-c3-os-c3 (Mon Aug 05 2019 - 12:51:36 PDT)
Stephan Schott
- Re: [AMBER] How to calculate the tilt angle of TM helix (Mon Aug 12 2019 - 03:37:26 PDT)
Sunita Patel
- Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 (Wed Aug 21 2019 - 04:52:06 PDT)
- Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 (Wed Aug 21 2019 - 01:20:21 PDT)
- Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 (Tue Aug 20 2019 - 22:41:08 PDT)
- Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 (Tue Aug 20 2019 - 22:26:41 PDT)
- Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 (Mon Aug 19 2019 - 22:54:23 PDT)
- [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 (Mon Aug 19 2019 - 22:41:59 PDT)
- Re: [AMBER] problems with Miniconda installation (Fri Aug 09 2019 - 04:44:39 PDT)
- Re: [AMBER] problems with Miniconda installation (Fri Aug 09 2019 - 01:52:59 PDT)
- Re: [AMBER] problems with Miniconda installation (Thu Aug 08 2019 - 23:43:27 PDT)
Supriyo Bhattacharya
- Re: [AMBER] Question about running MMPBSA.py with a mask to exclude certain residues (Fri Aug 23 2019 - 11:07:03 PDT)
Thomas Gaillard
- Re: [AMBER] error during the calculation of MMPBSA (Wed Aug 07 2019 - 02:30:47 PDT)
Tom Kurtzman
- Re: [AMBER] Simulations without PME (Tue Aug 06 2019 - 09:03:27 PDT)
- [AMBER] Simulations without PME (Mon Aug 05 2019 - 12:45:49 PDT)
Tyler Luchko (Lists)
- Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues (Fri Aug 16 2019 - 16:54:35 PDT)
viktor drobot
- Re: [AMBER] Bug in ambpdb in anaconda distribution? (Fri Aug 30 2019 - 11:13:29 PDT)
- Re: [AMBER] Bug in ambpdb in anaconda distribution? (Fri Aug 30 2019 - 10:36:38 PDT)
- Re: [AMBER] Combining sevaral frcmods into single file (Tue Aug 27 2019 - 08:31:58 PDT)
- [AMBER] Combining sevaral frcmods into single file (Tue Aug 27 2019 - 07:16:13 PDT)
- [AMBER] mdgx, improper terms and multifit (Thu Aug 22 2019 - 10:23:06 PDT)
- Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues (Sat Aug 17 2019 - 06:29:57 PDT)
- Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues (Sat Aug 17 2019 - 03:29:38 PDT)
- Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues (Fri Aug 16 2019 - 06:57:58 PDT)
- Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues (Thu Aug 15 2019 - 07:26:49 PDT)
- [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues (Tue Aug 13 2019 - 13:28:50 PDT)
Vivek Junghare
- [AMBER] Amber installation error (Mon Aug 19 2019 - 00:57:09 PDT)
YOGESH NARKHEDE
- [AMBER] MM-PBSA Alanine scanning issue (Fri Aug 09 2019 - 10:44:00 PDT)
- [AMBER] Alanine scan issue (Tue Aug 06 2019 - 10:59:51 PDT)
东庚
- [AMBER] 答复: probelm -- QMMM-MD with ZN（Znic atom）in QM region (Mon Aug 19 2019 - 01:51:21 PDT)
- [AMBER] 答复: probelm -- QMMM-MD with ZN（Znic atom）in QM region (Sat Aug 17 2019 - 19:20:03 PDT)
- [AMBER] probelm -- QMMM-MD with ZN（Znic atom）in QM region (Fri Aug 16 2019 - 19:10:11 PDT)
- [AMBER] probelm -- QMMM-MD with ZN（Znic atom）in QM region (Wed Aug 14 2019 - 23:20:20 PDT)
辛志宏
- [AMBER] Problem for the frcmod file from the amber tutorial (Tue Aug 13 2019 - 09:14:27 PDT)

Amber Archive Aug 2019 by author