Amber Archive Mar 2021 by thread
- Re: [AMBER] atom number difference in topology and simulated trajectory Ayesha Fatima (Sun Feb 28 2021 - 08:39:55 PST)
- [AMBER] Amber-forcefield for QM/MM calculation Rinsha Chk (Mon Mar 01 2021 - 05:05:28 PST)
- [AMBER] Superimpose mohamed marzouk (Mon Mar 01 2021 - 10:07:43 PST)
- [AMBER] Effect of different gamma_ln values Liao (Mon Mar 01 2021 - 12:29:29 PST)
- [AMBER] positional and NMR distance restraints together Qinghua Liao (Mon Mar 01 2021 - 17:15:31 PST)
- [AMBER] use orca in amber wangjianing_mail (Tue Mar 02 2021 - 01:37:05 PST)
- [AMBER] Free Energy Calculations using LIE and FEW Helena Damtoft Tjørnelund (Tue Mar 02 2021 - 02:21:27 PST)
- [AMBER] Using DFT-D3(BJ) during QM/MM calculations Zhiyi Wu (Tue Mar 02 2021 - 02:22:02 PST)
- [AMBER] How to plot the Phi-Psi picture in Section 7 of “Tutorial 6.6 Nudged Elastic Band (NEB) simulations”? Li Dailin (Tue Mar 02 2021 - 20:10:01 PST)
- [AMBER] MMPBSA/ Parmed error Jenny 148 (Tue Mar 02 2021 - 22:39:15 PST)
- [AMBER] Simulation of optimized ligand without docking Ramanathan Rajesh (Wed Mar 03 2021 - 04:19:38 PST)
- [AMBER] Practical questions on NMR-refinment Gustavo Seabra (Wed Mar 03 2021 - 12:33:51 PST)
- [AMBER] makeDIST_RST Ming Tang (Wed Mar 03 2021 - 21:04:27 PST)
- [AMBER] Problem Running E-REMD on GPUs Matthew Guberman-Pfeffer (Thu Mar 04 2021 - 19:13:20 PST)
- Re: [AMBER] gcc9 aishen.free.fr (Thu Mar 04 2021 - 23:05:50 PST)
- Re: [AMBER] Interaction energy by MM-PBSA for a superantigen with important Zn(II) center SATYAJIT KHATUA (Fri Mar 05 2021 - 02:53:07 PST)
- Re: [AMBER] Parametrization of Virtual sites in Halogens David Cerutti (Fri Mar 05 2021 - 07:28:51 PST)
- [AMBER] Pending deprecation of paramfit: Amber21 or Amber22? David Cerutti (Fri Mar 05 2021 - 08:01:22 PST)
- [AMBER] Ambertools20 with amber18 Pinky Mazumder (Fri Mar 05 2021 - 10:32:17 PST)
- [AMBER] How to define COM for groups in ASMD Matthew Guberman-Pfeffer (Sat Mar 06 2021 - 00:12:38 PST)
- [AMBER] Error when compiling AMBER20 fmying.xmu.edu.cn (Sun Mar 07 2021 - 22:38:32 PST)
- [AMBER] Is it possible to obtain vacuum charges (and only vacuum charges) with mdgx? Luis Simon (Mon Mar 08 2021 - 01:48:10 PST)
- [AMBER] The issue regarding to list index out of range 辛志宏 (Mon Mar 08 2021 - 04:12:03 PST)
- [AMBER] Generating library from cif file. sriram raghavan (Mon Mar 08 2021 - 07:24:10 PST)
- [AMBER] Single Point QM/MM energy using Amber-Q-Chem interface Bowleg, Jerrano (Mon Mar 08 2021 - 07:55:54 PST)
- [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler Samuel Mohan Dass, Premila (Mon Mar 08 2021 - 11:20:52 PST)
- Re: [AMBER] The issue regarding to list index out of range (???) 辛志宏 (Mon Mar 08 2021 - 16:07:57 PST)
- [AMBER] Pair interaction energy Eduardo R. Almeida (Tue Mar 09 2021 - 06:53:50 PST)
- [AMBER] Turning initial velocity off for continuous MD runs Aanshi Gandhi (Tue Mar 09 2021 - 09:35:24 PST)
- [AMBER] LJ parameters LOZANO ORDOÑEZ, HECTOR (Wed Mar 10 2021 - 08:59:33 PST)
- [AMBER] Problem with CG minimization in implicit solvent Alejandro Gil Ley (Wed Mar 10 2021 - 11:17:05 PST)
- [AMBER] pmemd.cuda unstable with ff19SB+OPC and HMassRepartition Tucker Burgin (Wed Mar 10 2021 - 11:25:22 PST)
- [AMBER] Secstruct error Kodituwakku,Dimuthu Nirmani (Wed Mar 10 2021 - 19:48:34 PST)
- [AMBER] sander/orca/xtb ：Low parallel efficiency wangjianing_mail (Wed Mar 10 2021 - 20:12:58 PST)
- [AMBER] GPU installation error amber18 Renato Araujo (Thu Mar 11 2021 - 04:53:14 PST)
- [AMBER] constant ph md Abhik Ghosh Moulick (Thu Mar 11 2021 - 08:00:46 PST)
- [AMBER] Why a target ion failed to move along the pathway in the simulated annealing version of Nudged Elastic Band (NEB) calculations? Li Dailin (Thu Mar 11 2021 - 17:55:57 PST)
- [AMBER] Error in tleap richa anand (Fri Mar 12 2021 - 02:04:28 PST)
- [AMBER] Tleap Fatal error richa anand (Fri Mar 12 2021 - 03:09:37 PST)
- [AMBER] Ligand moving out of active site after 250ns Sruthi Sudhakar (Fri Mar 12 2021 - 22:08:23 PST)
- Re: [AMBER] AMBER Digest, Vol 3300, Issue 1 richa anand (Sat Mar 13 2021 - 00:29:36 PST)
- [AMBER] Request for the sha256sum od amber20 Hector Martinez-Seara (Sat Mar 13 2021 - 02:43:07 PST)
- [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI Chuck is Busy (Sat Mar 13 2021 - 09:51:09 PST)
- [AMBER] AmberTools20 fails to compile with gcc10 (with workaround) Charo del Genio (Sat Mar 13 2021 - 12:06:20 PST)
- [AMBER] Energy minimization problem richa anand (Sun Mar 14 2021 - 00:15:39 PST)
- [AMBER] About the extract snapshop as input files from a trajectory files 辛志宏 (Sun Mar 14 2021 - 03:09:37 PDT)
- [AMBER] Installation Ambertools20 Mac M1 (arm64) Mailing list (Sun Mar 14 2021 - 05:59:40 PDT)
- [AMBER] x=sequence aishen.free.fr (Mon Mar 15 2021 - 00:30:05 PDT)
- [AMBER] hbond cpptraj Jon Uranga (Mon Mar 15 2021 - 06:47:17 PDT)
- [AMBER] MCPB.py ZINC Mediated interactions parameterization Rana Rehan Khalid (Mon Mar 15 2021 - 14:56:17 PDT)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules Ming Tang (Mon Mar 15 2021 - 16:28:21 PDT)
- [AMBER] Visualizing NetCDF in VMD - ERROR Jatin Kashyap (Mon Mar 15 2021 - 21:23:07 PDT)
- [AMBER] Missing atom types for ligand with chlorine atoms Aliakbartehrani Zahra (Tue Mar 16 2021 - 00:23:38 PDT)
- [AMBER] segmentation fault error richa anand (Tue Mar 16 2021 - 23:29:45 PDT)
- [AMBER] saving pdb and rst at specific frames in trajectory Sadaf Rani (Wed Mar 17 2021 - 06:23:17 PDT)
- [AMBER] Unit of Electric Field Frequency Shakir Ali Siddiqui (Thu Mar 18 2021 - 04:05:13 PDT)
- [AMBER] New In CPPTRAJ Daniel Roe (Thu Mar 18 2021 - 09:44:06 PDT)
- [AMBER] AMBER 18 Installation error Rituparna Roy (Fri Mar 19 2021 - 01:35:13 PDT)
- [AMBER] MMPBSA per residue decomposition - Calculation speed Jatin Kashyap (Fri Mar 19 2021 - 03:11:52 PDT)
- Re: [AMBER] New in CPPTRAJ Nikolay N. Kuzmich (Fri Mar 19 2021 - 12:35:57 PDT)
- [AMBER] How to assess mutant-induced instability with MM-GBSA Matthew Guberman-Pfeffer (Fri Mar 19 2021 - 13:49:37 PDT)
- [AMBER] Loading Topology & Trajectory Files Jatin Kashyap (Fri Mar 19 2021 - 14:24:41 PDT)
- [AMBER] Unknown PB option use_sav=0 Lennart Gundelach (Sat Mar 20 2021 - 01:07:50 PDT)
- [AMBER] Solvating my box with specified number of water molecules 库米尔 (Sat Mar 20 2021 - 09:20:21 PDT)
- [AMBER] SIRAH CG Protein with Implicit Solvent Leung, Jeremy (Sat Mar 20 2021 - 10:09:31 PDT)
- [AMBER] 3D-RISM solvent placement with MoFT He, Amy (Sun Mar 21 2021 - 19:10:45 PDT)
- [AMBER] cpptraj killed MYRIAN TORRES RICO (Mon Mar 22 2021 - 02:37:51 PDT)
- [AMBER] Pmemd to run TI on protein mutations zz sheng (Mon Mar 22 2021 - 11:00:27 PDT)
- [AMBER] Seeking suggestions for breaking a covalent link between atoms Amit Sharma (Asstt. Prof., MCARS) (Tue Mar 23 2021 - 01:54:59 PDT)
- [AMBER] Benchmarks for new RTX3060 Игорь Злотников (Tue Mar 23 2021 - 10:43:23 PDT)
- [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Renato Araujo (Wed Mar 24 2021 - 04:19:17 PDT)
- [AMBER] Discrepancy in pb binding energy (MMPBSA.py tutorial) Ali Saad Kusay (Wed Mar 24 2021 - 06:33:10 PDT)
- [AMBER] GB-HCP Example File and Setup Richard Kullmann (Wed Mar 24 2021 - 08:07:46 PDT)
- [AMBER] Electric Field Gradient Mani Radh (Thu Mar 25 2021 - 04:24:42 PDT)
- [AMBER] Addition of hydrogens - isoelectric point of protein Prasanth G, Research Scholar (Thu Mar 25 2021 - 12:11:49 PDT)
- [AMBER] Selection of forcefield for protein-ligand simulations Prasanth G, Research Scholar (Thu Mar 25 2021 - 12:22:18 PDT)
- [AMBER] Clustering based on predefined centroids Abhilash J (Thu Mar 25 2021 - 13:17:27 PDT)
- [AMBER] Problem with packmol-memgen when I try to installing Amber20 in GPU Dr. Gerardo Pérez Hernández (Fri Mar 26 2021 - 04:00:07 PDT)
- [AMBER] Conversion of CHARMM optimized pdb to AMBER compatible pdb Cato, Lee (Fri Mar 26 2021 - 09:34:32 PDT)
- [AMBER] Distance tolerance for identifying common atoms in thermodynamics integration zz sheng (Fri Mar 26 2021 - 11:19:11 PDT)
- [AMBER] Calculation halted on pmemd.cuda 库米尔 (Fri Mar 26 2021 - 17:10:06 PDT)
- [AMBER] Using average frame for nmode entropy calculation? Liao (Sat Mar 27 2021 - 12:10:42 PDT)
- [AMBER] Unit of Electric field frequency Shakir Ali Siddiqui (Sun Mar 28 2021 - 12:03:21 PDT)
- [AMBER] CHARMM Output - Empty Restraint File Aanshi Gandhi (Mon Mar 29 2021 - 08:46:46 PDT)
- [AMBER] Calculating SASA using Surf and Molsurf Loo Kang (Mon Mar 29 2021 - 19:10:28 PDT)
- [AMBER] Calculating displacement from PMF Pinky Mazumder (Tue Mar 30 2021 - 10:10:08 PDT)
- [AMBER] Convert SIRAH coarse-grained model back to all-atomic pdb file format? Michael Shokhen (Tue Mar 30 2021 - 23:39:57 PDT)
- [AMBER] Antechamber and mol2 file with .<TRIPOS>UNITY_ATOM_ATTR Alan (Wed Mar 31 2021 - 00:18:12 PDT)
- [AMBER] Calculating displacement from PMF Pinky Mazumder (Wed Mar 31 2021 - 06:58:49 PDT)
- Last message date: Wed Mar 31 2021 - 20:30:02 PDT
- Archived on: Wed Apr 17 2024 - 05:55:56 PDT
