Amber Archive Apr 2019 by thread
- [AMBER] How the instantaneous temperature is calculated in Amber ? Marek Maly (Sun Mar 31 2019 - 17:35:05 PDT)
- [AMBER] How to build the central fragment of a modified nucleotide in the AMBER force fields 21818674.zju.edu.cn (Sun Mar 31 2019 - 19:28:55 PDT)
- Re: [AMBER] huge reference.frc in MMPBSA Antoine Marion (Sun Mar 31 2019 - 21:20:27 PDT)
- [AMBER] Fwd: AMBER Digest, Vol 2600, Issue 1 SATYAJIT KHATUA (Mon Apr 01 2019 - 00:45:18 PDT)
- Re: [AMBER] NFE error: Cannot read &abmd namelist Jason Imamoto (Mon Apr 01 2019 - 00:54:59 PDT)
- [AMBER] Equilibration in multiple steps with decrement in force constants Priyabrata Das (Mon Apr 01 2019 - 03:19:34 PDT)
- [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Mon Apr 01 2019 - 05:04:14 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ David A Case (Mon Apr 01 2019 - 07:45:28 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ Daniel Roe (Mon Apr 01 2019 - 08:18:46 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Tue Apr 02 2019 - 00:27:58 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Tue Apr 02 2019 - 06:23:48 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ Hai Nguyen (Tue Apr 02 2019 - 06:26:56 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Tue Apr 02 2019 - 06:40:03 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ Hai Nguyen (Tue Apr 02 2019 - 07:20:23 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Tue Apr 02 2019 - 23:36:19 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ David A Case (Wed Apr 03 2019 - 07:36:59 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Thu Apr 04 2019 - 06:16:01 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ Daniel Roe (Thu Apr 04 2019 - 06:30:51 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Thu Apr 04 2019 - 06:54:53 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ David A Case (Fri Apr 05 2019 - 06:01:56 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ David A Case (Mon Apr 08 2019 - 04:57:11 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Mon Apr 08 2019 - 06:48:20 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ David A Case (Wed Apr 03 2019 - 05:24:27 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ Hai Nguyen (Wed Apr 03 2019 - 05:54:30 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ Hai Nguyen (Wed Apr 03 2019 - 05:59:45 PDT)
- Re: [AMBER] varying pressure conditions? Shayna Hilburg (Mon Apr 01 2019 - 08:21:07 PDT)
- Re: [AMBER] Problems calculating density over distance Lucas Bandeira (Mon Apr 01 2019 - 09:13:25 PDT)
- [AMBER] regarding simulation Charu Sharma (JRF) (Tue Apr 02 2019 - 00:55:53 PDT)
- [AMBER] Box with a “separator” Alessandro Mariani (Tue Apr 02 2019 - 02:59:01 PDT)
- [AMBER] Negative dihedral angle n glycan simulation Rajarshi Roy (Tue Apr 02 2019 - 04:04:58 PDT)
- [AMBER] leap duplicates bond ('triangular' bond) warning Fabian Glaser (Tue Apr 02 2019 - 05:16:39 PDT)
- [AMBER] rms2d analysis Debarati DasGupta (Tue Apr 02 2019 - 11:38:26 PDT)
- [AMBER] KeyError: 4018 for iron containing enzyme (prolyl hydroxylase) Mahesh kumar Teli (Tue Apr 02 2019 - 22:06:32 PDT)
- [AMBER] tests with different # of threads Vaibhav Dixit (Wed Apr 03 2019 - 03:26:04 PDT)
- [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol ( GeForce RTX 2080) bjyx20090941 (Wed Apr 03 2019 - 07:24:23 PDT)
- Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed bjyx20090941 (Wed Apr 03 2019 - 20:21:49 PDT)
- [AMBER] mmpbsa error MYRIAN TORRES RICO (Thu Apr 04 2019 - 01:08:44 PDT)
- [AMBER] mmpbsa error MYRIAN TORRES RICO (Thu Apr 04 2019 - 02:07:07 PDT)
- [AMBER] Problem calculating water density over distance Lucas Bandeira (Thu Apr 04 2019 - 13:35:38 PDT)
- Re: [AMBER] metal-oxide-metal interactions Pengfei Li (Thu Apr 04 2019 - 17:44:44 PDT)
- [AMBER] location related redox-potential? Feng, Zimin (Fri Apr 05 2019 - 09:15:00 PDT)
- [AMBER] Can Amber constant pH run with CHARMM force field? Chen Yifan (Fri Apr 05 2019 - 11:51:35 PDT)
- [AMBER] 2 job positions InterX Inc. Molecular Simulation and Molecular ForceField Scientists Ganesh Kamath (Fri Apr 05 2019 - 12:58:51 PDT)
- [AMBER] outtraj question Xiaoyu Wang (Fri Apr 05 2019 - 15:35:10 PDT)
- Re: [AMBER] metal parameters Fabian Glaser (Fri Apr 05 2019 - 21:56:51 PDT)
- [AMBER] pmemd.CUDA vs pmemd.MPI for equilibration of protein-ligand and trajectory identification for mmpbsa Prasanth G, Research Scholar (Fri Apr 05 2019 - 23:47:01 PDT)
- [AMBER] 2 job positions InterX Inc. Molecular Simulation and Molecular ForceField Scientists Ganesh Kamath (Sat Apr 06 2019 - 08:00:24 PDT)
- Re: [AMBER] preparing a new pdb Boutheïna KERKENI (Sun Apr 07 2019 - 03:56:11 PDT)
- [AMBER] Ligand Splitting Issue Tamsila Parveen (Sun Apr 07 2019 - 04:21:59 PDT)
- [AMBER] Error working with pytleap ARITRA MITRA (Mon Apr 08 2019 - 03:58:33 PDT)
- [AMBER] Problem in setting parameters for the modified nucleotide Xiaoting Mao (Mon Apr 08 2019 - 06:10:58 PDT)
- [AMBER] Creating a water model from scratch Gustavo Seabra (Mon Apr 08 2019 - 11:55:39 PDT)
- [AMBER] secstruct issue in CPPTRAJ SARAH JEANNE LEFAVE (Mon Apr 08 2019 - 13:22:18 PDT)
- [AMBER] Question about QM/MM simulation in vacuum connecting Amber and Gaussian 09 package 王婷婷 (Mon Apr 08 2019 - 17:36:31 PDT)
- [AMBER] mmpbsa MYRIAN TORRES RICO (Tue Apr 09 2019 - 01:22:16 PDT)
- [AMBER] Calculate zero point energy for a protein (no ligand) system Akshay Prabhakant (Tue Apr 09 2019 - 04:42:58 PDT)
- [AMBER] Force field parameters for modified amino acid residues (carboxy glutamates) Tanusree S (Tue Apr 09 2019 - 21:42:30 PDT)
- [AMBER] Patches for AmberTools18 viktor drobot (Wed Apr 10 2019 - 04:26:12 PDT)
- [AMBER] REGARDING MPI Charu Sharma (JRF) (Wed Apr 10 2019 - 11:06:10 PDT)
- [AMBER] Question about chemical reaction in vacuum with adding an extra reaction field (Specify dielectric constant in vacuum) 王婷婷 (Wed Apr 10 2019 - 18:03:59 PDT)
- [AMBER] parameters for isolated zwitter ion tyrosine angad sharma (Wed Apr 10 2019 - 23:15:25 PDT)
- [AMBER] Capping RNA Mihaljevic-Juric Paula (Mme) (Thu Apr 11 2019 - 02:56:08 PDT)
- [AMBER] T4 vs RTX2080Ti Giovanni Grazioso (Thu Apr 11 2019 - 08:00:42 PDT)
- [AMBER] COM Dihedral Restraint Kung, Ryan (Thu Apr 11 2019 - 08:23:17 PDT)
- [AMBER] Problem calculating water mass density over distance Lucas Bandeira (Thu Apr 11 2019 - 09:00:23 PDT)
- [AMBER] Electrostatic interactions in LIE method Debarati DasGupta (Thu Apr 11 2019 - 10:57:19 PDT)
- [AMBER] namd and amber md energies do not match Akshay Prabhakant (Thu Apr 11 2019 - 11:33:01 PDT)
- Re: [AMBER] charged residue mutation free energy Hosein Geraili Daronkola (Fri Apr 12 2019 - 00:04:12 PDT)
- [AMBER] Confusion regarding ff14SB and ff99SBildn forcefields RITUPARNA ROY (Fri Apr 12 2019 - 00:09:12 PDT)
- [AMBER] How to source oldff in tleap Saikat Pal (Fri Apr 12 2019 - 04:32:54 PDT)
- [AMBER] Question about NEB Lillian Chong (Fri Apr 12 2019 - 06:02:57 PDT)
- [AMBER] Problems in setting parameters for the modified nucleotide Xiaoting Mao (Fri Apr 12 2019 - 06:08:43 PDT)
- [AMBER] silver parameters Uroš Javornik (Fri Apr 12 2019 - 06:29:12 PDT)
- [AMBER] pdb4amber install w/ conda Paul, Austin (Fri Apr 12 2019 - 09:16:21 PDT)
- [AMBER] Save RST from mdcrd containing velocities Yuliana Bosken (Sat Apr 13 2019 - 02:40:05 PDT)
- Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine Xiaoting Mao (Sat Apr 13 2019 - 02:48:14 PDT)
- [AMBER] Guidance on WHAM Daniel Fernández Remacha (Sat Apr 13 2019 - 06:19:01 PDT)
- [AMBER] RTX 2070 GPU Card Ajeet Kumar Yadav (Mon Apr 15 2019 - 03:02:01 PDT)
- [AMBER] Atoms per processor Charo del Genio (Mon Apr 15 2019 - 04:36:10 PDT)
- [AMBER] mdgx CreateBellyMask error Anthony Bogetti (Mon Apr 15 2019 - 07:50:02 PDT)
- [AMBER] Fixing few box dimensions in semiisotropic/anisotropic pressure scaling Kyeong-jun Jeong (Mon Apr 15 2019 - 13:56:54 PDT)
- [AMBER] How to use GaMD in amber16 ATUL KUMAR (Tue Apr 16 2019 - 01:35:25 PDT)
- [AMBER] Problems in forcefield parameterization of Mercury Muthukumaran Rajagopalan (Tue Apr 16 2019 - 10:24:35 PDT)
- [AMBER] How to select dihedral angles to reweight accelerated molecular dynamics simulation of protein Mayank Dixit (Tue Apr 16 2019 - 17:48:47 PDT)
- [AMBER] pKa calculation Tanmoy Paul (Tue Apr 16 2019 - 23:18:58 PDT)
- [AMBER] mol2 files for FEW Zhonghua Xia (Wed Apr 17 2019 - 01:33:24 PDT)
- [AMBER] Mg2+_preparation_general_rule Antonio Amber Carlesso (Wed Apr 17 2019 - 08:27:11 PDT)
- [AMBER] More macOS compilation issues.... Gustaf Olsson (Thu Apr 18 2019 - 01:20:39 PDT)
- [AMBER] AMBER - Heating MD Systems An Ta (Thu Apr 18 2019 - 05:48:37 PDT)
- [AMBER] "Problem installing Miniconda" Seibold, Steve Allan (Thu Apr 18 2019 - 08:43:30 PDT)
- [AMBER] Force field for C-C Di-Tyrosine Linkage Bharat Manna (Thu Apr 18 2019 - 03:45:55 PDT)
- [AMBER] RTX-2070 supported(untested)? Yeyue Xiong (Thu Apr 18 2019 - 13:29:28 PDT)
- [AMBER] MM PBSA - clarification Prasanth G, Research Scholar (Fri Apr 19 2019 - 06:14:33 PDT)
- [AMBER] smflags in configure script viktor drobot (Fri Apr 19 2019 - 07:19:24 PDT)
- [AMBER] trouble in amberFATA: Atom doesn't have a type Maximilien BERNE (Fri Apr 19 2019 - 09:19:14 PDT)
- [AMBER] Change the trajectory format. Parviz Seifpanahi Shabane (Fri Apr 19 2019 - 12:12:39 PDT)
- [AMBER] possible bug in charmmlipid2amber.py liu junjun (Mon Apr 22 2019 - 00:14:17 PDT)
- [AMBER] Suggestions on running a qm-mm simulation for studying a group transfer reaction Prayagraj Fandilolu (Mon Apr 22 2019 - 05:43:24 PDT)
- [AMBER] regarding radius of gyration angad sharma (Mon Apr 22 2019 - 06:03:04 PDT)
- [AMBER] Computing forces by trajectory post-processing with sander Casalini Tommaso (Mon Apr 22 2019 - 12:54:10 PDT)
- [AMBER] problem in locating Aqvist Mg2+ parameter in amber ATUL KUMAR (Mon Apr 22 2019 - 21:52:18 PDT)
- [AMBER] A-DNA Charu Sharma (JRF) (Mon Apr 22 2019 - 22:17:26 PDT)
- [AMBER] Issue with cpptraj.MPI Benard, Dany (Tue Apr 23 2019 - 05:44:23 PDT)
- [AMBER] saving output of Gaussian accelerated MD Qinghua Liao (Tue Apr 23 2019 - 07:41:28 PDT)
- [AMBER] charge in constant redox cein file vs. prmtop file Feng, Zimin (Tue Apr 23 2019 - 15:03:24 PDT)
- [AMBER] styrene sulfonate molecule building using xleap Shilpa Gupta (Tue Apr 23 2019 - 23:32:36 PDT)
- [AMBER] Problem with heating the system ATUL KUMAR (Wed Apr 24 2019 - 01:57:34 PDT)
- [AMBER] secondary structure angad sharma (Wed Apr 24 2019 - 04:32:53 PDT)
- [AMBER] Targeted MD Elena Gomez (Thu Apr 25 2019 - 01:08:18 PDT)
- [AMBER] issues with pmemd.cuda Veenis, Andrew Jay (Thu Apr 25 2019 - 08:11:46 PDT)
- [AMBER] processing trajectories subjected to GIST analysis Alfredo Quevedo (Tue Apr 23 2019 - 23:19:47 PDT)
- [AMBER] Simulation with Protein, cofactor and Ligand Prasanth G, Research Scholar (Thu Apr 25 2019 - 11:41:05 PDT)
- [AMBER] Antechamber question David Poole (Thu Apr 25 2019 - 16:03:37 PDT)
- [AMBER] setting up triplicate runs Yin, Guowei (Thu Apr 25 2019 - 18:08:00 PDT)
- [AMBER] dihedral scanning with GAFF and GAFF2 Qasim Pars (Fri Apr 26 2019 - 03:22:33 PDT)
- [AMBER] Any help on how to implement it in cpptraj? Debarati DasGupta (Fri Apr 26 2019 - 09:25:11 PDT)
- [AMBER] Release of AmberTools19 David Case (Fri Apr 26 2019 - 17:59:43 PDT)
- [AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - clang Gustaf Olsson (Sat Apr 27 2019 - 05:58:27 PDT)
- [AMBER] NpT simulations in interfacial system Lucas Bandeira (Sat Apr 27 2019 - 07:38:33 PDT)
- [AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - GCC8.3 Gustaf Olsson (Sat Apr 27 2019 - 11:44:00 PDT)
- [AMBER] xleap display Yin, Guowei (Sat Apr 27 2019 - 14:49:20 PDT)
- [AMBER] Novel Force Field Parameters for Aromatic Dihedrals Erdem Yeler (Sun Apr 28 2019 - 13:09:41 PDT)
- [AMBER] WHAM umbrella PMF of ligand Z diffusion on lipid molecule zmatovic.kg.ac.rs (Mon Apr 29 2019 - 04:05:27 PDT)
- [AMBER] constant-pressure equilibration with a water droplet Anthony Bogetti (Mon Apr 29 2019 - 08:37:40 PDT)
- [AMBER] Why is SPAM throwing errors when I see none in my input files or trajectories. Debarati DasGupta (Mon Apr 29 2019 - 13:25:58 PDT)
- [AMBER] Regarding cosine content calculation in AMBER Rajarshi Roy (Mon Apr 29 2019 - 22:22:40 PDT)
- [AMBER] mmpbsa error MYRIAN TORRES RICO (Tue Apr 30 2019 - 02:01:54 PDT)
- [AMBER] CPPTRAJ gnu extension not working anu chandra (Tue Apr 30 2019 - 10:00:08 PDT)
- [AMBER] [rok.ucsd.edu: AT19 cpptraj MPI build issue (Linux, x86_64, gnu)] David A Case (Tue Apr 30 2019 - 12:55:23 PDT)
- Last message date: Tue Apr 30 2019 - 13:00:03 PDT
- Archived on: Wed Dec 11 2024 - 05:55:39 PST