Amber Archive Apr 2020 by thread
- [AMBER] sum of charges from parm file Lenka (Tue Mar 31 2020 - 15:27:36 PDT)
- Re: [AMBER] RTX 2020 Super GPU Random Memory Errors Giorgos Lambrinidis (Wed Apr 01 2020 - 00:21:50 PDT)
- Re: [AMBER] NPT equilibration is crashing Sunita Patel (Wed Apr 01 2020 - 05:45:40 PDT)
- [AMBER] Remove restraint mohamed marzouk (Wed Apr 01 2020 - 05:50:33 PDT)
- [AMBER] Running Steered MD Simulations using GPU Souvik Dey (Wed Apr 01 2020 - 08:48:18 PDT)
- [AMBER] Problem in configuring Sapna Shedge (Wed Apr 01 2020 - 21:34:48 PDT)
- Re: [AMBER] [External] Re: AmberTools19 update.8 fails to install mark.bergman.uphs.upenn.edu (Thu Apr 02 2020 - 08:29:23 PDT)
- [AMBER] AMBER 18 cuda installation: error: redefinition of ‘simulationConst cSim’ Sapna Shedge (Thu Apr 02 2020 - 10:58:23 PDT)
- [AMBER] pyramidal amide nitrogen Arnaud Bondon (Thu Apr 02 2020 - 11:17:38 PDT)
- [AMBER] cellulose chain Pinky Mazumder (Thu Apr 02 2020 - 12:09:59 PDT)
- [AMBER] Incorrect results when running MMPBSA example. Shum, Ho Hin (Thu Apr 02 2020 - 21:48:38 PDT)
- Re: [AMBER] Error: Could not find angle parameter Rosellen, Martin (Fri Apr 03 2020 - 01:04:51 PDT)
- [AMBER] Amber force field for SDS and DPC detergents Ricky Nencini (Fri Apr 03 2020 - 03:17:27 PDT)
- [AMBER] nmode entropy calculations gets stuck way too often Liao (Fri Apr 03 2020 - 16:42:58 PDT)
- Re: [AMBER] Contents of Amber Digest Pinky Mazumder (Sat Apr 04 2020 - 01:14:02 PDT)
- [AMBER] ff_amber_to_viparr.py Error iraklis litinas (Sat Apr 04 2020 - 02:04:58 PDT)
- Re: [AMBER] Abasic Site and Leap Polymerization Robert Molt (Sat Apr 04 2020 - 08:56:33 PDT)
- [AMBER] 12-6-4LJ for thermodynamic integration on PMEMD engine Paulius Kantakevicius (Sat Apr 04 2020 - 12:01:13 PDT)
- [AMBER] Sequence command to build the 4 - O glucuronuxylans chain Pinky Mazumder (Sat Apr 04 2020 - 19:26:03 PDT)
- [AMBER] Help for the sequence of residue name Pinky Mazumder (Sun Apr 05 2020 - 00:09:15 PDT)
- Re: [AMBER] Differences in Lennard-Jones interactions in CPU vs GPU pmemd? David A Case (Sun Apr 05 2020 - 10:15:15 PDT)
- [AMBER] PrmtopError: Inconsistent charge definition for atom DHEERAJ CHITARA (Sun Apr 05 2020 - 10:20:23 PDT)
- [AMBER] Installation of ambertools on 32 bit linux system Prasanth G, Research Scholar (Sun Apr 05 2020 - 22:12:12 PDT)
- [AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. Gallo, Angelo (Mon Apr 06 2020 - 02:12:26 PDT)
- [AMBER] command for building composite of cellulose microfibrils and hemicelullose Pinky Mazumder (Mon Apr 06 2020 - 15:05:16 PDT)
- [AMBER] Penalty score in frcmod file Sruthi Sudhakar (Mon Apr 06 2020 - 23:24:47 PDT)
- [AMBER] topology problems Seibold, Steve Allan (Tue Apr 07 2020 - 09:58:59 PDT)
- [AMBER] Ligand leaving binding site at high lambdas using TI softcore Juraj Dobias (Wed Apr 08 2020 - 13:39:52 PDT)
- [AMBER] peek_ewald_inpcrd: Box info not found in inpcrd Sunita Patel (Wed Apr 08 2020 - 21:01:18 PDT)
- Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial Pengfei Li (Thu Apr 09 2020 - 08:24:20 PDT)
- Re: [AMBER] tleap for Mg2+ data type Pengfei Li (Thu Apr 09 2020 - 09:19:19 PDT)
- [AMBER] ImportError: Could not import Amber Python modules Renato Araujo (Thu Apr 09 2020 - 10:24:18 PDT)
- [AMBER] Installing nglview Jatin Kashyap (Thu Apr 09 2020 - 20:18:53 PDT)
- [AMBER] Acetylated the truncated N- terminal Lod King (Thu Apr 09 2020 - 20:47:27 PDT)
- [AMBER] questions about paramfit ttz (Thu Apr 09 2020 - 21:54:12 PDT)
- [AMBER] Very low MMPBSA result Nada Afiva (Fri Apr 10 2020 - 14:18:47 PDT)
- [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? Erdem Yeler (Fri Apr 10 2020 - 16:01:59 PDT)
- [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests Cong Liu (Fri Apr 10 2020 - 16:52:16 PDT)
- [AMBER] Partial charge for ligand Lod King (Fri Apr 10 2020 - 17:00:05 PDT)
- [AMBER] Can I use paramfit for MM scan? Elif Çiğdem Calvin (Fri Apr 10 2020 - 18:31:06 PDT)
- [AMBER] Help for building lignin chain Pinky Mazumder (Sat Apr 11 2020 - 00:21:32 PDT)
- Re: [AMBER] AMBER 18 cuda installation ChenXingqiang (Sat Apr 11 2020 - 08:11:42 PDT)
- [AMBER] Antechamber/acpype for ligand parametrization and usage of yasara autosmiles Prasanth G, Research Scholar (Sat Apr 11 2020 - 10:37:10 PDT)
- [AMBER] integration algorithm of sander? And reference of sander? Erdem Yeler (Mon Apr 13 2020 - 09:12:12 PDT)
- [AMBER] Reg:MMPB(GB)SA Error Lara rajam (Mon Apr 13 2020 - 11:26:06 PDT)
- [AMBER] geometry of amino Song Hu (Mon Apr 13 2020 - 22:59:00 PDT)
- [AMBER] Simulating magnetite surfaces with AMBER Casalini Tommaso (Tue Apr 14 2020 - 02:44:23 PDT)
- [AMBER] RST File Corrupt Czarny,Ryan (Tue Apr 14 2020 - 10:54:45 PDT)
- [AMBER] CPPtraj PCA error Rana Rehan Khalid (Tue Apr 14 2020 - 10:57:54 PDT)
- [AMBER] 1 chain-1chain interactions between carbohydrates Pinky Mazumder (Tue Apr 14 2020 - 20:36:31 PDT)
- Re: [AMBER] Clustering analysis Debarati DasGupta (Wed Apr 15 2020 - 07:38:37 PDT)
- [AMBER] Generating an asymmetric box for Steered MD Souvik Dey (Wed Apr 15 2020 - 15:43:01 PDT)
- [AMBER] miniconda3 AmberTools MMPBSA.py ERROR 15501908560.163.com> (Wed Apr 15 2020 - 19:06:02 PDT)
- [AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Wed Apr 15 2020 - 20:13:45 PDT)
- Re: [AMBER] simulations of proteins with 2 domains connected by a linker Vlad Cojocaru (Thu Apr 16 2020 - 02:35:57 PDT)
- [AMBER] protein-protein complex dissociation Núbia Toman (Thu Apr 16 2020 - 06:17:53 PDT)
- [AMBER] Error when installing miniconda through AmberTools19 Gardezi,Shahbaz (Thu Apr 16 2020 - 10:40:06 PDT)
- [AMBER] Request for help in solving installation errors of Amber dhruvi.iiar.res.in (Fri Apr 17 2020 - 04:20:54 PDT)
- [AMBER] Force Field for small molecule ligands Sruthi Sudhakar (Fri Apr 17 2020 - 05:17:35 PDT)
- [AMBER] thanks for the GB/SA section of the manual Antoine MARION (Fri Apr 17 2020 - 07:46:10 PDT)
- [AMBER] Probable bug in tleap. Hector A. Baldoni (Fri Apr 17 2020 - 11:38:41 PDT)
- [AMBER] Amber18 PIMD tutorial Sapna Shedge (Fri Apr 17 2020 - 23:16:19 PDT)
- [AMBER] Request for help in solving installation errors of Amber dhruvi.iiar.res.in (Sat Apr 18 2020 - 06:13:11 PDT)
- [AMBER] FRCMOD file Sruthi Sudhakar (Sat Apr 18 2020 - 07:01:46 PDT)
- [AMBER] pytraj error Ravi Abrol (Mon Apr 20 2020 - 00:06:35 PDT)
- [AMBER] restraining many individual atoms Ignacio General (Mon Apr 20 2020 - 11:06:01 PDT)
- [AMBER] Sander can't calculate MBAR energy swjjin0015.163.com (Mon Apr 20 2020 - 18:31:19 PDT)
- [AMBER] Energy values from mdout (excluding solvent molecules) Eduardo R. Almeida (Mon Apr 20 2020 - 20:57:48 PDT)
- [AMBER] Problem in calculating pairwise interaction with CPPTRAJ Prathit Chatterjee (Tue Apr 21 2020 - 02:47:42 PDT)
- [AMBER] Restraint on certain atoms during MD Debarati DasGupta (Tue Apr 21 2020 - 05:45:15 PDT)
- [AMBER] Sander can't calculate Mbar energy swjjin0015.163.com (Tue Apr 21 2020 - 17:11:48 PDT)
- [AMBER] Targeted MD Hector A. Baldoni (Tue Apr 21 2020 - 17:53:36 PDT)
- [AMBER] Amber18, tools19, cuda 10.2 Christopher Benjamin Coffey (Wed Apr 22 2020 - 11:16:55 PDT)
- [AMBER] implicit water Fabian Glaser (Wed Apr 22 2020 - 11:53:45 PDT)
- [AMBER] Sander can not calculate Mbar energy Gini (Wed Apr 22 2020 - 17:21:53 PDT)
- [AMBER] How to change charge value for 1 residue for MD simulation? Devashish_Das (Thu Apr 23 2020 - 00:59:57 PDT)
- [AMBER] FATAL: allocation failure in ivector() error while running 3D-RISM calculations Leena Aggarwal (Thu Apr 23 2020 - 04:32:16 PDT)
- [AMBER] Energy values from mdout files (excluding solvent molecules) Eduardo R. Almeida (Thu Apr 23 2020 - 06:01:19 PDT)
- [AMBER] Run Amber as a job array Anna Sekuła (Thu Apr 23 2020 - 07:32:56 PDT)
- [AMBER] Fwd: FATAL: allocation failure in ivector() error while running 3D-RISM calculations Leena Aggarwal (Thu Apr 23 2020 - 11:25:47 PDT)
- [AMBER] wrong geometry amide nitrogen Arnaud Bondon (Fri Apr 24 2020 - 04:40:58 PDT)
- [AMBER] wrong geometry amide nitrogen Arnaud Bondon (Fri Apr 24 2020 - 06:56:37 PDT)
- [AMBER] unsubscribe Christopher Benjamin Coffey (Fri Apr 24 2020 - 08:19:20 PDT)
- [AMBER] minimizing a pyridine in water Debarati DasGupta (Sat Apr 25 2020 - 06:10:52 PDT)
- [AMBER] DNA-RNA duplex Sruthi Sudhakar (Sat Apr 25 2020 - 07:34:30 PDT)
- [AMBER] Ligand lose planarity Jenny 148 (Sat Apr 25 2020 - 08:09:45 PDT)
- [AMBER] Recurring problem: Ligand lose planarity Jenny 148 (Sat Apr 25 2020 - 21:49:45 PDT)
- [AMBER] NAB to create DNA/RNA hybrid? Jisha B (Sat Apr 25 2020 - 23:21:24 PDT)
- [AMBER] cylindrical Simulation mohamed marzouk (Sun Apr 26 2020 - 18:47:12 PDT)
- [AMBER] Tsolute and Tsolvent Eduardo R. Almeida (Mon Apr 27 2020 - 08:00:45 PDT)
- [AMBER] AMBER leap issues constructing non-standard residue Siddharth marwaha (Mon Apr 27 2020 - 11:50:30 PDT)
- [AMBER] How to get the eigenvalues from PCA SUNITA MUDULI (Mon Apr 27 2020 - 13:31:40 PDT)
- [AMBER] error tleap MYRIAN TORRES RICO (Tue Apr 28 2020 - 02:24:47 PDT)
- [AMBER] tlea MYRIAN TORRES RICO (Tue Apr 28 2020 - 02:25:58 PDT)
- [AMBER] Using tleap tho have the .inpcrd and crd file ABEL Stephane (Tue Apr 28 2020 - 04:51:39 PDT)
- [AMBER] Unavailability of AMBER tutorial on PCA Abhilash J (Tue Apr 28 2020 - 13:52:59 PDT)
- [AMBER] adding hydrogen to pdbqt ligand files Marawan Hussien (Tue Apr 28 2020 - 14:15:36 PDT)
- [AMBER] nativecontacts mohamed marzouk (Tue Apr 28 2020 - 23:35:04 PDT)
- [AMBER] tleap error MYRIAN TORRES RICO (Wed Apr 29 2020 - 03:23:30 PDT)
- [AMBER] Question about PCA tutorial Abhilash J (Wed Apr 29 2020 - 14:07:27 PDT)
- [AMBER] tMD and pmemd Francesco Gentile (Wed Apr 29 2020 - 17:00:17 PDT)
- [AMBER] Mutations in existing DNA PDB file Jisha B (Thu Apr 30 2020 - 09:36:38 PDT)
- [AMBER] TI simulations Debarati DasGupta (Thu Apr 30 2020 - 12:09:58 PDT)
- Re: [AMBER] SHAKE ALgorithm and frcmod file Carlos Simmerling (Thu Apr 30 2020 - 14:18:27 PDT)
- Last message date: Thu Apr 30 2020 - 20:30:02 PDT
- Archived on: Fri Sep 06 2024 - 05:55:56 PDT