Amber Archive Jul 2020 by thread
- [AMBER] Caping error mohamed marzouk (Tue Jun 30 2020 - 21:38:15 PDT)
- Re: [AMBER] Error in Installing Amber 20 on GPU Suchetana Gupta (Tue Jun 30 2020 - 22:28:23 PDT)
- [AMBER] MBAR with Amber 18 Ulf Ryde (Wed Jul 01 2020 - 03:25:00 PDT)
- [AMBER] how to create nice animated videos to show simulations Chetna Tyagi (Wed Jul 01 2020 - 03:31:34 PDT)
- Re: [AMBER] bulding a monosaccharide with N-acetylation Lachele Foley (Wed Jul 01 2020 - 04:55:06 PDT)
- Re: [AMBER] Hoogsteen H-bond Jisha B (Wed Jul 01 2020 - 08:18:10 PDT)
- Re: [AMBER] "Does not have a type" error in tleap David A Case (Wed Jul 01 2020 - 08:43:20 PDT)
- Re: [AMBER] Amber installation error ankita mehta (Wed Jul 01 2020 - 11:10:40 PDT)
- [AMBER] Amber20 installation Kliuchnikov, Evgenii (Wed Jul 01 2020 - 11:16:21 PDT)
- [AMBER] How to set salt concentration Nada Afiva (Wed Jul 01 2020 - 20:54:44 PDT)
- [AMBER] Amber 20 on Google Colab Suchetana Gupta (Wed Jul 01 2020 - 22:54:07 PDT)
- [AMBER] calculating methane parameters using RISM angad sharma (Thu Jul 02 2020 - 01:31:03 PDT)
- [AMBER] how to use triclinic box shape Nada Afiva (Thu Jul 02 2020 - 01:47:46 PDT)
- [AMBER] Problem of Steered MD Simulation for unfolding of RNA Vishal Singh (Thu Jul 02 2020 - 04:46:22 PDT)
- [AMBER] Installing Amber20 with cuda9 Schröder, David Christopher (Thu Jul 02 2020 - 06:58:38 PDT)
- [AMBER] Usage of the Density Peaks Algorithm. Gilberto Pereira (Thu Jul 02 2020 - 08:34:50 PDT)
- [AMBER] Defining new atoms in AMBER Kolattukudy P. Santo (Thu Jul 02 2020 - 08:47:00 PDT)
- [AMBER] Fortran error in constant pH MD Paul Meister (Thu Jul 02 2020 - 09:28:56 PDT)
- [AMBER] LJ potential for OPC water model Loki (Fri Jul 03 2020 - 05:07:04 PDT)
- [AMBER] Error while running Antechamber Shreeramesh (Fri Jul 03 2020 - 11:02:15 PDT)
- [AMBER] The most update force fields for DNA and RNA Nada Afiva (Fri Jul 03 2020 - 14:30:27 PDT)
- [AMBER] Solvent excluded volume Shilpa Gupta (Sat Jul 04 2020 - 03:21:31 PDT)
- [AMBER] generating methane parameters for rism angad sharma (Sat Jul 04 2020 - 05:22:17 PDT)
- [AMBER] Error in partial MINIMIZATION STEP Shreeramesh (Sat Jul 04 2020 - 09:39:01 PDT)
- [AMBER] MMGBSA and MMPBSA error (CalcError: failed with prmtop file complex.prmtop!) Nada Afiva (Sat Jul 04 2020 - 14:58:44 PDT)
- [AMBER] generating parameters of methane for RISM angad sharma (Sun Jul 05 2020 - 04:25:07 PDT)
- [AMBER] Using ntt=10 in PMEMD Sharif Nada (Mon Jul 06 2020 - 03:29:40 PDT)
- [AMBER] Question about SMD using polymer Pinky Mazumder (Mon Jul 06 2020 - 08:01:38 PDT)
- [AMBER] FW: restraint 10 kcal/mol Debarati DasGupta (Mon Jul 06 2020 - 08:16:07 PDT)
- [AMBER] Barostat and thermostat for membrane protein-ligand simulation ANDREA PASQUADIBISCEGLIE (Mon Jul 06 2020 - 08:49:36 PDT)
- [AMBER] Strip water job is killed after 10-40% completion Shreeramesh (Mon Jul 06 2020 - 09:23:26 PDT)
- [AMBER] Force Trajectory Output ABMD Jonathon Ferrell (Mon Jul 06 2020 - 09:56:24 PDT)
- [AMBER] Accounting for PBC in Density Plots An Ta (Mon Jul 06 2020 - 10:44:06 PDT)
- [AMBER] Install broke and compilation fails Gustaf Olsson (Tue Jul 07 2020 - 06:58:10 PDT)
- [AMBER] Amber prmtop and inpcrd of complex file with a water molecular cutoff 辛志宏 (Tue Jul 07 2020 - 07:54:04 PDT)
- [AMBER] Atomic Polarizability Thakur, Abhishek (Tue Jul 07 2020 - 09:58:48 PDT)
- [AMBER] fixatomorder Thakur, Abhishek (Tue Jul 07 2020 - 10:38:56 PDT)
- [AMBER] Asking for help: cross linking polymer SAKO MIRZAIE (Tue Jul 07 2020 - 17:28:10 PDT)
- [AMBER] amber14 gpu installation failed Carlos (Tue Jul 07 2020 - 20:42:57 PDT)
- [AMBER] Accelerated Molecular Dynamics and convergence Rosellen, Martin (Wed Jul 08 2020 - 06:58:20 PDT)
- [AMBER] Error in SMD running PRITI ROY (Wed Jul 08 2020 - 19:05:50 PDT)
- [AMBER] Amber prmtop and inpcrd of complex file with a water molecular cutoff 辛志宏 (Wed Jul 08 2020 - 21:11:32 PDT)
- [AMBER] Problem with running Python script in AMBER environment. Vishal Singh (Wed Jul 08 2020 - 23:51:52 PDT)
- [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Thirakorn Mokkawes (Thu Jul 09 2020 - 03:59:16 PDT)
- [AMBER] Forcefield for 5' phosphate in RNA dnlfr1994.gmail.com (Thu Jul 09 2020 - 05:01:36 PDT)
- [AMBER] GPU compatible with AMBER Isabelle Navizet (Thu Jul 09 2020 - 05:34:06 PDT)
- [AMBER] Error pmemd.cuda amber 20 GPU Camila Clemente (Thu Jul 09 2020 - 07:11:29 PDT)
- [AMBER] attach pull release method exploration for free energy calculations Debarati DasGupta (Thu Jul 09 2020 - 12:40:32 PDT)
- [AMBER] Mask behavior vs distance measurement? Kenneth Huang (Thu Jul 09 2020 - 17:04:10 PDT)
- Re: [AMBER] nmropt vs infe Feng Pan (Thu Jul 09 2020 - 22:01:21 PDT)
- [AMBER] REPEATED LINMIN FAILURE Akshay Prabhakant (Fri Jul 10 2020 - 04:20:12 PDT)
- [AMBER] About time-dependent positional restraints David Sáez (Fri Jul 10 2020 - 18:37:45 PDT)
- [AMBER] Reg. MMGBSA Calculations DHEERAJ CHITARA (Sat Jul 11 2020 - 11:26:52 PDT)
- [AMBER] Seg fault with pmemd.cuda.MPI using plumed Jacob Remington (Sat Jul 11 2020 - 12:16:54 PDT)
- [AMBER] Amber vs Namd energy values are different. Vishal Reddy (Sun Jul 12 2020 - 14:24:50 PDT)
- [AMBER] Problems with MC barostat Yessica (Sun Jul 12 2020 - 16:53:08 PDT)
- [AMBER] Using multiple distance restraints or creating exclusion sphere Amanda Buyan (Sun Jul 12 2020 - 18:20:16 PDT)
- [AMBER] XMGRACE giving error Sumra Abbasi (Mon Jul 13 2020 - 03:07:36 PDT)
- [AMBER] Default temperature regulation during production run: Missed to declare ntt option Jorden Cabal (Tue Jul 14 2020 - 04:26:02 PDT)
- [AMBER] EAMD_BOOST and reweighting of AMD runs Rosellen, Martin (Tue Jul 14 2020 - 08:00:51 PDT)
- [AMBER] Clarification of Amber Post on Heating Protocol Robert Molt (Tue Jul 14 2020 - 14:46:25 PDT)
- [AMBER] SPLIT method doubt Camila Clemente (Tue Jul 14 2020 - 15:01:49 PDT)
- [AMBER] Command for making atoms rigid Pinky Mazumder (Tue Jul 14 2020 - 15:55:40 PDT)
- Re: [AMBER] CPPTRAJ: Time Correlation Function (TCF) emanuele falbo (Wed Jul 15 2020 - 07:29:40 PDT)
- [AMBER] Questions on random seed Nada Afiva (Wed Jul 15 2020 - 20:35:37 PDT)
- [AMBER] matching paramters of methane angad sharma (Thu Jul 16 2020 - 08:27:44 PDT)
- [AMBER] OT: Job Posting Lachele Foley (Thu Jul 16 2020 - 16:40:13 PDT)
- [AMBER] mmpbsa error MYRIAN TORRES RICO (Fri Jul 17 2020 - 04:31:13 PDT)
- [AMBER] Several tutorial not found Michael F. Bruist (Fri Jul 17 2020 - 08:19:56 PDT)
- [AMBER] Reonstructing frames from PCA projection Michael F. Bruist (Fri Jul 17 2020 - 08:24:03 PDT)
- [AMBER] Tinker_to_amber problem Kliuchnikov, Evgenii (Fri Jul 17 2020 - 12:50:01 PDT)
- [AMBER] Amber20: Error in the linking of the pysander Wim R. Cardoen (Fri Jul 17 2020 - 13:54:04 PDT)
- Re: [AMBER] Cores, CPU RAM, GPU RAM James Kress (Fri Jul 17 2020 - 15:28:37 PDT)
- [AMBER] Error in incprd file while performing steered molecular dynamics simulation Pinky Mazumder (Sat Jul 18 2020 - 00:09:30 PDT)
- [AMBER] Modified cysteine parameters krishnendu sinha (Sun Jul 19 2020 - 00:49:40 PDT)
- [AMBER] Units from quasiharmonic analysis of Principal Components German P. Barletta (Sun Jul 19 2020 - 09:48:38 PDT)
- [AMBER] Amber SHAKE error when running REMD 변진영 (Sun Jul 19 2020 - 23:56:58 PDT)
- [AMBER] What would you like to see in visualization of chemical data? Jan Mičan (Mon Jul 20 2020 - 03:48:06 PDT)
- [AMBER] ABMD with RMSD and RoG: ** NFE-Error ** : Cannot read &colvar namelist! Diego Morone (Mon Jul 20 2020 - 06:37:31 PDT)
- [AMBER] libnetcdf.so.7 needed by /usr/local/src/amber18/lib/libcpptraj.so, not found when upgrading AT18 to AT19 Markowska (Mon Jul 20 2020 - 06:56:26 PDT)
- [AMBER] error in 3d rism calculation angad sharma (Mon Jul 20 2020 - 10:27:05 PDT)
- Re: [AMBER] Missing bond parameters after MCPB.py Pengfei Li (Mon Jul 20 2020 - 12:17:50 PDT)
- [AMBER] amber website down? Wim R. Cardoen (Mon Jul 20 2020 - 14:07:08 PDT)
- [AMBER] fatal error in 3D RISM calculation angad sharma (Tue Jul 21 2020 - 01:57:07 PDT)
- Re: [AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming Tim Travers (Tue Jul 21 2020 - 08:17:07 PDT)
- [AMBER] AMBER20 Error: No package metadata was found for pdb4amber Huang Tao (Tue Jul 21 2020 - 19:39:21 PDT)
- [AMBER] Undefined angle parameter and torsion terms in Antechamber Razil Tahir (Tue Jul 21 2020 - 21:03:20 PDT)
- [AMBER] problem with pdb4amber David A Case (Wed Jul 22 2020 - 07:59:02 PDT)
- [AMBER] Size of Solvent Box DHEERAJ CHITARA (Wed Jul 22 2020 - 11:14:20 PDT)
- [AMBER] tinker_to_amber force fields Kliuchnikov, Evgenii (Wed Jul 22 2020 - 11:37:33 PDT)
- [AMBER] Amber 20 - Support Multi GPU Adriano José Ferruzzi (Wed Jul 22 2020 - 12:31:29 PDT)
- [AMBER] tleap does not recognize nonstandard residue from lib file JoAnne Babula (Wed Jul 22 2020 - 12:43:59 PDT)
- [AMBER] Problem compiling Amber20 - undefined reference to 'plumedmain_create' Amanda Buyan (Wed Jul 22 2020 - 23:07:39 PDT)
- [AMBER] Download link for AmberTools17 Casalini Tommaso (Thu Jul 23 2020 - 01:44:20 PDT)
- [AMBER] AMBER trajectory analysis in MINT package Jisha B (Thu Jul 23 2020 - 05:40:18 PDT)
- [AMBER] smooth soft core potentials Debarati DasGupta (Thu Jul 23 2020 - 13:26:32 PDT)
- [AMBER] Using Orca to develop RESP Charges Lucas Bandeira (Thu Jul 23 2020 - 13:37:56 PDT)
- [AMBER] carboxylated Lys Állan Ferrari (Thu Jul 23 2020 - 14:30:32 PDT)
- [AMBER] Issue while installing Amber20 Alejandro Cagnoni (Fri Jul 24 2020 - 13:44:29 PDT)
- [AMBER] Error in Gausian file preparation using MCPB.py gagandeep singh (Fri Jul 24 2020 - 14:55:47 PDT)
- [AMBER] Steered molecular dynamics Simulation Pinky Mazumder (Fri Jul 24 2020 - 19:47:39 PDT)
- Re: [AMBER] steered MD with restraints on a selection Pinky Mazumder (Fri Jul 24 2020 - 19:51:46 PDT)
- [AMBER] How to calculate velocity in steered simulation Pinky Mazumder (Fri Jul 24 2020 - 20:58:05 PDT)
- [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol venkat (Sat Jul 25 2020 - 05:02:26 PDT)
- [AMBER] How to install Amber20 with pmemd.amoeba? Kliuchnikov, Evgenii (Sat Jul 25 2020 - 12:29:56 PDT)
- [AMBER] Maximum system size Jack Shepherd (Sat Jul 25 2020 - 17:57:01 PDT)
- [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." 辛志宏 (Sun Jul 26 2020 - 04:59:21 PDT)
- [AMBER] Amber20 Compiling problem with b2 and Boost.Regex Amanda Buyan (Sun Jul 26 2020 - 18:35:07 PDT)
- [AMBER] Charges for modified DNA base at the termini? Kenneth Huang (Sun Jul 26 2020 - 23:50:39 PDT)
- [AMBER] Error building Amber Walton Smith (Mon Jul 27 2020 - 07:04:33 PDT)
- [AMBER] Problems generating charges with RESP Lucas Bandeira (Mon Jul 27 2020 - 13:39:01 PDT)
- [AMBER] Problem installing AmberMD with MPI support on Cray XC40 Jakub Jalowiec (Mon Jul 27 2020 - 15:27:13 PDT)
- [AMBER] Problems deriving charges with RESP Lucas Bandeira (Mon Jul 27 2020 - 17:23:52 PDT)
- [AMBER] ASMD equil4 not producing output files Hantz, Eric R. (Tue Jul 28 2020 - 06:51:23 PDT)
- [AMBER] Tracking lifetime distance by closest of specific water IDs? Kenneth Huang (Tue Jul 28 2020 - 07:28:51 PDT)
- Re: [AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Tue Jul 28 2020 - 08:48:49 PDT)
- [AMBER] Issue heating system in equilibration step Samuel A. Ratliff (Tue Jul 28 2020 - 10:05:00 PDT)
- [AMBER] AMD parameter: protein residue should count ligand or not Lod King (Tue Jul 28 2020 - 10:55:43 PDT)
- [AMBER] 6. Re: Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." (???) 辛志宏 (Wed Jul 29 2020 - 02:10:13 PDT)
- [AMBER] Refitting charges with MCPB destabilizes the active site Casalini Tommaso (Wed Jul 29 2020 - 04:23:44 PDT)
- [AMBER] Adding ions to implicit solvent models Conrad F Li (Wed Jul 29 2020 - 18:17:34 PDT)
- [AMBER] Erro Amber18 GPU Renato Araujo (Thu Jul 30 2020 - 12:55:42 PDT)
- Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." 辛志宏 (Thu Jul 30 2020 - 20:46:21 PDT)
- [AMBER] How to make pass extra argument "--bind-to none" to mpirun for ORCA when running QMMM from sander? Francesca Lønstad Bleken (Fri Jul 31 2020 - 02:42:32 PDT)
- [AMBER] Amber nc trajectory file analysis by x3dna Jenny 148 (Fri Jul 31 2020 - 08:05:56 PDT)
- [AMBER] amber trajectory nc file to pdb ensemble Athena N (Fri Jul 31 2020 - 09:28:26 PDT)
- [AMBER] Structure Artifact After Autoimage Mikhael, Simoun (Fri Jul 31 2020 - 14:01:52 PDT)
- Last message date: Fri Jul 31 2020 - 14:30:04 PDT
- Archived on: Fri Dec 20 2024 - 05:56:01 PST
