Amber Archive Oct 2018 by thread
- [AMBER] Regarding calculation of RMSD DHEERAJ CHITARA (Mon Oct 01 2018 - 05:38:49 PDT)
- [AMBER] Query regarding Amber installation Rakesh Srivastava (Mon Oct 01 2018 - 05:49:29 PDT)
- [AMBER] Water Density Seibold, Steve Allan (Mon Oct 01 2018 - 12:03:00 PDT)
- [AMBER] Total system charge and TI simulations Veenis, Andrew Jay (Mon Oct 01 2018 - 12:29:05 PDT)
- [AMBER] ligand_preparation_general_rule Antonio Amber Carlesso (Tue Oct 02 2018 - 00:31:14 PDT)
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphälinger (Tue Oct 02 2018 - 02:33:18 PDT)
- [AMBER] add12_6_4 Parmed error Nikolay N. Kuzmich (Tue Oct 02 2018 - 10:06:28 PDT)
- Re: [AMBER] Reducing memory usage in lifetime analyses Daniel Roe (Tue Oct 02 2018 - 11:20:34 PDT)
- [AMBER] NFE _Lib error Hugo Macdermott-Opeskin (Tue Oct 02 2018 - 17:19:16 PDT)
- [AMBER] Number of inter-conversions between minima on a FEL Chetna Tyagi (Wed Oct 03 2018 - 04:59:35 PDT)
- [AMBER] AMBER18 compilation using intel compiler pavel.banas.upol.cz (Wed Oct 03 2018 - 06:13:47 PDT)
- [AMBER] get energy of some residues of the molecule Johannes Kalliauer (Wed Oct 03 2018 - 07:13:44 PDT)
- [AMBER] Cpptraj bond deforming Aashish Bhatt (Wed Oct 03 2018 - 07:52:42 PDT)
- [AMBER] Part of protein going out of the box Leena Aggarwal (Wed Oct 03 2018 - 07:57:32 PDT)
- Re: [AMBER] Problems with MPI compilation gb_force.F90 Ruben Ramos Horta (Wed Oct 03 2018 - 10:10:58 PDT)
- Re: [AMBER] pmemd.MPI won't work in Amber 18 Hai Long (Wed Oct 03 2018 - 19:57:17 PDT)
- [AMBER] Problem in saving amber prmtop file from DNA pdb file creacted using server http://structure.usc.edu/make-na/server.html) ? Subrata Paul (Thu Oct 04 2018 - 00:37:08 PDT)
- [AMBER] Amber 18 installation problem MR. RABINDRANATH PAUL (Thu Oct 04 2018 - 00:44:25 PDT)
- [AMBER] How to run the test in HPC cluster and GPU Saikat Pal (Thu Oct 04 2018 - 04:15:53 PDT)
- [AMBER] Amber to gromacs topology Saikat Pal (Thu Oct 04 2018 - 04:37:46 PDT)
- [AMBER] FW: Problem running the adqmmm test, one mdcrd file only Dreab, Ana (Thu Oct 04 2018 - 06:17:30 PDT)
- Re: [AMBER] R.E.D. Server is down Stéphane Téletchéa (Thu Oct 04 2018 - 07:43:25 PDT)
- [AMBER] Setting up parameters for a simulation at 350K Dmitry Suplatov (Thu Oct 04 2018 - 08:39:51 PDT)
- [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Ross Walker (Fri Oct 05 2018 - 05:32:07 PDT)
- [AMBER] number of reaction coordinate in a ASMD run sangita kachhap (Fri Oct 05 2018 - 06:14:38 PDT)
- [AMBER] questions on pmemd.cuda for thermodynamic integration Song-Ho Chong (Fri Oct 05 2018 - 08:06:49 PDT)
- [AMBER] acpype_error Antonio Amber Carlesso (Fri Oct 05 2018 - 11:11:06 PDT)
- [AMBER] Warning for MMPBSA.py calculation maryam azimzadehirani (Sat Oct 06 2018 - 00:01:19 PDT)
- Re: [AMBER] Problem with antechamber/acdoctor David Case (Sat Oct 06 2018 - 05:54:35 PDT)
- [AMBER] Lipid Order Parameters somdev pahari (Sat Oct 06 2018 - 08:03:48 PDT)
- [AMBER] Amber Install on Mojave (ld: library not found for -lmc) Fix Andrew Schaub (Sun Oct 07 2018 - 17:02:03 PDT)
- [AMBER] Testing C++11 support: Not present Gustaf Olsson (Mon Oct 08 2018 - 01:04:12 PDT)
- [AMBER] Parameters for atom CE in lj_1264_pol.dat Nikolay N. Kuzmich (Mon Oct 08 2018 - 02:20:52 PDT)
- [AMBER] Full: Parameters for atom CE in lj_1264_pol.dat Nikolay N. Kuzmich (Mon Oct 08 2018 - 02:29:17 PDT)
- [AMBER] Antechamber on unknown residue Keiran Corbett (Mon Oct 08 2018 - 03:44:25 PDT)
- [AMBER] GPU memory usage with center-of-mass restratints David Case (Mon Oct 08 2018 - 06:08:03 PDT)
- [AMBER] Restrain distance for Umbrella Sampling emanuele falbo (Mon Oct 08 2018 - 07:03:44 PDT)
- [AMBER] torsion angles of carbon allotropes Ibrahim Said (Mon Oct 08 2018 - 11:57:08 PDT)
- [AMBER] RTX 2080 Benchmarks Bisignano, Paola (Mon Oct 08 2018 - 13:05:14 PDT)
- [AMBER] constant pH pmemd.cuda error andreas.tosstorff.cup.uni-muenchen.de (Mon Oct 08 2018 - 13:20:30 PDT)
- [AMBER] Errors when installing with MPI Felipe Franco Gonzalez (Mon Oct 08 2018 - 13:49:03 PDT)
- [AMBER] Regarding Leap Charu Sharma (JRF) (Mon Oct 08 2018 - 21:33:15 PDT)
- [AMBER] Fwd: The results of your email commands Charu Sharma (JRF) (Mon Oct 08 2018 - 21:35:22 PDT)
- [AMBER] Rigid body simulation of Nitrogenase's FeMo cluster Sadra Aghajani (Tue Oct 09 2018 - 00:32:17 PDT)
- [AMBER] Selecting specific set of molecules for output trajectory anu chandra (Tue Oct 09 2018 - 04:29:36 PDT)
- [AMBER] viscosity calculation Lorenzo Gontrani (Tue Oct 09 2018 - 07:48:45 PDT)
- [AMBER] hydrogen bond analysis Qinghua Liao (Tue Oct 09 2018 - 16:03:44 PDT)
- [AMBER] Regarding calculation of RMSD using AMBER-18 CPPTRAJ V-18.01 DHEERAJ CHITARA (Tue Oct 09 2018 - 23:15:50 PDT)
- [AMBER] Unkown residue to AMBER Keiran Corbett (Wed Oct 10 2018 - 00:55:52 PDT)
- [AMBER] Striping distance based water residues Kshatresh Dutta Dubey (Wed Oct 10 2018 - 03:29:30 PDT)
- [AMBER] Cationic dummy Zinc atom in accelerated molecular dynamics M RCC (Wed Oct 10 2018 - 06:06:18 PDT)
- [AMBER] FW: Fatal error in RESP calculation fateme haghighi (Wed Oct 10 2018 - 06:52:52 PDT)
- [AMBER] Water do not see the system.... Vito GENNA (Wed Oct 10 2018 - 09:18:40 PDT)
- [AMBER] .gesp file is not generated for Antechamber M RCC (Wed Oct 10 2018 - 09:43:37 PDT)
- [AMBER] AMBER and plumed Pierre GIRARD (Wed Oct 10 2018 - 11:05:05 PDT)
- [AMBER] RTX2080 Performance Update for AMBER 18 Ross Walker (Wed Oct 10 2018 - 20:15:37 PDT)
- [AMBER] AMBER 18 INSTALLATION ON CLUSTER - ERROR Midhun K Madhu (Wed Oct 10 2018 - 22:32:49 PDT)
- [AMBER] error in RESP calculation fateme haghighi (Thu Oct 11 2018 - 00:36:23 PDT)
- [AMBER] RTX2080TI Performance Ross Walker (Thu Oct 11 2018 - 04:19:47 PDT)
- [AMBER] calculation of free binding energy when a residue is mutated to residues other than alanine? ali akbar (Thu Oct 11 2018 - 05:08:27 PDT)
- [AMBER] SIRAH 2.0: a finer taste in coarse-grained protiens Matias Machado (Thu Oct 11 2018 - 08:17:17 PDT)
- [AMBER] Installation issues on Mac OSX 10.14 Matthew Fisher (Thu Oct 11 2018 - 10:02:18 PDT)
- [AMBER] Commented AmberTools functions Ruben Ramos Horta (Thu Oct 11 2018 - 10:09:21 PDT)
- Re: [AMBER] AMBER Digest, Vol 2436, Issue 1 Midhun K Madhu (Fri Oct 12 2018 - 01:36:25 PDT)
- [AMBER] How to use ff99SB-ILDN in Amber16 Yang, Tianyi (Fri Oct 12 2018 - 14:26:13 PDT)
- [AMBER] Fondaparinux Amber Force Field Marcelo Andrade Chagas (Sun Oct 14 2018 - 07:31:42 PDT)
- [AMBER] GAMD not running in CPU cluster Midhun K Madhu (Mon Oct 15 2018 - 04:19:18 PDT)
- [AMBER] more on building Amber18 on Mojave David A Case (Mon Oct 15 2018 - 07:39:27 PDT)
- [AMBER] GLYCAM Amber Force Field to Fondaparinux...? Marcelo Andrade Chagas (Mon Oct 15 2018 - 13:24:14 PDT)
- Re: [AMBER] Using custom non-bonding potential, drude oscillator in Amber18 Kyeong-jun Jeong (Mon Oct 15 2018 - 15:46:22 PDT)
- [AMBER] Using custom non-bonding potential, drude oscillator in Amber18 Kyeong-jun Jeong (Tue Oct 16 2018 - 10:11:42 PDT)
- [AMBER] using parmed (python api) to merge two parm7 files for TI Wesley Michael Botello-Smith (Tue Oct 16 2018 - 13:35:33 PDT)
- [AMBER] does surf command use for stripped trajectory? g.bakrani.sci.ui.ac.ir (Wed Oct 17 2018 - 04:30:56 PDT)
- [AMBER] error in Resp fateme haghighi (Wed Oct 17 2018 - 05:33:22 PDT)
- [AMBER] Problem with tleap Ali Khodayari (Wed Oct 17 2018 - 11:05:01 PDT)
- [AMBER] sugar derivatives parametrization Bisignano, Paola (Wed Oct 17 2018 - 15:49:34 PDT)
- [AMBER] Parametarization error senal dinuka (Wed Oct 17 2018 - 21:34:09 PDT)
- [AMBER] Amber workshop in Europe? Albert (Wed Oct 17 2018 - 23:31:44 PDT)
- [AMBER] Question about stripping waters Maria Clelia Milletti (Thu Oct 18 2018 - 10:22:31 PDT)
- [AMBER] Alternative way to do targeted MD Xiaoling Leng (Thu Oct 18 2018 - 11:53:33 PDT)
- [AMBER] pi-pi And Aromatic Interactions Meng Wu (Thu Oct 18 2018 - 19:11:02 PDT)
- [AMBER] Constrained QM.MM minimization Vito GENNA (Fri Oct 19 2018 - 06:29:12 PDT)
- [AMBER] Amber force field for non-natural amino acids Mijiddorj B (Fri Oct 19 2018 - 21:53:42 PDT)
- [AMBER] tleap gamma-carboxyglutamic acid linkage error Rajbinder Kaur Virk (Sun Oct 21 2018 - 20:06:30 PDT)
- [AMBER] The make_na web service, and corresponding code David A Case (Mon Oct 22 2018 - 06:27:48 PDT)
- [AMBER] Error in Running tLEaP for Protein File Amartya Pradhan (Mon Oct 22 2018 - 11:30:00 PDT)
- [AMBER] Simulating a covalently bound ligand senal dinuka (Mon Oct 22 2018 - 21:48:53 PDT)
- [AMBER] Effective born radii calculations - No correct statistics returned at the end of the mdout file Eric Lang (Tue Oct 23 2018 - 08:28:16 PDT)
- [AMBER] Struggling to convert AMBER .frcmod and .mol2 to GROMACS for HEME Matthew Fisher (Tue Oct 23 2018 - 14:10:32 PDT)
- [AMBER] Material simulation using Amber and Interface FF Sundar (Tue Oct 23 2018 - 14:42:51 PDT)
- [AMBER] Topological error for Mg in .prepin file. Anuja Ware (Wed Oct 24 2018 - 06:22:55 PDT)
- [AMBER] Temperature-Replica Exchange MD Gilberto Pereira (Wed Oct 24 2018 - 07:26:32 PDT)
- [AMBER] MD_Box_size_and_counterions_counting_general_rule Antonio Amber Carlesso (Thu Oct 25 2018 - 04:54:55 PDT)
- [AMBER] Ca ion bond distances restraints with chelator ? Michael Shokhen (Thu Oct 25 2018 - 05:25:35 PDT)
- [AMBER] Measuring Membrane Curvature somdev pahari (Thu Oct 25 2018 - 11:31:05 PDT)
- [AMBER] Sander and Thermodynamic integration and softcore Khabiri, Morteza (Thu Oct 25 2018 - 12:07:24 PDT)
- [AMBER] Na+ ion got stuck at one C-terminal end Rakesh Srivastava (Thu Oct 25 2018 - 23:25:13 PDT)
- [AMBER] error in distance restraint input file Michael Shokhen (Fri Oct 26 2018 - 03:31:12 PDT)
- [AMBER] parmchk2 frcmod file Jon Uranga (Fri Oct 26 2018 - 03:36:12 PDT)
- [AMBER] Question Regarding GRID Saikat Pal (Fri Oct 26 2018 - 07:44:09 PDT)
- [AMBER] non-bonded params hosein geraili (Fri Oct 26 2018 - 09:30:36 PDT)
- [AMBER] Post-process calculation of atomic forces SARAH JEANNE LEFAVE (Fri Oct 26 2018 - 17:00:10 PDT)
- [AMBER] the unperturbed charge of the unit is not zero soukaina louerdi (Sat Oct 27 2018 - 16:17:49 PDT)
- [AMBER] Interplane angles using vector and vectormath in cpptraj Matthew Turner (Mon Oct 29 2018 - 15:35:09 PDT)
- [AMBER] AMBER18: user-defined reaction coordinate in umbrella sampling 李耀 (Tue Oct 30 2018 - 07:06:20 PDT)
- [AMBER] Fortran runtime error: Bad value during integer read Thomas Evangelidis (Tue Oct 30 2018 - 15:55:14 PDT)
- [AMBER] Amber Error (an illegal memory access) Avirup Ghosh (Tue Oct 30 2018 - 21:22:45 PDT)
- [AMBER] amber18 installation problem Mary Dutta (Wed Oct 31 2018 - 03:48:13 PDT)
- [AMBER] Problem regarding radial command Saikat Pal (Wed Oct 31 2018 - 05:01:13 PDT)
- [AMBER] CUDA 10.0 vs CUDA 9.2 for Amber18&1080Ti GTX - any gain in performance? Nikolay N. Kuzmich (Wed Oct 31 2018 - 07:31:56 PDT)
- Last message date: Wed Oct 31 2018 - 13:30:03 PDT
- Archived on: Fri Apr 19 2024 - 05:55:30 PDT
