Amber Archive Jun 2016 by thread
- Re: [AMBER] cpptraj clustering based on ligand cavity Neha Gandhi (Tue May 31 2016 - 18:28:22 PDT)
- [AMBER] rdf or watershell Neha Gandhi (Tue May 31 2016 - 18:31:54 PDT)
- [AMBER] QMS-QMMM Odin Zeus (Tue May 31 2016 - 20:51:50 PDT)
- [AMBER] radial (rdf) computation time Neha Gandhi (Wed Jun 01 2016 - 00:28:03 PDT)
- [AMBER] FW: MMPBSA.py issue with complex prmtop file Kalenkiewicz, Andrew (NIH/NICHD) [F] (Wed Jun 01 2016 - 11:34:44 PDT)
- [AMBER] Amber Cpptraj troubleshoot Angelina Malagodi (Wed Jun 01 2016 - 15:55:50 PDT)
- [AMBER] mmgbsa calculation chemjxn (Wed Jun 01 2016 - 17:25:53 PDT)
- [AMBER] parmchk and parmchk2 segmentation fault Neha Gandhi (Wed Jun 01 2016 - 18:41:51 PDT)
- [AMBER] Unreadable rst7 Elisa Pieri (Thu Jun 02 2016 - 01:51:14 PDT)
- [AMBER] mmpbsa analys Ziba Bahadori (Thu Jun 02 2016 - 10:05:21 PDT)
- Re: [AMBER] Replacing water with a H2O2 and restart the simulation Morteza Chehel Amirani (Thu Jun 02 2016 - 13:37:09 PDT)
- Re: [AMBER] mdl file for 1d-rism Jingyi Yan (Thu Jun 02 2016 - 14:51:58 PDT)
- [AMBER] Some problems about heme 163邮箱 (Fri Jun 03 2016 - 02:25:01 PDT)
- [AMBER] iwrap and mmpbsa Mary Varughese (Fri Jun 03 2016 - 03:16:40 PDT)
- [AMBER] re imaging doubt Mary Varughese (Fri Jun 03 2016 - 03:58:20 PDT)
- [AMBER] Amber16 won't install Gulsevin,Alican (Fri Jun 03 2016 - 04:01:23 PDT)
- [AMBER] proper box size to calculate binding enthalpy of host-guest in explicit solvent Budhathoki, Dipesh (Fri Jun 03 2016 - 10:27:42 PDT)
- Re: [AMBER] GAFF2 setup Igor Marques (Fri Jun 03 2016 - 12:40:19 PDT)
- [AMBER] TI calculation with ligand dimer Hu, Yuan (Fri Jun 03 2016 - 15:39:31 PDT)
- [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 mmaestre (Fri Jun 03 2016 - 22:41:40 PDT)
- [AMBER] Principle Component Analysis (PCA) in cpptraj Himanshu Joshi (Sat Jun 04 2016 - 06:14:43 PDT)
- [AMBER] Some problems about Heme 163邮箱 (Sat Jun 04 2016 - 06:29:09 PDT)
- [AMBER] mmpbsa problem Ziba Bahadori (Sat Jun 04 2016 - 07:05:50 PDT)
- [AMBER] Ambertools16 test failed for leap zoran matovic (Sat Jun 04 2016 - 14:18:22 PDT)
- [AMBER] pulling a zn ion with SMD Fabian gmail (Sun Jun 05 2016 - 04:29:05 PDT)
- [AMBER] [Amber] Build parameters on HEME-Fe-HIS system 163邮箱 (Sun Jun 05 2016 - 08:28:22 PDT)
- [AMBER] Protein - ligand tutorials - reg arthivenkat2.gmail.com (Sun Jun 05 2016 - 11:13:59 PDT)
- [AMBER] proper box size to calculate binding enthalpy of host-guest in explicit solvent Budhathoki, Dipesh (Sun Jun 05 2016 - 14:16:12 PDT)
- [AMBER] test 4096wat mmaestre (Sun Jun 05 2016 - 22:16:35 PDT)
- [AMBER] Issue of AMBER 2016 with CUDA Huian Li (Mon Jun 06 2016 - 06:24:07 PDT)
- [AMBER] restarting a run Thomas Pochapsky (Mon Jun 06 2016 - 06:27:54 PDT)
- [AMBER] cpinutil.py problem Elisa Pieri (Mon Jun 06 2016 - 06:46:53 PDT)
- Re: [AMBER] proper box size to calculate binding enthalpy of host-guest Budhathoki, Dipesh (Mon Jun 06 2016 - 11:06:55 PDT)
- Re: [AMBER] Clustering of MD trajectories: ptraj, cpptraj Daniel Roe (Mon Jun 06 2016 - 12:57:41 PDT)
- [AMBER] setMolecules failed Damiano Spadoni (Mon Jun 06 2016 - 13:01:52 PDT)
- [AMBER] cpptraj reading a reference coordinate for analyses Neha Gandhi (Tue Jun 07 2016 - 01:43:18 PDT)
- [AMBER] Amber14 & Cuda 7.5 Nikolay N. Kuzmich (Tue Jun 07 2016 - 05:03:52 PDT)
- [AMBER] Umbrella sampling with two degrees of freedom Airy Sanjeev (Tue Jun 07 2016 - 21:16:50 PDT)
- [AMBER] Energy decomposition in MM/GBSA mish (Tue Jun 07 2016 - 22:35:21 PDT)
- [AMBER] neuraminic acid mmaestre (Wed Jun 08 2016 - 00:44:00 PDT)
- [AMBER] Error while trying to upgrade AmberTools 15 Nikolay N. Kuzmich (Wed Jun 08 2016 - 02:48:28 PDT)
- [AMBER] MD simulations with jar=1 and more than one nmropt restraint James Murdock (Wed Jun 08 2016 - 03:39:46 PDT)
- [AMBER] How to define COM group of atoms greater than 1024 atoms when nmropt=1 and pmemd.cuda.MPI Shuntaro Chiba (Wed Jun 08 2016 - 08:07:55 PDT)
- [AMBER] Umbrella Sampling Airy Sanjeev (Wed Jun 08 2016 - 09:15:58 PDT)
- [AMBER] Dismal QM/MM Efficiency Nisler, Collin R. (Wed Jun 08 2016 - 11:52:45 PDT)
- [AMBER] hanging test mdgx/1p7e for installation to 'long' path Kenneth Hoste (Wed Jun 08 2016 - 13:28:23 PDT)
- [AMBER] Principal Component Analysis Kat G (Wed Jun 08 2016 - 18:10:47 PDT)
- [AMBER] buffer OR buffer_xyz_list in setBox command mish (Wed Jun 08 2016 - 18:35:35 PDT)
- [AMBER] energy decomposition Sanjib Paul (Wed Jun 08 2016 - 23:55:35 PDT)
- [AMBER] INDIGO-DataCloud Newsletter, May 2016 galileo.galile22.yahoo.com (Thu Jun 09 2016 - 02:28:03 PDT)
- [AMBER] THF parametrization Norbert GARNIER (Thu Jun 09 2016 - 05:39:54 PDT)
- [AMBER] PCA error not Lara rajam (Thu Jun 09 2016 - 11:28:30 PDT)
- [AMBER] RMSD for the backbone atoms of residues Aishani Prem (Thu Jun 09 2016 - 12:14:32 PDT)
- [AMBER] QM/MM MD problem Debodyuti Dutta (Thu Jun 09 2016 - 21:31:55 PDT)
- [AMBER] Issue with with the nocenter in tLeap Sushil Mishra (Thu Jun 09 2016 - 23:39:02 PDT)
- [AMBER] FF14SB implementation Miroslav Krepl (Fri Jun 10 2016 - 06:37:38 PDT)
- [AMBER] Error in tleap for the atom type of OCT1 and OCT2 of glutamic acid at C-terminal Shreeramesh (Fri Jun 10 2016 - 07:16:49 PDT)
- [AMBER] addition of hydrogen to unionised the -COO group Martina Devi (Fri Jun 10 2016 - 08:00:42 PDT)
- [AMBER] Regarding error in MMPBSA MOHD HOMAIDUR RAHMAN (Fri Jun 10 2016 - 14:35:26 PDT)
- [AMBER] radial distribution function tails for liquids using GAFF conor parks (Fri Jun 10 2016 - 18:51:35 PDT)
- [AMBER] Free energy decomposition of QM/MM-GBSA Allen Zou (Sat Jun 11 2016 - 07:48:37 PDT)
- [AMBER] Help me with double ambiguous noe.map files!!! PLEASE tanfei777.sina.cn (Sun Jun 12 2016 - 00:28:05 PDT)
- [AMBER] Problem in Calculating Rotational diffusion ATUL KUMAR (Sun Jun 12 2016 - 06:22:52 PDT)
- [AMBER] 回复：Re: Help me with double ambiguous noe.map files!!! PLEASE tanfei777.sina.cn (Sun Jun 12 2016 - 21:15:45 PDT)
- [AMBER] Can I turn off group coordinate averaging? tanfei777.sina.cn (Sun Jun 12 2016 - 21:59:17 PDT)
- [AMBER] problems with building sulfo sialil-lacnac mmaestre (Mon Jun 13 2016 - 01:00:37 PDT)
- [AMBER] umbrella sampling with two degrees of freedom Airy Sanjeev (Mon Jun 13 2016 - 05:06:29 PDT)
- [AMBER] Choose reference frame for rmsd Jean-Patrick Francoia (Mon Jun 13 2016 - 05:55:31 PDT)
- [AMBER] umbrella sampling long axex problem Airy Sanjeev (Mon Jun 13 2016 - 08:50:11 PDT)
- [AMBER] Radial Distribution Function Angelina Malagodi (Mon Jun 13 2016 - 10:38:24 PDT)
- [AMBER] 回复：Re: Help me with double ambiguous noe.map files!!! PLEASE tanfei777.sina.cn (Mon Jun 13 2016 - 20:06:30 PDT)
- [AMBER] Fwd: eChemInfo Workshop on Rational Drug Design in Milano Thomas Exner (Mon Jun 13 2016 - 23:01:44 PDT)
- [AMBER] antechamber error message Martina Devi (Tue Jun 14 2016 - 00:02:07 PDT)
- [AMBER] Errors in my installation Abdul-Rashid Iii Sampaco (Tue Jun 14 2016 - 01:22:56 PDT)
- [AMBER] Problem: Do not receive mails from Amber list but Amber digest SHAILESH KUMAR (Tue Jun 14 2016 - 02:10:42 PDT)
- [AMBER] Difference between radius of gyration and max radius of gyration Jean-Patrick Francoia (Tue Jun 14 2016 - 04:42:12 PDT)
- [AMBER] [ANN] Release of NGLView for interactive trajectory visualization in Jupyter notebooks. Hai Nguyen (Tue Jun 14 2016 - 11:05:11 PDT)
- [AMBER] amber16 pmemd cuda rst file Neha Gandhi (Tue Jun 14 2016 - 14:29:43 PDT)
- [AMBER] Visualizing QM/MM Simulations Nisler, Collin R. (Tue Jun 14 2016 - 19:26:07 PDT)
- [AMBER] Density File Wong Li Zhe (Tue Jun 14 2016 - 19:27:36 PDT)
- [AMBER] Reminder: Training and Innovation Course in Drug Design Thomas Exner (Tue Jun 14 2016 - 23:59:22 PDT)
- [AMBER] Lipidorder/No output Batuhan Kav (Wed Jun 15 2016 - 02:56:31 PDT)
- [AMBER] ABOUT the GaMD patch for Amber14 Yeng-Tseng Wang (Wed Jun 15 2016 - 08:50:45 PDT)
- [AMBER] Which of charge methods in antechamber are appropriate? Atila Petrosian (Wed Jun 15 2016 - 11:10:54 PDT)
- [AMBER] Imaging problem? colvin (Wed Jun 15 2016 - 21:11:39 PDT)
- [AMBER] QMMM-MD Odin Zeus (Wed Jun 15 2016 - 22:36:37 PDT)
- [AMBER] mmpbsa doubt Mary Varughese (Thu Jun 16 2016 - 00:42:36 PDT)
- [AMBER] extremely slow cluster analysis with cpptraj Michael Shokhen (Thu Jun 16 2016 - 01:17:18 PDT)
- [AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR (Thu Jun 16 2016 - 06:33:21 PDT)
- [AMBER] Entropy normal mode error George Tzotzos (Thu Jun 16 2016 - 08:08:16 PDT)
- [AMBER] script for calculation of dihedral angle frequency Sehrish Naz Aijaz (Fri Jun 17 2016 - 00:36:14 PDT)
- [AMBER] Une demande d'aide avec GAFF ( 2 ) Chloe Renard (Fri Jun 17 2016 - 01:36:44 PDT)
- [AMBER] NMR restraints on GPU (asterisks in output) Miroslav Krepl (Fri Jun 17 2016 - 02:21:15 PDT)
- [AMBER] volmap: densities too low Jean-Patrick Francoia (Sat Jun 18 2016 - 03:38:35 PDT)
- [AMBER] GIST calculation Sanjib Paul (Sat Jun 18 2016 - 04:46:05 PDT)
- [AMBER] Saving the coordinates during a simulation Aishani Prem (Mon Jun 20 2016 - 11:31:12 PDT)
- [AMBER] Bad atom type: FE when calculating free energy using mmpbsa 163邮箱 (Tue Jun 21 2016 - 01:08:34 PDT)
- [AMBER] Principle component analysis: percentage contribution of eigenvectors Hirdesh Kumar (Tue Jun 21 2016 - 05:52:11 PDT)
- [AMBER] Amber16+CUDA8.0 pmemd.cuda worked, and then stopped working, saying "cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" Zack Scholl (Tue Jun 21 2016 - 08:03:19 PDT)
- [AMBER] Problem analysing output with process_mdout.perl script Ruth Helena Tichauer (Tue Jun 21 2016 - 08:46:40 PDT)
- [AMBER] Problem with PCA projection Kat G (Tue Jun 21 2016 - 09:26:01 PDT)
- [AMBER] Amber16 and CUDA8.0 pmemd.cuda worked, and then stopped working, saying "cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" Zack Scholl (Tue Jun 21 2016 - 09:44:14 PDT)
- [AMBER] Problem with PCA projection (cont) Kat G (Tue Jun 21 2016 - 10:41:32 PDT)
- [AMBER] AMBER support for gtx1080 Anton Perera (Tue Jun 21 2016 - 21:56:06 PDT)
- [AMBER] Query regarding dihedral angles Sehrish Naz Aijaz (Tue Jun 21 2016 - 22:17:51 PDT)
- [AMBER] convergence criteria in enhanced md techniques Neha Gandhi (Wed Jun 22 2016 - 05:43:18 PDT)
- [AMBER] RESP charges amir sadeghi (Wed Jun 22 2016 - 11:53:14 PDT)
- [AMBER] MMPBSA.PY Error :LengthError: length mismatch in energy vectors 徐明远 (Thu Jun 23 2016 - 04:07:06 PDT)
- [AMBER] Running pmemd.MPI across the nodes Himanshu Joshi (Thu Jun 23 2016 - 04:30:35 PDT)
- [AMBER] MMPBSA.py nmode output problem Xiao-Lei Wang (Thu Jun 23 2016 - 05:38:00 PDT)
- [AMBER] measures of data reliability in Steered MD Asmita Gupta (Thu Jun 23 2016 - 07:25:30 PDT)
- [AMBER] Error in MMPBSA Shreeramesh (Thu Jun 23 2016 - 07:50:16 PDT)
- [AMBER] Error in MCPB.py Fabrício Bracht (Thu Jun 23 2016 - 09:19:31 PDT)
- [AMBER] Amber16 + GTX1080 - working well Beavil, Andrew (Thu Jun 23 2016 - 13:49:26 PDT)
- [AMBER] cpptraj analysis of water in cavity Michael Shokhen (Fri Jun 24 2016 - 00:58:04 PDT)
- Re: [AMBER] SHAKE Error bharat gupta (Fri Jun 24 2016 - 03:42:55 PDT)
- [AMBER] HYDROGEN BONDING ANALYSIS chemjxn (Fri Jun 24 2016 - 04:35:19 PDT)
- [AMBER] How to compare protein dynamics in free and bound-ligands states with cpptraj Kat G (Fri Jun 24 2016 - 11:38:37 PDT)
- [AMBER] solvent equilibration Shilpa Gupta (Sat Jun 25 2016 - 06:03:57 PDT)
- [AMBER] Fw: Ziba Bahadori (Sat Jun 25 2016 - 23:00:04 PDT)
- [AMBER] Mmpbsa problem Ziba Bahadori (Sat Jun 25 2016 - 23:08:40 PDT)
- [AMBER] Regarding run.rst file generation Vishal Nemaysh (Sun Jun 26 2016 - 07:10:59 PDT)
- Re: [AMBER] AMBER Digest, Vol 1616, Issue 1 bharat gupta (Sun Jun 26 2016 - 08:09:49 PDT)
- [AMBER] can we sample ligand conformation in Amber Albert (Sun Jun 26 2016 - 11:31:43 PDT)
- Re: [AMBER] AMBER Digest, Vol 1618, Issue 1 bharat gupta (Sun Jun 26 2016 - 18:06:36 PDT)
- [AMBER] Thermodynamic Integration with QM/MM Hamiltonian Xiangyu Jia (Mon Jun 27 2016 - 00:07:30 PDT)
- [AMBER] Distorted and clumped structures after cpptraj average structure calculation Prayagraj Fandilolu (Mon Jun 27 2016 - 03:52:57 PDT)
- [AMBER] MCPB Fabrício Bracht (Mon Jun 27 2016 - 12:56:17 PDT)
- [AMBER] problem:hydrogen bonding analysis contain water molecular chemjxn (Mon Jun 27 2016 - 21:35:00 PDT)
- [AMBER] charge of aminoacids in an special pH Atila Petrosian (Tue Jun 28 2016 - 00:18:01 PDT)
- Re: [AMBER] QM/MM - SCF converge error bharat gupta (Tue Jun 28 2016 - 02:12:06 PDT)
- [AMBER] Hidden parameters for tleap Lea Natalia Toledo Carvajal (Tue Jun 28 2016 - 04:22:01 PDT)
- [AMBER] prepin to mol2 Martina Devi (Tue Jun 28 2016 - 09:37:23 PDT)
- [AMBER] convert mol2 to prepin Martina Devi (Tue Jun 28 2016 - 09:40:39 PDT)
- [AMBER] difference in ptraj for ambertools-12 and 15 Thakur, Abhishek (Tue Jun 28 2016 - 13:54:54 PDT)
- [AMBER] Error: [cluster] Not all arguments handled: [ pdb ] Thakur, Abhishek (Tue Jun 28 2016 - 13:59:18 PDT)
- [AMBER] the meaning of NONBON in frcmod Zhenyu Meng (Tue Jun 28 2016 - 21:26:18 PDT)
- [AMBER] equilibration problem esther nehu (Tue Jun 28 2016 - 22:40:59 PDT)
- [AMBER] Does Amber14 work with CUDA higher than 6.5? Karolina Markowska (Wed Jun 29 2016 - 00:25:44 PDT)
- Re: [AMBER] QM/MM simulation bharat gupta (Wed Jun 29 2016 - 01:44:46 PDT)
- Re: [AMBER] Slow performance of Amber12 on cluster bharat gupta (Wed Jun 29 2016 - 01:56:28 PDT)
- [AMBER] RMSD PLot ankita mehta (Wed Jun 29 2016 - 02:22:14 PDT)
- [AMBER] Using Gromcas trajectories with CPPTRAJ anu chandra (Wed Jun 29 2016 - 02:57:01 PDT)
- Re: [AMBER] 9. Hidden parameters for tleap Lea Natalia Toledo Carvajal (Wed Jun 29 2016 - 03:09:26 PDT)
- [AMBER] TIP3PFBOX: water model Shilpa Gupta (Wed Jun 29 2016 - 05:32:49 PDT)
- [AMBER] Advice for Implicit Solvent MD with Nucleic Acids Kasprzak, Wojciech (NIH/NCI) [C] (Wed Jun 29 2016 - 07:22:16 PDT)
- [AMBER] Structural refinement of the protein complexed with metalo-ions James Starlight (Wed Jun 29 2016 - 07:39:21 PDT)
- [AMBER] convert mol2 to pdb Martina Devi (Wed Jun 29 2016 - 07:57:36 PDT)
- [AMBER] Ambertools16 error compiling Esteban Gabriel Vega Hissi (Wed Jun 29 2016 - 10:43:36 PDT)
- [AMBER] Library errors while using NAB on Amber16 Slava Chushak (Wed Jun 29 2016 - 12:01:04 PDT)
- [AMBER] cutoff and switching Bisignano, Paola (Wed Jun 29 2016 - 17:24:15 PDT)
- [AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt Jose Manuel Gally (Thu Jun 30 2016 - 00:48:14 PDT)
- [AMBER] compiling reduce with gcc6 David A Case (Thu Jun 30 2016 - 05:45:07 PDT)
- [AMBER] one more point about gcc6 David A Case (Thu Jun 30 2016 - 06:06:24 PDT)
- [AMBER] addAtomType problem Lea Natalia Toledo Carvajal (Thu Jun 30 2016 - 08:58:49 PDT)
- [AMBER] how to calculate the correlation function for first water shell? Parviz Seifpanahi Shabane (Thu Jun 30 2016 - 09:20:10 PDT)
- [AMBER] Regarding ho parameter in gaff MOHD HOMAIDUR RAHMAN (Thu Jun 30 2016 - 11:01:35 PDT)
- [AMBER] GB-neck2 MD with nucleic acids Kasprzak, Wojciech (NIH/NCI) [C] (Thu Jun 30 2016 - 11:29:48 PDT)
- [AMBER] bad atom type decomp Bruno Falcone (Thu Jun 30 2016 - 11:33:39 PDT)
- Re: [AMBER] Progress with testing GB-neck2 MD with nucleic acids Kasprzak, Wojciech (NIH/NCI) [C] (Thu Jun 30 2016 - 13:16:19 PDT)
- Last message date: Thu Jun 30 2016 - 19:30:03 PDT
- Archived on: Fri Dec 20 2024 - 05:55:24 PST
