Amber Archive Mar 2022 by thread
- Re: [AMBER] Clarification in 3DRISM Alexis Azucena (Mon Feb 28 2022 - 17:54:20 PST)
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces Állan Ferrari (Tue Mar 01 2022 - 05:08:08 PST)
- Re: [AMBER] CPPTRAJ, Dipole autocorrelation? David A Case (Tue Mar 01 2022 - 16:43:01 PST)
- [AMBER] Error in using multiple distance restraints in a single RST file Prathit Chatterjee (Tue Mar 01 2022 - 18:37:04 PST)
- Re: [AMBER] CUDART lib not found during install Charlotta Lebedenko (Wed Mar 02 2022 - 13:27:27 PST)
- Re: [AMBER] Cpptraj - Density Action Command Units Gerardo Zerbetto De Palma (Thu Mar 03 2022 - 14:05:32 PST)
- [AMBER] Asking MMPBSA.PY Purnawan pontana putra (Fri Mar 04 2022 - 02:52:15 PST)
- [AMBER] How to use artificial covariance matrix in PCA analysis of cpptraj? wangjianing_mail (Fri Mar 04 2022 - 06:10:46 PST)
- Re: [AMBER] error preparing ligand parameters Vaibhav Dixit (Fri Mar 04 2022 - 07:04:37 PST)
- [AMBER] Watershell like command for lipids Vic De Roo (Mon Mar 07 2022 - 03:56:47 PST)
- [AMBER] TLEAP error when adding Ag+ Alysia Mandato (Mon Mar 07 2022 - 12:23:56 PST)
- [AMBER] glibc causing amber install error Bruno Cramer (Mon Mar 07 2022 - 12:56:34 PST)
- [AMBER] Failed to generate rst file in partially deleted structure Yen Nguyen (Mon Mar 07 2022 - 14:44:57 PST)
- [AMBER] Constant pH MD Simulations for General Organic Compounds Nathan Black (Mon Mar 07 2022 - 20:36:53 PST)
- [AMBER] [Amber]Not able to generate eq_density.cpptraj file while doing QM/MM calculations Anita Meena (Mon Mar 07 2022 - 21:18:33 PST)
- [AMBER] EZAFF force field Elisa Frezza (Mon Mar 07 2022 - 23:51:06 PST)
- [AMBER] Entropy calculations in GIST Daniella Hares (Tue Mar 08 2022 - 05:44:10 PST)
- [AMBER] Penalty Scores for Amino Acid Dihedral Parameters Nathan Black (Tue Mar 08 2022 - 21:35:32 PST)
- Re: [AMBER] Calculate Lipid Surface Pressure/Tension from Lipid-Water Interface Mirza Ahmed Hammad (Wed Mar 09 2022 - 01:15:40 PST)
- [AMBER] Unit cell size changed and coords overlap problems chanyann06.stu.scu.edu.cn (Wed Mar 09 2022 - 23:45:38 PST)
- [AMBER] tleap: keep crystallographic waters? Daniel Konstantinovsky (Thu Mar 10 2022 - 16:05:54 PST)
- [AMBER] Unit cell size changed and coords overlap problems chanyann06.stu.scu.edu.cn (Thu Mar 10 2022 - 18:00:49 PST)
- [AMBER] calculate entropy using MMPBSA.py Ming Tang (Thu Mar 10 2022 - 22:11:31 PST)
- [AMBER] Convergence issue in rism1d angad sharma (Thu Mar 10 2022 - 23:07:17 PST)
- [AMBER] problems installing Amber20 + AmberTools21 parallel version with open-mpi Antonija Tomić (Fri Mar 11 2022 - 04:28:07 PST)
- [AMBER] Request help modifying a force field russ.brown.yahoo.com (Fri Mar 11 2022 - 09:19:43 PST)
- [AMBER] Stripping waters from trajectory except those forming bridged H-bond between Protein and Ligand Rakesh Srivastava (Fri Mar 11 2022 - 21:12:50 PST)
- [AMBER] Error when using mmpbsa_py_nabnmode in parallel Ming Tang (Sun Mar 13 2022 - 03:36:01 PDT)
- [AMBER] Non-Integer Charge for Systems Comprised of Large Number of Residues Nathan Black (Sun Mar 13 2022 - 11:32:05 PDT)
- [AMBER] How to read netcdf files on VMD Windows version? Suchetana Gupta (Sun Mar 13 2022 - 22:09:15 PDT)
- [AMBER] Modeling cis-amide bonds in diketopiperazines Christian Schafmeister (Mon Mar 14 2022 - 08:03:20 PDT)
- [AMBER] NFE-Error Tanmoy Paul (Mon Mar 14 2022 - 11:00:22 PDT)
- Re: [AMBER] tleap error: "expected 'default'" Scott Brozell (Mon Mar 14 2022 - 18:05:29 PDT)
- [AMBER] I cannot find NAB in AmberTools 21 russ.brown.yahoo.com (Mon Mar 14 2022 - 22:29:36 PDT)
- [AMBER] Regarding treating ligand with QM level of theory Soumyajit Karmakar (Wed Mar 16 2022 - 03:53:03 PDT)
- [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer (Wed Mar 16 2022 - 06:45:28 PDT)
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Kenneth Huang (Wed Mar 16 2022 - 07:37:57 PDT)
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Daniel Roe (Wed Mar 30 2022 - 12:27:12 PDT)
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer (Wed Mar 30 2022 - 13:39:25 PDT)
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Daniel Roe (Wed Mar 30 2022 - 13:54:23 PDT)
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Daniel Roe (Wed Mar 30 2022 - 13:54:47 PDT)
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer (Wed Mar 30 2022 - 14:00:42 PDT)
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer (Wed Mar 30 2022 - 13:58:44 PDT)
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Daniel Roe (Wed Mar 30 2022 - 16:05:17 PDT)
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer (Wed Mar 30 2022 - 16:12:06 PDT)
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Daniel Roe (Wed Mar 30 2022 - 16:31:07 PDT)
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer (Wed Mar 30 2022 - 16:34:19 PDT)
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Daniel Roe (Wed Mar 30 2022 - 17:14:34 PDT)
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer (Wed Mar 30 2022 - 17:22:13 PDT)
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Daniel Roe (Wed Mar 30 2022 - 17:44:26 PDT)
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer (Wed Mar 30 2022 - 17:51:17 PDT)
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer (Thu Mar 31 2022 - 10:23:37 PDT)
- [AMBER] question about ATP-Mg2+ binding system liu kai (Wed Mar 16 2022 - 08:46:05 PDT)
- [AMBER] A way to stop simulations when certain criteria are met? Chris Lee (Wed Mar 16 2022 - 12:31:47 PDT)
- [AMBER] Query regarding AMBER meta dynamics Sruthi Sudhakar (Thu Mar 17 2022 - 02:00:19 PDT)
- [AMBER] Hubbard derivative not found and element Na not supported for a QM/MM system Pau Mayorga Delgado (Thu Mar 17 2022 - 02:36:07 PDT)
- [AMBER] CPPTRAJ, Conflicting H-Bonding Results Matthew Guberman-Pfeffer (Thu Mar 17 2022 - 09:23:00 PDT)
- Re: [AMBER] AMBER Digest, Vol 3660, Issue 1 liu kai (Thu Mar 17 2022 - 19:15:06 PDT)
- [AMBER] T-REMD Juliette Newell (Fri Mar 18 2022 - 02:57:03 PDT)
- [AMBER] PySander availability in PyTraj David Poole (Fri Mar 18 2022 - 05:08:08 PDT)
- [AMBER] Installation errors of AmberTools 21 on Ubuntu 20.04 WSL2 M. Reza Ganjalikhany (Sun Mar 20 2022 - 03:39:09 PDT)
- [AMBER] Cannot install AmberTools 21 due to errors in getline.c file Сергей Горелов (Sun Mar 20 2022 - 11:45:09 PDT)
- [AMBER] Problems with DFTB3 and Na in Amber Pau Mayorga Delgado (Mon Mar 21 2022 - 05:46:51 PDT)
- [AMBER] Small Cutoffs Not Supported for Implicit Solvent GPU Simulation Runs Nathan Black (Mon Mar 21 2022 - 07:28:16 PDT)
- [AMBER] Problem with production run of cyclic peptide Suchetana Gupta (Mon Mar 21 2022 - 16:41:10 PDT)
- [AMBER] Query related to TIMD SATYAJIT KHATUA (Mon Mar 21 2022 - 23:09:09 PDT)
- [AMBER] 1D-RISM with 4-Point water models Grunewald, Lukas (Tue Mar 22 2022 - 03:32:44 PDT)
- Re: [AMBER] Error - corrupted size vs. prev_size saranya.cbmm.lodz.pl (Tue Mar 22 2022 - 08:02:58 PDT)
- [AMBER] MMPBSA.py.MPI and pytraj bugs David Poole (Tue Mar 22 2022 - 08:12:28 PDT)
- Re: [AMBER] The tutorial 6.8 Westpa Tutorials Maria Nagan (Tue Mar 22 2022 - 18:33:49 PDT)
- [AMBER] D-amino acids Daniel Konstantinovsky (Wed Mar 23 2022 - 09:05:53 PDT)
- [AMBER] ** NFE-Error ** : Selection weight overflows, try smaller selection constant Sruthi Sudhakar (Wed Mar 23 2022 - 21:57:29 PDT)
- [AMBER] [AMBER ] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered. Anita Meena (Wed Mar 23 2022 - 22:05:29 PDT)
- [AMBER] How to visualize the results generated from the analysis of MD trajectory using Cpptraj in AMBER16 ? priya murugan (Thu Mar 24 2022 - 05:01:36 PDT)
- [AMBER] PMEMD does not support single H residues! Huimin Tian (Thu Mar 24 2022 - 19:44:27 PDT)
- [AMBER] Atom coordinate disagreement error in running the TI calculation Bhakti Hirlekar (Thu Mar 24 2022 - 22:33:59 PDT)
- [AMBER] mmpbsa divalent ion bug xiangyu (Fri Mar 25 2022 - 00:26:58 PDT)
- [AMBER] Error while running minimization run while doing thermodynamic integration. Divya Rai (Fri Mar 25 2022 - 00:48:31 PDT)
- [AMBER] Amber20 installation error Chen, Guoquan (Fri Mar 25 2022 - 15:23:03 PDT)
- [AMBER] Is it possible to use less replicas by freezing some atoms of protein in which I'm not interested? 云之彼端 (Fri Mar 25 2022 - 17:23:59 PDT)
- [AMBER] ** NFE-Error ** : Selection weight overflows, try smaller selection constant Sruthi Sudhakar (Mon Mar 28 2022 - 05:29:16 PDT)
- [AMBER] Tyrosine anion simulation Пушкарев Сергей (Mon Mar 28 2022 - 22:54:39 PDT)
- [AMBER] Error in parameter file preparation Debasish Mandal (Tue Mar 29 2022 - 00:04:07 PDT)
- [AMBER] Distance Restraints and/or Periodic Boundaries for Implicit Solvent Nathan Black (Tue Mar 29 2022 - 09:58:38 PDT)
- [AMBER] Is there a way to restart MMPBSA.py calculation? Ming Tang (Tue Mar 29 2022 - 16:58:50 PDT)
- [AMBER] mmpbsa.py divalent ion issue xiangyu (Tue Mar 29 2022 - 21:57:13 PDT)
- [AMBER] How to use GPU and GLYCAM force fields s.ohno.tohoku-mpu.ac.jp (Tue Mar 29 2022 - 23:24:03 PDT)
- [AMBER] Entropy calculations upon covalent modification Aravind R (Wed Mar 30 2022 - 04:09:12 PDT)
- [AMBER] Toluene solvent box equilibration Pedro Miguel Reis Figueiredo (Wed Mar 30 2022 - 13:17:02 PDT)
- [AMBER] problem with using amber Feng Su (Wed Mar 30 2022 - 22:04:59 PDT)
- Re: [AMBER] Unit 9 Error on OPEN: inpcrd When Running GPU Simulation on PMEMD.CUDA Nathan Black (Thu Mar 31 2022 - 06:47:45 PDT)
- Last message date: Thu Mar 31 2022 - 10:30:02 PDT
- Archived on: Fri Apr 19 2024 - 05:55:57 PDT
