Amber Archive May 2018 by thread
- Re: [AMBER] QM/MM minimization issue using sander (AMBER 18) Goetz, Andreas (Mon Apr 30 2018 - 17:01:55 PDT)
- [AMBER] Computing interaction energies from trajectory Aravind Ravichandran (Tue May 01 2018 - 06:59:32 PDT)
- Re: [AMBER] Cremer Pucker values using Pytraj Vivek Bharadwaj (Tue May 01 2018 - 07:31:34 PDT)
- [AMBER] Using infe = 1, &pmd, and pmemd.cuda (AMBER16) Lenz, Stefan (Tue May 01 2018 - 09:04:27 PDT)
- [AMBER] CPPTRAJ Ensemble Keyword: "Too Many Open Files" Jason Ku Wang (Tue May 01 2018 - 16:55:15 PDT)
- Re: [AMBER] Boost not linking when compiling on Mac Gustaf Olsson (Tue May 01 2018 - 23:44:30 PDT)
- [AMBER] GPU benchmark - Amber18 Hadházi Ádám (Wed May 02 2018 - 02:00:19 PDT)
- [AMBER] update ambertools Tousif Hossen (Wed May 02 2018 - 02:28:52 PDT)
- [AMBER] update Ambertools Tousif Hossen (Wed May 02 2018 - 02:33:16 PDT)
- [AMBER] PhD/Junior position, AMBER sims DNA/RNA Jiri Sponer (Wed May 02 2018 - 03:54:35 PDT)
- [AMBER] How to extract frames with particular hydrogen bonds only Stejskal, Lenka (Wed May 02 2018 - 08:31:59 PDT)
- Re: [AMBER] .rst and .mdcrd file outputted in ascii David A Case (Wed May 02 2018 - 11:36:59 PDT)
- [AMBER] need QMMM interface for TURBOMOLE 陈金峰 (Wed May 02 2018 - 16:38:09 PDT)
- [AMBER] Multiple temperature groups I Lőrincz (Thu May 03 2018 - 07:03:13 PDT)
- [AMBER] input files from AmberTools 16/17 run on Amber14 pmemd.cuda engine problem Chetna Tyagi (Thu May 03 2018 - 07:18:54 PDT)
- Re: [AMBER] Configure CUDA issues Kadir Ozcan (Thu May 03 2018 - 08:55:34 PDT)
- Re: [AMBER] AMBER Digest, Vol 2280, Issue 1 Kadir Ozcan (Thu May 03 2018 - 15:19:23 PDT)
- [AMBER] calculation of cavity water Tousif Hossen (Fri May 04 2018 - 04:11:33 PDT)
- [AMBER] Problem in distance restraint Kshatresh Dutta Dubey (Fri May 04 2018 - 05:01:57 PDT)
- Re: [AMBER] Simulation does not restart from restart file written in previous step. Abhilash J (Fri May 04 2018 - 05:19:38 PDT)
- [AMBER] Setting initial velocities diego.soler.uam.es (Fri May 04 2018 - 05:42:39 PDT)
- [AMBER] SGLD Piotr Fajer (Sat May 05 2018 - 12:52:40 PDT)
- [AMBER] Poly amino acid helix form topology files roja rahmani (Sat May 05 2018 - 23:53:31 PDT)
- [AMBER] nativecontacts command in CPPTRAJ Ruth Helena Tichauer (Sun May 06 2018 - 03:31:06 PDT)
- [AMBER] PC modes per residue from existing evecs file? Kenneth Huang (Mon May 07 2018 - 08:15:27 PDT)
- [AMBER] Amber 18 Thermodynamic integration question David Wifling (Mon May 07 2018 - 12:27:18 PDT)
- [AMBER] Advice on SMD QM/MM for Cyanogenic Glucoside senal dinuka (Mon May 07 2018 - 23:34:21 PDT)
- [AMBER] GBNSR6 with MMPBSA.py Jose Manuel Granadino Roldán (Tue May 08 2018 - 02:08:38 PDT)
- [AMBER] MMPBSA.py.MPI and matching topology files a problem Kasprzak, Wojciech (NIH/NCI) [C] (Tue May 08 2018 - 09:17:21 PDT)
- [AMBER] Parametrization: consistency with gaff force field Alechania Misturini (Tue May 08 2018 - 11:25:50 PDT)
- [AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory Chris Neale (Tue May 08 2018 - 16:58:41 PDT)
- [AMBER] what are the benefits of cuda9 vs. 8 with amber 18? Chris Neale (Tue May 08 2018 - 21:41:11 PDT)
- [AMBER] Extracting infromation from topology file anu chandra (Tue May 08 2018 - 22:36:23 PDT)
- [AMBER] Query related to the Umbrella sampling method Saikat Pal (Tue May 08 2018 - 23:00:50 PDT)
- [AMBER] adding NME and ACE terminals roja rahmani (Wed May 09 2018 - 03:40:10 PDT)
- [AMBER] Different outputs of external electric field Meng Wu (Wed May 09 2018 - 04:05:42 PDT)
- [AMBER] Error: No data sets selected - Problem or not? Gustaf Olsson (Wed May 09 2018 - 04:15:55 PDT)
- [AMBER] QM/MM issue with boron containing compound (AMBER16) Bodee Nutho (Thu May 10 2018 - 08:04:32 PDT)
- [AMBER] MMPBSA.py execution error Jose Manuel Granadino Roldán (Thu May 10 2018 - 09:14:27 PDT)
- [AMBER] Angle calculation between three amino acids maryam azimzadehirani (Thu May 10 2018 - 23:45:27 PDT)
- [AMBER] MMPBSA.py.MPI: questions about output warnings and discrepancies Kasprzak, Wojciech (NIH/NCI) [C] (Fri May 11 2018 - 06:59:40 PDT)
- [AMBER] TMD : Doubts regarding TGTMDFRC Aravind Ravichandran (Fri May 11 2018 - 23:25:58 PDT)
- [AMBER] change the charge of the chlorine ion Saikat Pal (Sat May 12 2018 - 05:13:21 PDT)
- [AMBER] lipid MSD values for lipid 14 FF Chitrak Gupta (Sat May 12 2018 - 14:56:12 PDT)
- Re: [AMBER] Novice Question: MD Visualisation in VMD Horn, Anselm (Sun May 13 2018 - 05:07:40 PDT)
- [AMBER] lipid 14 MSD with OPC water Chitrak Gupta (Sun May 13 2018 - 12:30:48 PDT)
- [AMBER] tleap error 'FATAL: Atom .R<NMET 1>.A<CAY 20> does not have a type' Midhun K Madhu (Mon May 14 2018 - 00:26:01 PDT)
- [AMBER] combining trajectories with different parameter files Chetna Tyagi (Mon May 14 2018 - 04:31:36 PDT)
- [AMBER] GUI for TI setup Hadházi Ádám (Mon May 14 2018 - 06:38:43 PDT)
- [AMBER] autoimage problem Ming Tang (Mon May 14 2018 - 06:59:14 PDT)
- [AMBER] NetCDF error: NetCDF: Not a valid ID Midhun K Madhu (Mon May 14 2018 - 14:12:46 PDT)
- [AMBER] Creating a Gold surface library file Timothy Cholko (Mon May 14 2018 - 17:35:06 PDT)
- [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters. with pmemd.cuda David Sáez (Mon May 14 2018 - 18:49:05 PDT)
- [AMBER] MMPBSA.py - PrmtopError: Inconsistent charge definition for atom Rodrigo Galindo-Murillo (Tue May 15 2018 - 14:41:50 PDT)
- [AMBER] Electrostatic potential calculation Meng Wu (Tue May 15 2018 - 19:52:18 PDT)
- [AMBER] pmemd.MPI compatible for REMD simulation IN AMBER package Saikat Pal (Tue May 15 2018 - 22:48:07 PDT)
- [AMBER] I: help please giuseppe gatti (Wed May 16 2018 - 08:10:19 PDT)
- [AMBER] MMPBSA energy decomposition Yuxin Xie (Wed May 16 2018 - 11:38:47 PDT)
- [AMBER] Reservoir REMD using GPUs Hurst, Travis C (MU-Student) (Wed May 16 2018 - 15:25:55 PDT)
- [AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version). DHEERAJ CHITARA (Thu May 17 2018 - 01:04:54 PDT)
- [AMBER] MD stops due to the distortion of a molecule Sergey Samsonov (Thu May 17 2018 - 01:23:57 PDT)
- [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" PRITI ROY (Thu May 17 2018 - 02:45:51 PDT)
- [AMBER] DFT method for calculating amino acids partial charges in AMBER99 roja rahmani (Thu May 17 2018 - 03:10:43 PDT)
- [AMBER] Reg. generating empty frcmod file for ligand molecule DHEERAJ CHITARA (Thu May 17 2018 - 05:03:01 PDT)
- [AMBER] GPU questions 陈金峰 (Thu May 17 2018 - 07:54:17 PDT)
- [AMBER] Parametrization of Small Molecules Johannes Loeffler (Fri May 18 2018 - 02:44:56 PDT)
- [AMBER] [cpptraj] Angle between atom and two centroids Eiros Zamora, Juan (Fri May 18 2018 - 04:14:11 PDT)
- [AMBER] Facing problem to generate ala10_chir.dat in REMD tutorial Saikat Pal (Fri May 18 2018 - 05:29:21 PDT)
- [AMBER] QMMM surface scan 陈金峰 (Fri May 18 2018 - 07:55:39 PDT)
- [AMBER] Amber16 pmemd.cuda.MPI simulation can drop a frame with an inopportune node crash Chris Neale (Sat May 19 2018 - 00:07:06 PDT)
- [AMBER] Restart From Check point File Midhun K Madhu (Sun May 20 2018 - 05:47:24 PDT)
- [AMBER] Total Energy Decomposition daniele selli (Mon May 21 2018 - 04:06:56 PDT)
- [AMBER] info grafic about MD Rosellen, Martin (Mon May 21 2018 - 05:45:42 PDT)
- [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model Sadegh Faramarzi Ganjabad (Mon May 21 2018 - 11:24:52 PDT)
- [AMBER] 1x PCI-E Riser card for MD/TI? Hadházi Ádám (Tue May 22 2018 - 07:20:46 PDT)
- [AMBER] Possible memory leak with LMOD Charo del Genio (Tue May 22 2018 - 09:39:08 PDT)
- [AMBER] Scabilility of the code in cpus Ana Luisa Novo de Oliveira (Tue May 22 2018 - 09:45:39 PDT)
- [AMBER] Hydrogen Bond Occupancy Jerrano Bowleg (Tue May 22 2018 - 10:13:42 PDT)
- [AMBER] R: Re: SHAKEH: Extra bond between hydrogen atoms of TIP3 water model Sadegh Faramarzi Ganjabad (Tue May 22 2018 - 12:59:21 PDT)
- [AMBER] VMD window Karla Galdamez (Tue May 22 2018 - 20:43:23 PDT)
- [AMBER] update_amber URL time out problem Meng Wu (Wed May 23 2018 - 01:29:11 PDT)
- [AMBER] S-S bond roja rahmani (Wed May 23 2018 - 02:47:29 PDT)
- [AMBER] Use of Amber12 and 14 on the same simulation JoAnne Babula (Wed May 23 2018 - 09:09:08 PDT)
- [AMBER] parmed/chamber verify including CMAP corrections David Sáez (Wed May 23 2018 - 12:00:26 PDT)
- [AMBER] Amber 18 manual shows TI as not supported in pmemd.cuda Patricio German Barletta Roldan (Wed May 23 2018 - 13:47:48 PDT)
- [AMBER] pmemd.MPI won't work in Amber 18 Hai Long (Wed May 23 2018 - 14:37:27 PDT)
- [AMBER] optimization of QM zone in QM/MM-GBSA calculations. mish (Thu May 24 2018 - 00:10:19 PDT)
- [AMBER] Error in using pdb4amber command senal dinuka (Thu May 24 2018 - 03:14:03 PDT)
- Re: [AMBER] eCheminfo Milano July 16-29, Training and Innovation Course in Drug Design 2018, bursary and early-bird deadline ending soon Thomas Exner (Thu May 24 2018 - 04:43:18 PDT)
- [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Markowska (Thu May 24 2018 - 05:07:20 PDT)
- [AMBER] Plotting phi-psi plots with free energy scale Chetna Tyagi (Thu May 24 2018 - 07:01:19 PDT)
- [AMBER] How to evaluate the impact of PH on protein structures by Amber Lei Zhao (Thu May 24 2018 - 07:49:38 PDT)
- [AMBER] AMBER TI more examples Omoto, Kiyoyuki (Thu May 24 2018 - 08:30:55 PDT)
- [AMBER] ABMD with multiple walkers Qinghua Liao (Fri May 25 2018 - 16:00:01 PDT)
- [AMBER] CUDA v9.0 with AMBER16 Question Korey M Reid (Fri May 25 2018 - 16:56:43 PDT)
- [AMBER] Using multiple CPU threads senal dinuka (Sat May 26 2018 - 01:17:55 PDT)
- [AMBER] Troubleshooting SHAKE problems in minimization Alen Ahmetovic (Sat May 26 2018 - 21:07:29 PDT)
- [AMBER] DEADLINE EXTENDED: Call for Papers, GCC 2018, 14th German Conference on Chemoinformatics Stefan.Guessregen.sanofi.com (Mon May 28 2018 - 04:56:58 PDT)
- [AMBER] error in rst file during Minimization Subrata Paul (Mon May 28 2018 - 05:37:08 PDT)
- [AMBER] AMBER NFE SMD calculation with new collective variable georg.kuenze.vanderbilt.edu (Mon May 28 2018 - 13:51:41 PDT)
- [AMBER] AMBER: trouble while running constant pH simulation 李耀 (Mon May 28 2018 - 19:35:06 PDT)
- [AMBER] Automatic patching failed! senal dinuka (Tue May 29 2018 - 21:10:54 PDT)
- [AMBER] Request of help on Leap PDB preparation error "atom does not have a type" 符哲瀚 (Tue May 29 2018 - 21:32:33 PDT)
- [AMBER] sander failed with prmtop complex.top! Urszula Uciechowska (Tue May 29 2018 - 23:52:54 PDT)
- [AMBER] TI for side chain mutation in dimer protein Josephine la sala (Wed May 30 2018 - 02:55:48 PDT)
- [AMBER] problems with MCPY.py step 2 Cristián Ferretti (Wed May 30 2018 - 03:03:02 PDT)
- [AMBER] TiMergeError: Cannot have dihedral cross through softcore region Jissy Akkarapattiakal Kuriappan (Wed May 30 2018 - 06:07:15 PDT)
- [AMBER] TI for side chain mutation in dimer protein Josephine la sala (Wed May 30 2018 - 06:29:22 PDT)
- Re: [AMBER] AMBER: trouble while running constant pH simulation > (Cruzeiro, Vinicius Wilian D) 李耀 (Wed May 30 2018 - 08:48:29 PDT)
- [AMBER] Conda Installation error andreas.tosstorff.cup.uni-muenchen.de (Wed May 30 2018 - 10:51:25 PDT)
- Re: [AMBER] Problem with g++ compiler with boost (AmberTools18) Matias Machado (Wed May 30 2018 - 19:12:28 PDT)
- [AMBER] Dimension Box visualization Aashish Bhatt (Wed May 30 2018 - 23:00:50 PDT)
- [AMBER] Ubuntu 18 Sepideh Jafari (Thu May 31 2018 - 06:22:00 PDT)
- [AMBER] Initial configuration of ADP and ion simulation using AMBER. Abhilash J (Thu May 31 2018 - 09:45:12 PDT)
- Last message date: Thu May 31 2018 - 13:00:03 PDT
- Archived on: Mon Apr 22 2024 - 05:55:34 PDT
