Amber Archive Dec 2014 by thread
- Re: [AMBER] hydophobicity Mary Varughese (Sun Nov 30 2014 - 17:38:19 PST)
- Re: [AMBER] Monitoring pi-cationic interaction asdda asa (Sun Nov 30 2014 - 19:37:03 PST)
- Re: [AMBER] installing amber12 in GPU Vijay Achari (Sun Nov 30 2014 - 23:30:21 PST)
- [AMBER] LEaP Error Aronica, Pietro (Mon Dec 01 2014 - 03:23:28 PST)
- Re: [AMBER] Problem with triangular point in parameter file David A Case (Mon Dec 01 2014 - 04:24:52 PST)
- [AMBER] tleap segmentation fault George Tzotzos (Mon Dec 01 2014 - 11:44:32 PST)
- [AMBER] Problems with amber14 intallation in parallel Dailin Li (Mon Dec 01 2014 - 17:39:58 PST)
- [AMBER] Ambertools14 Installation Appears to Reset Edward Kalkreuter (Mon Dec 01 2014 - 18:16:12 PST)
- Re: [AMBER] TI and FEW Nadine Homeyer (Mon Dec 01 2014 - 23:34:40 PST)
- [AMBER] bug in "natural language" system to define nmropt restraints: generalized distance coordinate Marc van der Kamp (Tue Dec 02 2014 - 01:29:50 PST)
- [AMBER] accelerated MD set up Asmita Gupta (Tue Dec 02 2014 - 03:15:27 PST)
- [AMBER] how to retain the MG++ coordination geometry during simulation BERGY (Tue Dec 02 2014 - 11:59:57 PST)
- [AMBER] On the significant dG error in the MMGBSA results.dat James Starlight (Tue Dec 02 2014 - 13:29:27 PST)
- [AMBER] Linker Attached to DNA Brittany Boykin (Tue Dec 02 2014 - 13:58:41 PST)
- [AMBER] DMPC lipids are slightly charged in lipid14? Matthew Harrigan (Tue Dec 02 2014 - 22:00:41 PST)
- [AMBER] MMGBSA.py cpptraj - autoimaging issue de Manzanos Guinot, Angela (Wed Dec 03 2014 - 02:54:09 PST)
- [AMBER] B-factor values George Tzotzos (Wed Dec 03 2014 - 10:49:28 PST)
- [AMBER] Help regarding error in top n crd generation Ruchika Bhat (Wed Dec 03 2014 - 23:14:29 PST)
- [AMBER] How to calculate energy change between two conformations Kshatresh Dutta Dubey (Thu Dec 04 2014 - 07:28:57 PST)
- [AMBER] Docking with Dock6 Wong, Sook (NIH/NCATS) [V] (Thu Dec 04 2014 - 09:28:28 PST)
- [AMBER] Monitoring GPU voltage Kenneth Lam (Thu Dec 04 2014 - 12:08:32 PST)
- [AMBER] xleap segmentation fault when removing residues Mickey Richards (Thu Dec 04 2014 - 15:03:42 PST)
- [AMBER] TINKER and SANDER minimization (AMOEBA force field) 양지현 (Thu Dec 04 2014 - 18:17:11 PST)
- Re: [AMBER] CHAMBER error Abhishek TYAGI (Thu Dec 04 2014 - 19:25:06 PST)
- [AMBER] closeness Sylvester Tumusiime (Thu Dec 04 2014 - 21:12:36 PST)
- [AMBER] MMGBSA.py - issues with molsurf de Manzanos Guinot, Angela (Fri Dec 05 2014 - 02:29:41 PST)
- [AMBER] Problems with implicit solvent Carlo Guardiani (Fri Dec 05 2014 - 03:11:56 PST)
- Re: [AMBER] problem with unknown compiler: gnu Narendar Kolimi (Fri Dec 05 2014 - 04:20:40 PST)
- [AMBER] Alignment before calculation? Soumendranath Bhakat (Fri Dec 05 2014 - 07:12:38 PST)
- [AMBER] error creating mol2 files Anupam Goel (Fri Dec 05 2014 - 08:26:13 PST)
- [AMBER] Can i combine the result given by sander and pmemd together wangmt (Sat Dec 06 2014 - 01:21:54 PST)
- [AMBER] Use of special characters * and ? in ambermask Emilio Lence (Sat Dec 06 2014 - 11:31:27 PST)
- [AMBER] Problems with amber14 intallation in parallel Dailin Li (Sat Dec 06 2014 - 17:42:10 PST)
- [AMBER] acetate params for mtkpp Francesco Pietra (Sun Dec 07 2014 - 09:41:32 PST)
- [AMBER] ERROR USING tleap ROOPALI VERMA (Mon Dec 08 2014 - 03:08:15 PST)
- [AMBER] Calculating of charge MOHD HOMAIDUR RAHMAN (Mon Dec 08 2014 - 03:57:47 PST)
- [AMBER] single strand DNA Urszula Uciechowska (Mon Dec 08 2014 - 05:45:34 PST)
- [AMBER] Problem with AMBER mail list wangmt (Mon Dec 08 2014 - 06:26:47 PST)
- [AMBER] help in calculating diffusion coefficient Robin Jain (Mon Dec 08 2014 - 06:40:52 PST)
- Re: [AMBER] MMPBSA.py bad atom type Jason Swails (Mon Dec 08 2014 - 07:10:22 PST)
- [AMBER] Wrong bond types in Antechamber MOL2 Denis Schmidt (Mon Dec 08 2014 - 07:21:11 PST)
- Re: [AMBER] Instructions on How to install Amber on Suse Linux Jin Zhang (Mon Dec 08 2014 - 07:55:55 PST)
- [AMBER] analyze.x error when dealing with the system containing ions in tinker Ya Gao (Mon Dec 08 2014 - 08:47:05 PST)
- [AMBER] Lipid 14 PDB format Romero, Raquel (Mon Dec 08 2014 - 10:56:58 PST)
- [AMBER] selecting the best docking pose with MM/PBSA Thomas Evangelidis (Mon Dec 08 2014 - 15:22:39 PST)
- [AMBER] Software announcement: Release of PUPIL 3.0 Joan Torras (Mon Dec 08 2014 - 15:36:14 PST)
- [AMBER] sander.PUPIL compile error 汪盛 (Mon Dec 08 2014 - 19:12:49 PST)
- [AMBER] questions about bcc charge 徐晓庶 (Mon Dec 08 2014 - 22:07:11 PST)
- [AMBER] Antechamber problem Atila Petrosian (Mon Dec 08 2014 - 22:49:45 PST)
- [AMBER] Empirical force fields: release of R.E.D. Server Dev./PyRED Nov. 2014 FyD (Tue Dec 09 2014 - 00:30:32 PST)
- [AMBER] Query about MMPBSA.py de Manzanos Guinot, Angela (Tue Dec 09 2014 - 08:49:04 PST)
- [AMBER] getting the input files for antechamber Ahmet yıldırım (Tue Dec 09 2014 - 11:49:05 PST)
- [AMBER] AmberTools suppose program Yu Chen (Tue Dec 09 2014 - 12:27:28 PST)
- [AMBER] Add MgCl2 salts Haining Liu (Tue Dec 09 2014 - 13:13:58 PST)
- [AMBER] TLEAP issues Wong, Sook (NIH/NCATS) [V] (Tue Dec 09 2014 - 13:59:01 PST)
- [AMBER] switch digest model to normal fjliu (Tue Dec 09 2014 - 19:17:07 PST)
- [AMBER] Failure to restart H-REMD Carlo Guardiani (Wed Dec 10 2014 - 01:57:03 PST)
- [AMBER] another segfault with sander14 and TI/softcore Hannes Loeffler (Wed Dec 10 2014 - 02:04:48 PST)
- [AMBER] Amber12 parallel installation error Kanin Wichapong (Wed Dec 10 2014 - 06:43:05 PST)
- [AMBER] PM6-DH+ simulation problem Marcos Serrou do Amaral (Wed Dec 10 2014 - 09:05:57 PST)
- [AMBER] Information on ff12polA and ff12polL Manikanthan Bhavaraju (Wed Dec 10 2014 - 10:55:18 PST)
- [AMBER] MMPBSA-ERROR for firstmolecule-dna Abhishek TYAGI (Wed Dec 10 2014 - 19:05:46 PST)
- [AMBER] Is BUG in cpptraj of version 14?? Chris Gao (Wed Dec 10 2014 - 22:51:43 PST)
- [AMBER] steered MD based on PCA Guillaume Roellinger (Thu Dec 11 2014 - 00:34:12 PST)
- Re: [AMBER] Free energy landscape Carlos Simmerling (Thu Dec 11 2014 - 06:08:55 PST)
- [AMBER] Generate pmf of small molecule membrane insertion wmsmith (Thu Dec 11 2014 - 14:34:02 PST)
- [AMBER] Problem with simulation of protein-DNA complex Aditya Sarkar (Fri Dec 12 2014 - 00:49:20 PST)
- [AMBER] script to convert the Gromacs topology to Amber topology? Ravi Tripathi (Fri Dec 12 2014 - 01:19:47 PST)
- [AMBER] MM-PBSA (addions) Atila Petrosian (Fri Dec 12 2014 - 03:20:02 PST)
- [AMBER] AmberTools14/Amber10 Francesco Pietra (Fri Dec 12 2014 - 03:40:56 PST)
- [AMBER] change the mode of my AMBER mail list from digest to normal fjliu (Fri Dec 12 2014 - 03:56:56 PST)
- [AMBER] MM-PBSA (addions) Atila Petrosian (Fri Dec 12 2014 - 04:54:15 PST)
- [AMBER] conversion of AMBER trajectory to Gromacs trajectory Robin Jain (Fri Dec 12 2014 - 23:14:24 PST)
- [AMBER] Generation of 3D structure of polypeptides with modified amino acids Suman Chakrabarty (Sat Dec 13 2014 - 02:01:47 PST)
- [AMBER] 8Mureabox URE residue unknown CHAMI F. (Sat Dec 13 2014 - 06:13:21 PST)
- [AMBER] PCA 2dprojection with xtal data and energy information BERGY (Sat Dec 13 2014 - 14:39:58 PST)
- [AMBER] "Unit 18 Error on OPEN: logfile" kurisaki (Sat Dec 13 2014 - 16:57:28 PST)
- [AMBER] production run for diffusion constant Robin Jain (Sun Dec 14 2014 - 07:39:17 PST)
- [AMBER] Looking for AMBER FF12SB for CHARMM Zhang, Sixue (Sun Dec 14 2014 - 14:52:03 PST)
- [AMBER] Glycan-protein h-bond ptraj maryam azimzadehirani (Sun Dec 14 2014 - 19:40:05 PST)
- [AMBER] Error in Box Dimension 杨川 (Sun Dec 14 2014 - 20:13:13 PST)
- [AMBER] Optimization under restraint atoms using ibelly option Akihiro Yamane (Mon Dec 15 2014 - 04:12:08 PST)
- [AMBER] gas phase, nonperiodic system with AMOEBA ff in AMBER Lawrenz, Morgan (Mon Dec 15 2014 - 12:17:51 PST)
- [AMBER] Missing psi dihedral at cationic N-terminus of protein/peptide? nealec (Mon Dec 15 2014 - 13:32:42 PST)
- [AMBER] error while saving prmtop and inpcrd Anupam Goel (Mon Dec 15 2014 - 14:38:07 PST)
- [AMBER] Analyzing multiple trajectories in cpptraj Gard Nelson (Mon Dec 15 2014 - 17:37:32 PST)
- [AMBER] Different convergence in pmemd.cuda against CPU Hiromasa WATANABE (Mon Dec 15 2014 - 20:42:18 PST)
- [AMBER] How to analyze REMD results Wang Moye (Mon Dec 15 2014 - 22:42:04 PST)
- [AMBER] Fwd: RED-III.52-Tools stopped to work suddenly. Zeinab Emami (Tue Dec 16 2014 - 03:05:19 PST)
- [AMBER] Amber 12 on K20 GPUs -- how am I doing? Baker D.J. (Tue Dec 16 2014 - 04:22:22 PST)
- [AMBER] phosphoserine parameters Jacopo Sgrignani (Tue Dec 16 2014 - 07:17:06 PST)
- [AMBER] clustering problem in ambertool14 Mahendra B Thapa (Tue Dec 16 2014 - 10:28:13 PST)
- [AMBER] excluding atom sets from MMPB/GB-SA calculations Hallel Freedman (Tue Dec 16 2014 - 16:49:18 PST)
- [AMBER] TiMergeError fjliu (Tue Dec 16 2014 - 22:18:15 PST)
- Re: [AMBER] subscribe amber wliu (Tue Dec 16 2014 - 23:53:07 PST)
- [AMBER] error in parallel installation of Amber 12 with AmberTools13 Robin Jain (Wed Dec 17 2014 - 01:47:07 PST)
- [AMBER] error running equilibration (wall clock called) Anupam Goel (Wed Dec 17 2014 - 11:41:00 PST)
- [AMBER] leap crashes and set: Improper number of arguments! Francesco Pietra (Wed Dec 17 2014 - 13:52:57 PST)
- [AMBER] help in calculation of diffusion coefficient Robin Jain (Thu Dec 18 2014 - 07:28:33 PST)
- [AMBER] installing error Amber 12 Error Houcemeddine Othman (Thu Dec 18 2014 - 07:37:54 PST)
- [AMBER] help on the AMBER Tutorial B0 Dabing Chen (Thu Dec 18 2014 - 08:37:52 PST)
- Re: [AMBER] how can i use acpype yaser (Thu Dec 18 2014 - 08:55:18 PST)
- [AMBER] unclear leap crashing Francesco Pietra (Thu Dec 18 2014 - 10:53:21 PST)
- [AMBER] Improper torsions in NMA Ganesh Kamath (Thu Dec 18 2014 - 14:13:17 PST)
- [AMBER] pseudo F-statistic (pSF) Jonathan Gough (Thu Dec 18 2014 - 14:54:39 PST)
- [AMBER] error in install amber Yaser Hosseini (Fri Dec 19 2014 - 02:05:24 PST)
- [AMBER] Free Energy Workshop, Münster, March 9-11, 2015 Vlad Cojocaru (Fri Dec 19 2014 - 04:58:42 PST)
- [AMBER] Hydrogen charge site and Oxygen V-site displacement Sylvester Tumusiime (Sun Dec 21 2014 - 04:29:18 PST)
- [AMBER] Error in pmemd.amoeba.MPI run Ya Gao (Sun Dec 21 2014 - 05:17:01 PST)
- [AMBER] pmemd.MPI fails to run Fabian Glaser (Sun Dec 21 2014 - 06:02:10 PST)
- [AMBER] pmemd.MPI fails Fabian Glaser (Sun Dec 21 2014 - 07:39:31 PST)
- [AMBER] error in acpype Yaser Hosseini (Sun Dec 21 2014 - 08:34:13 PST)
- [AMBER] Singe point QM/MM energy using Gaussian interface Bence Hégely (Sun Dec 21 2014 - 10:37:43 PST)
- [AMBER] How to analyze REMD results Wang Moye (Sun Dec 21 2014 - 16:13:15 PST)
- [AMBER] NVE simulation Robin Jain (Sun Dec 21 2014 - 21:48:07 PST)
- [AMBER] Laccase studies of 2013 mmaestre.gate.sinica.edu.tw (Sun Dec 21 2014 - 22:24:12 PST)
- [AMBER] target dynamics problem antonio.coluccia.uniroma1.it (Mon Dec 22 2014 - 05:31:20 PST)
- [AMBER] antechamber script Ahmet yıldırım (Mon Dec 22 2014 - 07:05:48 PST)
- [AMBER] Umbrella sampling for molecules moving Helen Lvy (Mon Dec 22 2014 - 13:22:38 PST)
- [AMBER] Parameter could not be saved Harmeet Kaur (Tue Dec 23 2014 - 03:00:25 PST)
- [AMBER] a problem in MM-GBSA calculation 朱亚莉 (Tue Dec 23 2014 - 05:22:11 PST)
- [AMBER] ifqnt chemjxn (Tue Dec 23 2014 - 18:24:56 PST)
- [AMBER] Errors during Adding hydrogen atoms to the PDB file（MCPB program） wjli (Tue Dec 23 2014 - 20:42:50 PST)
- Re: [AMBER] Forcefield for DNA Nihal Korkmaz (Wed Dec 24 2014 - 19:44:59 PST)
- [AMBER] WHAM tolerance Sun (Thu Dec 25 2014 - 19:46:20 PST)
- [AMBER] conversion of amber outputs to gromacs shahab shariati (Thu Dec 25 2014 - 23:48:35 PST)
- [AMBER] conversion of amber outputs to gromacs shahab shariati (Thu Dec 25 2014 - 23:55:43 PST)
- [AMBER] conversion of amber outputs to gromacs shahab shariati (Fri Dec 26 2014 - 05:16:41 PST)
- [AMBER] charmmlipid2amber.py Jacopo Sgrignani (Fri Dec 26 2014 - 06:21:24 PST)
- [AMBER] Amber 14 Performance and Other Questions Novosielski, Ryan (Fri Dec 26 2014 - 13:16:05 PST)
- [AMBER] lipid conversion Jacopo Sgrignani (Sat Dec 27 2014 - 08:17:37 PST)
- [AMBER] Error during Adding Fragment（about MCPB ） wjli (Sat Dec 27 2014 - 20:26:35 PST)
- [AMBER] Enthalpy calculation of protein. Abhilash J (Sat Dec 27 2014 - 23:42:46 PST)
- [AMBER] amber force field 王珍 (Sun Dec 28 2014 - 03:51:25 PST)
- [AMBER] Total energy of system is positive MOHD HOMAIDUR RAHMAN (Sun Dec 28 2014 - 21:40:26 PST)
- [AMBER] convergence problem in antechamber with Ambertools14 Rebeca García Fandiño (Mon Dec 29 2014 - 05:05:12 PST)
- [AMBER] Fwd: pmemd.MPI fails to run Fabian Glaser (Mon Dec 29 2014 - 05:28:09 PST)
- [AMBER] TI calculation using pmemd wangmt (Mon Dec 29 2014 - 06:21:51 PST)
- [AMBER] rms fit Sylvester Tumusiime (Mon Dec 29 2014 - 12:47:16 PST)
- [AMBER] Peter Kollman lectureship, Jan 8 David A Case (Mon Dec 29 2014 - 14:11:49 PST)
- [AMBER] Imaging membrane proteins Parker de Waal (Mon Dec 29 2014 - 16:37:26 PST)
- [AMBER] Need help in SMD Kshatresh Dutta Dubey (Tue Dec 30 2014 - 09:32:34 PST)
- [AMBER] amber14 CUDA GPU for workstation? Michael Shokhen (Tue Dec 30 2014 - 11:31:33 PST)
- [AMBER] Need help in Targeted MD Pallavi Mohanty (Wed Dec 31 2014 - 03:57:14 PST)
- [AMBER] Solvation free energy using soft core potential Teerapong Pirojsirikul (Wed Dec 31 2014 - 17:08:02 PST)
- Last message date: Wed Dec 31 2014 - 17:30:03 PST
- Archived on: Wed Dec 25 2024 - 05:55:03 PST
