Amber Archive Apr 2018 by thread
- Re: [AMBER] Help with mdcrd in VMD Abdul-Rashid III Sampaco (Sat Mar 31 2018 - 10:35:54 PDT)
- Re: [AMBER] Query for force field parameters of 'R' and 'S' enantiomers Chetna Tyagi (Sun Apr 01 2018 - 03:32:55 PDT)
- [AMBER] superimpose two atoms in cpptraj Mark Rance (Sun Apr 01 2018 - 05:55:34 PDT)
- [AMBER] ZnS force field parameters roja rahmani (Sun Apr 01 2018 - 11:17:43 PDT)
- [AMBER] no output results for heating process wangjy.dicp.ac.cn (Mon Apr 02 2018 - 01:47:11 PDT)
- Re: [AMBER] Problem with parallel install Maria Clelia Milletti (Mon Apr 02 2018 - 12:59:52 PDT)
- [AMBER] Fwd: Postdoctoral Positions in Computational Biophysics at Westlake University Pengfei Li (Tue Apr 03 2018 - 09:00:38 PDT)
- Re: [AMBER] center of mass restraint in pmemd.cuda Rajarshi Roy (Tue Apr 03 2018 - 23:27:13 PDT)
- [AMBER] Converting gromacs TRX file to mdcrd.nc and mdvel.nc Mohd Farid Ismail (Wed Apr 04 2018 - 03:20:15 PDT)
- [AMBER] RNA with Amber16 Elisa FREZZA (Wed Apr 04 2018 - 04:05:57 PDT)
- [AMBER] A Problem about Alanine Scan of Proline 忠彦 (Wed Apr 04 2018 - 04:55:01 PDT)
- [AMBER] When did SCEE and SCNB make it into the force-field files Karl Kirschner (Wed Apr 04 2018 - 06:28:08 PDT)
- [AMBER] Are the equations for FF14SB and FF15IPQ same or different Dmitry Suplatov (Wed Apr 04 2018 - 06:32:52 PDT)
- [AMBER] parmed CharmmError: Could not convert dihedral phase to <type 'float'> Sadegh Faramarzi Ganjabad (Wed Apr 04 2018 - 11:05:50 PDT)
- [AMBER] Changing box size M Conte (Wed Apr 04 2018 - 17:47:13 PDT)
- [AMBER] Fix for fixed sized cmd in nab Åke Sandgren (Thu Apr 05 2018 - 03:35:29 PDT)
- [AMBER] Query about Constant pH cpout file Saikat Dutta chowdhury (Thu Apr 05 2018 - 05:33:07 PDT)
- [AMBER] Replica Exchange: an illegal memory access was encountered launching kernel kClearForces Jason Ku Wang (Thu Apr 05 2018 - 13:58:35 PDT)
- [AMBER] Calculate minimum distance between two groups of atoms David Sáez (Thu Apr 05 2018 - 14:13:55 PDT)
- [AMBER] Replica Exchange: an illegal memory access was encountered launching kernel kClearForces Jason Ku Wang (Thu Apr 05 2018 - 14:37:46 PDT)
- [AMBER] Temperatured-Based Replica Exchange: an illegal memory access was encountered launching kernel kClearForces Jason Ku Wang (Thu Apr 05 2018 - 14:45:06 PDT)
- [AMBER] Questions about SEBOMD with Divide and Conqure method Mingyuan_xu (Fri Apr 06 2018 - 04:35:07 PDT)
- [AMBER] ERROR TUTORIAL AMBER --- Step 3.3.3) "Visualizing the trajectories with VMD" Edjan Silva (Fri Apr 06 2018 - 05:07:09 PDT)
- [AMBER] atomic radius data in amber library Rakesh Srivastava (Sat Apr 07 2018 - 03:51:09 PDT)
- [AMBER] MMGBSA calculation for complex with two ligangs using three trajectoris cuiyinglukitty (Sun Apr 08 2018 - 01:36:55 PDT)
- [AMBER] RED Server deriving charges for hybrid molecule using GLYCAM ff Neha Gandhi (Sun Apr 08 2018 - 23:26:32 PDT)
- [AMBER] Unable to perform MD because of Fortran runtime error: End of file Sehrish Naz (Mon Apr 09 2018 - 03:28:18 PDT)
- [AMBER] Extracting forces from the mdcrd file Nikolay N. Kuzmich (Mon Apr 09 2018 - 04:28:06 PDT)
- Re: [AMBER] Amber16+AT17: Several checks failing w/Intel Parallel Studio XE 2018.1 David A Case (Mon Apr 09 2018 - 06:14:20 PDT)
- [AMBER] residue looks like it is not a part of protein Thakur, Abhishek (Mon Apr 09 2018 - 14:54:27 PDT)
- [AMBER] protons Carlos Romero (Mon Apr 09 2018 - 16:36:13 PDT)
- [AMBER] Regarding input files Midhun K Madhu (Mon Apr 09 2018 - 23:45:01 PDT)
- Re: [AMBER] Count water in active site Daniel Roe (Tue Apr 10 2018 - 06:17:39 PDT)
- Re: [AMBER] Volume occupied during MD Daniel Roe (Tue Apr 10 2018 - 06:24:00 PDT)
- Re: [AMBER] Resume AMD simulation Daniel Roe (Tue Apr 10 2018 - 06:25:58 PDT)
- Re: [AMBER] Calculate water density in the protein water channel by Amber 16 Daniel Roe (Tue Apr 10 2018 - 06:32:05 PDT)
- Re: [AMBER] AMBER Digest, Vol 2256, Issue 1 Sehrish Naz (Tue Apr 10 2018 - 07:01:01 PDT)
- [AMBER] PB calculation is failing varun dewaker (Tue Apr 10 2018 - 07:54:38 PDT)
- [AMBER] Cpptraj and Sander Question Portillo, Jennifer (Tue Apr 10 2018 - 17:24:58 PDT)
- [AMBER] Problem building Amber16 with -cuda Ryan Novosielski (Wed Apr 11 2018 - 00:28:19 PDT)
- [AMBER] ATP hydrolysis Abhilash J (Wed Apr 11 2018 - 00:42:36 PDT)
- [AMBER] Thioester Bond:leap Aravind Ravichandran (Wed Apr 11 2018 - 02:54:12 PDT)
- [AMBER] Problem in disance restraints for atom groups Huan He (Wed Apr 11 2018 - 04:00:36 PDT)
- [AMBER] MMPBSA runs GB but fails in PB for RNA-ligand complex Kasprzak, Wojciech (NIH/NCI) [C] (Wed Apr 11 2018 - 07:47:44 PDT)
- [AMBER] Help with building a non-standard RNA structure Debostuti Ghoshdastidar (Wed Apr 11 2018 - 23:52:47 PDT)
- [AMBER] Ambertools17 error: 3D-RISM calculation Fabian Herrera Olivares (Thu Apr 12 2018 - 00:49:40 PDT)
- [AMBER] How can I run PMEMD with multiple distance restraints? Markowska (Thu Apr 12 2018 - 06:32:17 PDT)
- [AMBER] MM-GBSA on pH constant MD simulations Giovanni Grazioso (Thu Apr 12 2018 - 07:27:43 PDT)
- [AMBER] Simulation between DNA and small molecules. Edjan Silva (Thu Apr 12 2018 - 08:35:37 PDT)
- [AMBER] Building Amber16 CPU with Intel Compiler and GPU with GNU Compiler vs. MPI Ryan Novosielski (Thu Apr 12 2018 - 10:14:20 PDT)
- [AMBER] Two-Dimensional Replica Exchange in AMBER Jason Ku Wang (Fri Apr 13 2018 - 00:56:17 PDT)
- [AMBER] Replica exchange in explicit solvent Maya Hauss (Fri Apr 13 2018 - 12:23:12 PDT)
- [AMBER] "bad atom type: DU" error Sharon D. Morris (Fri Apr 13 2018 - 21:25:35 PDT)
- [AMBER] Amber94 charges for neutral amino acids Rinsha Chk (Fri Apr 13 2018 - 21:33:23 PDT)
- [AMBER] md simulation of modified nucleotides in RNA leila karami (Sat Apr 14 2018 - 08:47:19 PDT)
- [AMBER] GPU Atila Petrosian (Sat Apr 14 2018 - 08:59:32 PDT)
- [AMBER] (pmemd.cuda.MPI) Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL Amen Shamim (Sun Apr 15 2018 - 06:30:42 PDT)
- Re: [AMBER] Simple normal mode analysis in amber Lorena.Rosaleny.uv.es (Sun Apr 15 2018 - 23:08:57 PDT)
- [AMBER] query regarding nonlinear pbsa Rakesh Srivastava (Mon Apr 16 2018 - 01:02:15 PDT)
- [AMBER] Regarding AuCl force field Aashish Bhatt (Mon Apr 16 2018 - 06:58:08 PDT)
- [AMBER] Configure cuda Kadir Ozcan (Mon Apr 16 2018 - 16:53:15 PDT)
- [AMBER] convert psf to prmtop Ashutosh Shandilya (Mon Apr 16 2018 - 17:00:04 PDT)
- [AMBER] Weight the xyz components of restraints Huan He (Tue Apr 17 2018 - 06:24:03 PDT)
- [AMBER] QMMM Replica exchange with TeraChem Raimon Fabregat (Tue Apr 17 2018 - 08:12:58 PDT)
- [AMBER] How fast is Amber's new GPU code? Are CPUs ever coming back? David Cerutti (Tue Apr 17 2018 - 08:40:14 PDT)
- Re: [AMBER] Configure cuda (David A Case) Kadir Ozcan (Tue Apr 17 2018 - 12:27:37 PDT)
- [AMBER] Release of Amber18 and AmberTools18 David A Case (Tue Apr 17 2018 - 14:28:42 PDT)
- [AMBER] Multisander: No scale up Aravind Ravichandran (Tue Apr 17 2018 - 23:31:57 PDT)
- [AMBER] How to solve the problem of molecule box jumping? golshan bakrani (Wed Apr 18 2018 - 21:42:54 PDT)
- [AMBER] Brand new GPU card testing Nikolay N. Kuzmich (Thu Apr 19 2018 - 00:28:06 PDT)
- [AMBER] Python installation while installing AmberTools18 Debostuti Ghoshdastidar (Thu Apr 19 2018 - 02:04:22 PDT)
- [AMBER] Error generating gau_job.inp Giovanni Grazioso (Thu Apr 19 2018 - 03:16:47 PDT)
- [AMBER] eCheminfo Milano July 16-29, Training and Innovation Course in Drug Design 2018, bursary and early-bird deadline ending soon Thomas Exner (Thu Apr 19 2018 - 03:40:13 PDT)
- [AMBER] Error compiling AmberTools18 cpptraj with Intel 16 Niel Henriksen (Thu Apr 19 2018 - 07:34:38 PDT)
- [AMBER] native contacts Sowmya Indrakumar (Thu Apr 19 2018 - 09:26:27 PDT)
- [AMBER] Aligning frames and printing pdb files Christopher Warren (Thu Apr 19 2018 - 10:04:05 PDT)
- [AMBER] mac installation problem Jiyong Su (Thu Apr 19 2018 - 21:54:22 PDT)
- [AMBER] installation problem wuxc (Fri Apr 20 2018 - 01:53:06 PDT)
- [AMBER] NEB simulations: Inputs from TMD ? Aravind Ravichandran (Fri Apr 20 2018 - 02:33:41 PDT)
- [AMBER] NEB simulations: Inputs from TMD ? Aravind Ravichandran (Fri Apr 20 2018 - 02:36:24 PDT)
- [AMBER] Amber18 and Amber14 Günther H.J. Peters (Fri Apr 20 2018 - 08:48:56 PDT)
- [AMBER] pmemd.cuda error; Exiting due to the presence of inconsistent SHAKEH hydrogen clusters Sadegh Faramarzi Ganjabad (Fri Apr 20 2018 - 10:49:31 PDT)
- [AMBER] pH as a Dimension in Multidimensional (2D) Replica Exchange Jason Ku Wang (Fri Apr 20 2018 - 11:08:57 PDT)
- [AMBER] accelerated MD cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Ashutosh Shandilya (Fri Apr 20 2018 - 14:59:09 PDT)
- [AMBER] How to solve the problem of molecule box jumping? g.bakrani.sci.ui.ac.ir (Fri Apr 20 2018 - 23:39:54 PDT)
- [AMBER] Constant Redox potential MD simulations Fernando Ogata (Sat Apr 21 2018 - 14:20:51 PDT)
- [AMBER] Jumping from simulation box g.bakrani.sci.ui.ac.ir (Sun Apr 22 2018 - 12:49:33 PDT)
- [AMBER] average between structures with different residue numbering Rosellen, Martin (Mon Apr 23 2018 - 04:31:52 PDT)
- [AMBER] Amber18 and Titan V graphic cards Nikolay N. Kuzmich (Mon Apr 23 2018 - 05:24:48 PDT)
- [AMBER] Amino acid GROMACS topology file roja rahmani (Mon Apr 23 2018 - 06:50:41 PDT)
- [AMBER] Problem with g++ compiler with boost (AmberTools18) Abdul-Rashid III Sampaco (Mon Apr 23 2018 - 22:48:11 PDT)
- [AMBER] Charmm36 modified forcefield in Amber Midhun K Madhu (Tue Apr 24 2018 - 03:05:10 PDT)
- [AMBER] PMF analysis Tousif Hossen (Tue Apr 24 2018 - 04:06:16 PDT)
- [AMBER] Trouble Running/Understanding Wavelet Analysis Moataz Noureddine (Tue Apr 24 2018 - 10:42:01 PDT)
- [AMBER] Atom position changes when setting up QM/MM calculation James Kress (Tue Apr 24 2018 - 11:37:54 PDT)
- [AMBER] Parmchk roja rahmani (Tue Apr 24 2018 - 11:52:40 PDT)
- [AMBER] Issue running alanine scanning Núbia Prates (Tue Apr 24 2018 - 14:49:23 PDT)
- [AMBER] Boost not linking when compiling on Mac Gustaf Olsson (Wed Apr 25 2018 - 02:53:11 PDT)
- [AMBER] Analyzing Multidimensional REMD Simulations Jason Ku Wang (Wed Apr 25 2018 - 02:58:06 PDT)
- [AMBER] Call for Papers, GCC 2018, 14th German Conference on Chemoinformatics Stefan.Guessregen.sanofi.com (Wed Apr 25 2018 - 05:35:41 PDT)
- [AMBER] topology file roja rahmani (Wed Apr 25 2018 - 05:51:18 PDT)
- [AMBER] simulation with duration of 5000 Ps Edjan Silva (Wed Apr 25 2018 - 06:52:29 PDT)
- [AMBER] Paramfit issues - Improvement of R^2 value Alechania Misturini (Wed Apr 25 2018 - 07:51:54 PDT)
- [AMBER] QM/MM-MD charges Thakur, Abhishek (Wed Apr 25 2018 - 08:38:17 PDT)
- [AMBER] Solvateoct Distance Parameter Kung, Ryan (Wed Apr 25 2018 - 15:42:09 PDT)
- [AMBER] Multi-Dimensional REMD: rem.log shows exchanges along Hamiltonian dimension, but .mdout files do not Jason Ku Wang (Wed Apr 25 2018 - 17:44:45 PDT)
- [AMBER] AmberError: FLAG ATOMIC_NUMBER Sharon D. Morris (Wed Apr 25 2018 - 23:14:24 PDT)
- [AMBER] Simulation of bilayer with negative pressure Debostuti Ghoshdastidar (Thu Apr 26 2018 - 02:13:10 PDT)
- [AMBER] packmol-memgen and parmed packages import error Chetna Tyagi (Thu Apr 26 2018 - 03:04:09 PDT)
- Re: [AMBER] AMBER Digest, Vol 2271, Issue 1 Kadir Ozcan (Thu Apr 26 2018 - 09:07:59 PDT)
- [AMBER] QM/MM-MD Mulliken Charge calculation output atom name changed Thakur, Abhishek (Thu Apr 26 2018 - 11:50:54 PDT)
- [AMBER] Amber Lipid Force Field Tutorial: update? Matthias.Nachtschatt.csiro.au (Thu Apr 26 2018 - 19:35:23 PDT)
- [AMBER] Suggestions to pick up right methodology anu chandra (Fri Apr 27 2018 - 02:52:00 PDT)
- [AMBER] Fwd: Paramfit issues - Improvement of R^2 value. Alechania Misturini (Fri Apr 27 2018 - 07:29:19 PDT)
- [AMBER] Segmentation fault - invalid memory reference, during the minimization Nikolay N. Kuzmich (Fri Apr 27 2018 - 08:20:27 PDT)
- [AMBER] Forces on atoms Yuliana Bosken (Sat Apr 28 2018 - 01:29:54 PDT)
- [AMBER] Continuous hydrogen bond time correlation function S(t) Tousif Hossen (Sat Apr 28 2018 - 04:07:06 PDT)
- [AMBER] variety of errors in membrane/umbrella sampling simulations Baker, Joseph (Sat Apr 28 2018 - 11:51:13 PDT)
- [AMBER] GTX 1080Ti Problem. 汪盛 (Sun Apr 29 2018 - 03:16:54 PDT)
- [AMBER] QM/MM minimization issue using sander (AMBER 18) Abhilash J (Mon Apr 30 2018 - 01:16:17 PDT)
- [AMBER] MMPBSA.py.MPI TypeError when using &pb Eiros Zamora, Juan (Mon Apr 30 2018 - 10:49:48 PDT)
- [AMBER] Thermodynamic integration with sander + using nosoftcore Khabiri, Morteza (Mon Apr 30 2018 - 10:58:32 PDT)
- [AMBER] Cremer Pucker values using Pytraj Vivek Bharadwaj (Mon Apr 30 2018 - 11:13:38 PDT)
- Last message date: Mon Apr 30 2018 - 20:30:01 PDT
- Archived on: Sun Nov 24 2024 - 05:55:52 PST
