Amber Archive Mar 2015 by thread
- [AMBER] Fwd: help in sdf Robin Jain (Sun Mar 01 2015 - 06:40:44 PST)
- [AMBER] Param PROC does not exist (MM-PBSA) Atila Petrosian (Sun Mar 01 2015 - 06:49:33 PST)
- [AMBER] tleap box neutralization Sergio Decherchi (Mon Mar 02 2015 - 01:13:58 PST)
- [AMBER] R: Re: GTX980 PERFORMANCE carmendigiovanni75.alice.it (Mon Mar 02 2015 - 01:22:28 PST)
- [AMBER] Error while creating force field Swithin Hanosh (Mon Mar 02 2015 - 02:21:07 PST)
- [AMBER] COM restrain support in Amber14 Srinivasaraghavan Kannan (Mon Mar 02 2015 - 02:29:42 PST)
- Re: [AMBER] Cofactor parametrization Francesca Tessaro (Mon Mar 02 2015 - 03:08:08 PST)
- [AMBER] ERROR no map function for FE2 FE2 :data= 91 CYS SG 170 FE2 FE2 2.4 Pragya Priyadarshini (Mon Mar 02 2015 - 03:37:48 PST)
- [AMBER] using internal geometry newamber list (Mon Mar 02 2015 - 10:07:47 PST)
- [AMBER] Replacing water with oxygen molecules Shukla, Saurabh (Mon Mar 02 2015 - 10:19:51 PST)
- Re: [AMBER] Chamber problem Shukla, Saurabh (Mon Mar 02 2015 - 11:50:29 PST)
- [AMBER] ATP and ADP-Pi simulations Joseph Baker (Mon Mar 02 2015 - 13:04:45 PST)
- [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Jordan Graziadei (Mon Mar 02 2015 - 14:01:41 PST)
- [AMBER] Problem with Creating Unit for Non-standard N-Cap Residue Huang Tao (Mon Mar 02 2015 - 17:33:51 PST)
- [AMBER] Problem in capping ACE and NME. Harshala Haldankar (Mon Mar 02 2015 - 22:13:19 PST)
- [AMBER] Problem in calculation per residue free energy decomposition maryam azimzadehirani (Tue Mar 03 2015 - 02:04:42 PST)
- [AMBER] Error while creating force field Swithin Hanosh (Tue Mar 03 2015 - 03:35:37 PST)
- [AMBER] Decomposition of the MMGBSA based on multi trajectory input James Starlight (Tue Mar 03 2015 - 03:58:44 PST)
- [AMBER] SMD average work Mahmood Jasim (Tue Mar 03 2015 - 07:58:09 PST)
- [AMBER] matrix newtransform command Sylvester Tumusiime (Tue Mar 03 2015 - 12:03:24 PST)
- [AMBER] Tutorial B0 Sanmeet Chahal (Tue Mar 03 2015 - 15:05:57 PST)
- [AMBER] How to calculate interaction energy between any two residues of one protein danieldefoe (Tue Mar 03 2015 - 21:04:40 PST)
- [AMBER] Param PROC does not exist --- MM-PBSA problem Atila Petrosian (Tue Mar 03 2015 - 23:49:18 PST)
- [AMBER] Targeted MD shows blank output file! Pallavi Mohanty (Wed Mar 04 2015 - 02:44:22 PST)
- Re: [AMBER] REMD jobs crashing repeatedly on GPUs Christina Bergonzo (Wed Mar 04 2015 - 10:19:35 PST)
- [AMBER] GTX TITAN X was introduced filip fratev (Wed Mar 04 2015 - 13:38:54 PST)
- [AMBER] Solvent Box Issue When Running AMBER Dynamics Zhang, Sixue (Wed Mar 04 2015 - 14:46:37 PST)
- [AMBER] error in MMPBSA.py Emilio Angelina (Thu Mar 05 2015 - 03:26:43 PST)
- [AMBER] mm-pbsa & extra-point Emilio Angelina (Thu Mar 05 2015 - 13:42:19 PST)
- Re: [AMBER] Improper torsions in NMA FyD (Fri Mar 06 2015 - 00:02:49 PST)
- [AMBER] a question on molecular dynamics simulation Brett (Fri Mar 06 2015 - 05:14:35 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Fri Mar 06 2015 - 07:22:58 PST)
- [AMBER] cpptraj H-bond: clarification sought George Tzotzos (Fri Mar 06 2015 - 09:44:55 PST)
- [AMBER] Reading two units from same .mol2 file Sanmeet Chahal (Fri Mar 06 2015 - 17:16:10 PST)
- Re: [AMBER] Inability to use antechamber on Anion Robert Molt (Fri Mar 06 2015 - 17:43:23 PST)
- [AMBER] General question about MM-PB(GB)SA Atila Petrosian (Fri Mar 06 2015 - 21:56:14 PST)
- [AMBER] ideal range values for distance restraint b/w 2 non-bonded atoms. GG Smith (Sat Mar 07 2015 - 03:22:59 PST)
- [AMBER] acetyl lysine Dhiraj Srivastava (Sat Mar 07 2015 - 14:15:29 PST)
- [AMBER] on the force field Brett (Sat Mar 07 2015 - 19:04:55 PST)
- [AMBER] free energy plot zahra khatti (Sat Mar 07 2015 - 22:09:59 PST)
- [AMBER] force field parameter for fructose 1 6 bisphosphate Dhiraj Srivastava (Sat Mar 07 2015 - 22:13:55 PST)
- [AMBER] free energy plot zahra khatti (Sat Mar 07 2015 - 22:12:53 PST)
- [AMBER] free energy plot zahra khatti (Sun Mar 08 2015 - 08:18:25 PDT)
- [AMBER] Syntax Confusion on Radial Command Robert Molt (Sun Mar 08 2015 - 14:55:59 PDT)
- [AMBER] Invitation to Computational Chemical Biology Conference (Aug 6th to 9th 2015), Cairns, Australia (http://tinyurl.com/nyblv7o) Ross Walker (Sun Mar 08 2015 - 18:14:45 PDT)
- [AMBER] clustering in ptraj Mary Varughese (Sun Mar 08 2015 - 23:48:43 PDT)
- [AMBER] PCA_representation_in_Cpptraj abdennour braka (Mon Mar 09 2015 - 02:14:51 PDT)
- Re: [AMBER] calculating HB lifetime Vijay Achari (Mon Mar 09 2015 - 23:52:03 PDT)
- [AMBER] Evaluating hydrogen boding lifetime Vijay Achari (Tue Mar 10 2015 - 01:53:39 PDT)
- [AMBER] Sudden RMSD blow-up in trajectory analysis Anasuya Dighe (Tue Mar 10 2015 - 02:54:17 PDT)
- [AMBER] MMPBSA tutorial: MMPBSA.py camm-kansai (Tue Mar 10 2015 - 04:32:06 PDT)
- Re: [AMBER] Lipid14 POPE lipids Joseph Baker (Tue Mar 10 2015 - 10:08:57 PDT)
- [AMBER] Reg: Query on distance restrain and its effect on conformation GG Smith (Tue Mar 10 2015 - 21:41:18 PDT)
- [AMBER] calculating angle between to vectors Vijay Achari (Wed Mar 11 2015 - 01:01:28 PDT)
- [AMBER] help in getting 3D isodensity surface Robin Jain (Wed Mar 11 2015 - 01:09:48 PDT)
- [AMBER] D- amino acids in ff10 Neha Gandhi (Wed Mar 11 2015 - 06:45:07 PDT)
- [AMBER] mmpbsa conflict with Ca2+ ? Jinfeng Huang (Wed Mar 11 2015 - 07:52:10 PDT)
- [AMBER] Truncated octahedron Arjun Sharma (Wed Mar 11 2015 - 08:24:31 PDT)
- [AMBER] : Dimer Imaging Problem Waldner, Birgit (Wed Mar 11 2015 - 09:28:35 PDT)
- [AMBER] Putting oxygen molecules around protein structure Shukla, Saurabh (Wed Mar 11 2015 - 20:38:24 PDT)
- [AMBER] Fitting velocity autocorrelation data DEBOSTUTI GHOSHDASTIDAR (Thu Mar 12 2015 - 03:27:00 PDT)
- [AMBER] finding angles Vijay Achari (Thu Mar 12 2015 - 07:00:31 PDT)
- [AMBER] RNA Simulation jacob wick (Thu Mar 12 2015 - 11:28:59 PDT)
- [AMBER] Predefined number of water molecules in waterbox jacob wick (Thu Mar 12 2015 - 22:17:44 PDT)
- [AMBER] error in antechamber: Bond types are assigned for valence state 1 with penalty of 1 Rebeca García Fandiño (Fri Mar 13 2015 - 02:24:20 PDT)
- [AMBER] Problem in protonating. Harshala Haldankar (Fri Mar 13 2015 - 04:16:02 PDT)
- [AMBER] Force field for Inositol triphosphate anu chandra (Fri Mar 13 2015 - 05:35:00 PDT)
- [AMBER] leap and centering Hannes Loeffler (Fri Mar 13 2015 - 08:20:35 PDT)
- Re: [AMBER] [q4md-fft] Fwd: D- amino acids in ff10 FyD (Fri Mar 13 2015 - 09:51:04 PDT)
- [AMBER] Errors in AmberTools14 Jonathan Gough (Fri Mar 13 2015 - 10:52:33 PDT)
- [AMBER] Unable to load OLS OLT NLN in tleap (AmberTools14) Pedro Swagger (Fri Mar 13 2015 - 17:28:43 PDT)
- [AMBER] 10-12 Potentials, HBOND David Poole (Fri Mar 13 2015 - 20:37:13 PDT)
- [AMBER] Fwd: [Fwd: Purchase of Amber-14] N.R. Jena (Sat Mar 14 2015 - 12:14:23 PDT)
- [AMBER] set command and VMD Arjun Sharma (Sat Mar 14 2015 - 15:44:23 PDT)
- [AMBER] RNA's sugar modification jacob wick (Sun Mar 15 2015 - 11:05:20 PDT)
- [AMBER] Nuclicacid forcefield in AMBER mish (Sun Mar 15 2015 - 12:12:49 PDT)
- [AMBER] ** No torsion terms Evans, Shalton (Sun Mar 15 2015 - 17:57:30 PDT)
- Re: [AMBER] [q4md-fft] Modify RNA's sugar and adding partial charges FyD (Mon Mar 16 2015 - 00:15:03 PDT)
- [AMBER] Using WHAM to get 3D free energy surface in AMBER12 Wang Moye (Mon Mar 16 2015 - 00:30:40 PDT)
- [AMBER] facing problem to create a prmtop file for oxonium cation Sohag Biswas (Mon Mar 16 2015 - 02:59:06 PDT)
- [AMBER] diisopropylethylene parameter Jennifer Vo (Mon Mar 16 2015 - 03:06:47 PDT)
- [AMBER] organic molecule Lara rajam (Mon Mar 16 2015 - 06:45:47 PDT)
- [AMBER] Per-residue decomposition energy MMGBSA.py maryam azimzadehirani (Mon Mar 16 2015 - 06:49:12 PDT)
- [AMBER] ante-mmpbsa.py: problem with the mask syntax George Tzotzos (Mon Mar 16 2015 - 10:26:16 PDT)
- [AMBER] pmemd.MPI error George Tzotzos (Mon Mar 16 2015 - 13:07:55 PDT)
- [AMBER] HMR Adrian Roitberg (Mon Mar 16 2015 - 14:40:23 PDT)
- [AMBER] Format of solventhb.dat file in hydrogen bonding calculation Vijay Achari (Mon Mar 16 2015 - 19:10:40 PDT)
- Re: [AMBER] AMBER Digest, Vol 1160, Issue 1 Sohag Biswas (Tue Mar 17 2015 - 01:39:53 PDT)
- [AMBER] unfolding protein and solvent density Ibrahim Said (Tue Mar 17 2015 - 02:32:03 PDT)
- [AMBER] Differences in AMBER force fields Thomas Exner (Tue Mar 17 2015 - 02:46:24 PDT)
- Re: [AMBER] script to convert the Gromacs topology to Amber topology? Josep Maria Campanera Alsina (Tue Mar 17 2015 - 02:57:59 PDT)
- [AMBER] Backbone Rmsd jacob wick (Tue Mar 17 2015 - 03:17:46 PDT)
- [AMBER] About TIP4-Ew water model usage Saikat Dutta chowdhury (Tue Mar 17 2015 - 03:31:56 PDT)
- [AMBER] Dielectric constant for dna-ligand in TIP3P system Him Shweta (Tue Mar 17 2015 - 07:45:13 PDT)
- [AMBER] Dielectric constant for dna-ligand in TIP3P system Him Shweta (Tue Mar 17 2015 - 07:49:59 PDT)
- [AMBER] **No Torsion terms Evans, Shalton (Tue Mar 17 2015 - 09:28:47 PDT)
- [AMBER] Starting antechamber for preparing ligand molecule Anasuya Dighe (Tue Mar 17 2015 - 10:23:51 PDT)
- Re: [AMBER] Amber on Red Hat? Agnieszka Szarecka (Tue Mar 17 2015 - 12:23:04 PDT)
- [AMBER] topology file, segment id and the pathways plugin Shoresh Shafei (Tue Mar 17 2015 - 13:33:32 PDT)
- [AMBER] Non-Standard Residue / Non-Integer Charge Maral Aminpour (Tue Mar 17 2015 - 14:09:50 PDT)
- [AMBER] PMF for dimer dissociation Sanmeet Chahal (Tue Mar 17 2015 - 14:18:33 PDT)
- [AMBER] MMGBSA pairwise decomposition - differences in Non-Polar Solv. & TOTAL for same residue pairs Cassandra Churchill (Tue Mar 17 2015 - 14:53:43 PDT)
- [AMBER] help in hbond analysis Robin Jain (Tue Mar 17 2015 - 23:26:35 PDT)
- [AMBER] CHAMBER and CMAP difficulty Brian Radak (Wed Mar 18 2015 - 08:03:53 PDT)
- [AMBER] how to use cpptraj for pdb files generated from external software Mahendra B Thapa (Wed Mar 18 2015 - 09:34:29 PDT)
- [AMBER] trajectory of minimization using generalized Born Edwin Helbert Aponte Angarita (Wed Mar 18 2015 - 09:41:43 PDT)
- Re: [AMBER] FW: how to use cpptraj for pdb files generated from external software Mahendra B Thapa (Wed Mar 18 2015 - 09:57:18 PDT)
- [AMBER] Amber 14 tests errors Gustavo Avelar Molina (Wed Mar 18 2015 - 16:34:26 PDT)
- [AMBER] Fwd: CPPTRAJ trajout results "weird" pdb Chinh Su Tran To (Wed Mar 18 2015 - 20:40:59 PDT)
- [AMBER] Error during Adding Fragment（about MCPB ） wjli (Thu Mar 19 2015 - 03:33:23 PDT)
- [AMBER] Amber standard residue name wjli (Thu Mar 19 2015 - 03:45:34 PDT)
- [AMBER] NetCDF AMBER file corrupted Jacopo Sgrignani (Thu Mar 19 2015 - 07:20:09 PDT)
- [AMBER] On the clustering of the ligand position within the cavity James Starlight (Thu Mar 19 2015 - 08:50:12 PDT)
- [AMBER] sander.MPI error George Tzotzos (Thu Mar 19 2015 - 11:02:40 PDT)
- [AMBER] | ERROR: PMEMD does not support intermolecular PRFs! Jorgen Simonsen (Thu Mar 19 2015 - 11:15:30 PDT)
- [AMBER] post processing temperature replica exchange trajectories Sandeep Somani (Thu Mar 19 2015 - 13:00:49 PDT)
- [AMBER] Problem with heating lipid bilayer in amber 12 Chris Gaughan (Thu Mar 19 2015 - 14:31:26 PDT)
- [AMBER] Drifting molecules despite strong restraints Sanmeet Chahal (Thu Mar 19 2015 - 15:32:42 PDT)
- [AMBER] Reduce not working properly Francesco Gentile (Thu Mar 19 2015 - 21:47:14 PDT)
- [AMBER] loading molecule in xleap and saving it in mol2 format jacob wick (Fri Mar 20 2015 - 00:17:05 PDT)
- [AMBER] Bond distance and Box shape Arjun Sharma (Fri Mar 20 2015 - 07:21:58 PDT)
- [AMBER] error with mmpbsa.py Norbert GARNIER (Fri Mar 20 2015 - 08:32:24 PDT)
- [AMBER] Leap warning George Tzotzos (Fri Mar 20 2015 - 10:55:18 PDT)
- [AMBER] heat capacity Ahmet yıldırım (Fri Mar 20 2015 - 13:07:34 PDT)
- [AMBER] [Fwd: ] vladimir.palivec.marge.uochb.cas.cz (Sat Mar 21 2015 - 04:46:19 PDT)
- [AMBER] Error message from FEW in Amber14 tutorial A24 Michael Shokhen (Sun Mar 22 2015 - 06:44:30 PDT)
- [AMBER] Immediate Postdoctoral Position Opening In Dr. Khaled Barakat’s Lab, Faculty Of Pharmacy, University Of Alberta Marawan Hussien (Sun Mar 22 2015 - 14:01:11 PDT)
- [AMBER] error when doing lifetime calculation Vijay Achari (Sun Mar 22 2015 - 23:32:36 PDT)
- [AMBER] "Error opening unit 30: File "inpcrd" is missing or unreadable" on Tutorial A15 christian.yongky.ui.ac.id (Sun Mar 22 2015 - 23:47:08 PDT)
- [AMBER] Fwd: Regarding the MCPB tutorial Garisekurthi Satheesh (Mon Mar 23 2015 - 02:41:35 PDT)
- [AMBER] CUDA problems Beale, John (Mon Mar 23 2015 - 07:41:30 PDT)
- [AMBER] Replica Exchange on a single Titan-X GPU amr hamed (Mon Mar 23 2015 - 08:19:09 PDT)
- [AMBER] RMSF & changes of the secondary structure of protein shahab shariati (Mon Mar 23 2015 - 11:45:41 PDT)
- [AMBER] vdw energy and electrostatic energy calculation for osmolyte Subrata Paul (Tue Mar 24 2015 - 00:31:49 PDT)
- [AMBER] About generalized restraints in AMBER14 with GPU support Attilio Vittorio Vargiu (Tue Mar 24 2015 - 07:29:28 PDT)
- [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA psu4.uic.edu (Tue Mar 24 2015 - 10:06:49 PDT)
- [AMBER] CpHMD-pHREX AMBER14 Arjun Sharma (Tue Mar 24 2015 - 10:37:29 PDT)
- [AMBER] concave edge on torus has mismatched atoms Sylvester Tumusiime (Tue Mar 24 2015 - 12:28:12 PDT)
- [AMBER] The unperturbed charge of the unit: -2.980000 is not integral 王华 (Tue Mar 24 2015 - 18:40:20 PDT)
- [AMBER] iterative calculation in CPPTRAJ using "for... do... done" Vijay Achari (Wed Mar 25 2015 - 04:42:16 PDT)
- [AMBER] trouble running pmemd.cuda Brian Radak (Wed Mar 25 2015 - 10:30:23 PDT)
- [AMBER] Free energy calculation: Thermodynamic integration with use of restraints vladimir.palivec.marge.uochb.cas.cz (Wed Mar 25 2015 - 10:55:45 PDT)
- Re: [AMBER] AMBER Digest, Vol 1169, Issue 1 Arjun Sharma (Wed Mar 25 2015 - 14:54:31 PDT)
- [AMBER] Implicit solvent simulation with Andersen thermostat Glenn Carrington [bs10g3c] (Wed Mar 25 2015 - 16:41:38 PDT)
- [AMBER] vdw energy and electrostatic energy calculation for osmolyte MOHD HOMAIDUR RAHMAN (Wed Mar 25 2015 - 22:59:40 PDT)
- [AMBER] MMGBSA error Abhishek TYAGI (Wed Mar 25 2015 - 23:06:44 PDT)
- [AMBER] Antechamber - TURBOMOLE Sanja Zivanovic (Thu Mar 26 2015 - 04:48:26 PDT)
- [AMBER] Water sigma parameters Paolo Tosco (Thu Mar 26 2015 - 13:16:44 PDT)
- [AMBER] combinatorial library Hector A. Baldoni (Thu Mar 26 2015 - 17:22:05 PDT)
- [AMBER] problem regarding different pmf graph Shubhadip Das (Thu Mar 26 2015 - 21:21:52 PDT)
- [AMBER] Histogram analysis of the dihedral distributions using cpptraj James Starlight (Fri Mar 27 2015 - 08:13:10 PDT)
- [AMBER] aMD boost parameters for CHARMM force field? Brian Radak (Fri Mar 27 2015 - 08:39:13 PDT)
- Re: [AMBER] MMPBSA error Abhishek Tyagi (Fri Mar 27 2015 - 09:39:50 PDT)
- [AMBER] Intel Compiler and MKL Novosielski, Ryan (Fri Mar 27 2015 - 11:03:32 PDT)
- [AMBER] REGARDING ATOM TYPE ERROR Swithin Hanosh (Sat Mar 28 2015 - 05:01:43 PDT)
- [AMBER] Gromacs towards Amber conversion Simone Fulle (Sat Mar 28 2015 - 07:25:27 PDT)
- [AMBER] Projection on modes calculated by distcovar matrix Vishal Kumar Jaiswal (Sun Mar 29 2015 - 02:53:00 PDT)
- [AMBER] Restrained MD James Starlight (Sun Mar 29 2015 - 03:50:31 PDT)
- [AMBER] flag for fast water FyD (Sun Mar 29 2015 - 07:54:06 PDT)
- [AMBER] Problem Regarding Different PMF Graph Shubhadip Das (Sun Mar 29 2015 - 22:02:34 PDT)
- [AMBER] Problem Regarding Different PMF Graphs Shubhadip Das (Sun Mar 29 2015 - 22:04:22 PDT)
- [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12 Wang Moye (Mon Mar 30 2015 - 05:39:03 PDT)
- [AMBER] Projection on distance covariance modes Vishal Kumar Jaiswal (Mon Mar 30 2015 - 06:11:55 PDT)
- [AMBER] Manual still ambiguous about igb=8 and pmemd Edwin Helbert Aponte Angarita (Mon Mar 30 2015 - 09:32:44 PDT)
- [AMBER] Help regarding appropriate analysis for correlated motion using cpptraj Kshatresh Dutta Dubey (Mon Mar 30 2015 - 12:44:39 PDT)
- [AMBER] issue with LRT calculation in sander Emilio Angelina (Mon Mar 30 2015 - 13:01:18 PDT)
- [AMBER] temp ramping in tutorial A5 Robert Wohlhueter (Mon Mar 30 2015 - 15:33:31 PDT)
- [AMBER] Stability MMPBSA Parker de Waal (Mon Mar 30 2015 - 18:44:20 PDT)
- [AMBER] Multiple MEPs option in R.E.D tools Yip Yew Mun (Mon Mar 30 2015 - 19:26:05 PDT)
- [AMBER] Problems with Amber installation Pinchas Aped (Tue Mar 31 2015 - 06:45:53 PDT)
- [AMBER] Pressure units in 1D-RISM Maksim Mišin (Tue Mar 31 2015 - 07:27:00 PDT)
- [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files Himanshu Joshi (Tue Mar 31 2015 - 10:58:51 PDT)
- Last message date: Wed Apr 01 2015 - 00:00:03 PDT
- Archived on: Wed Dec 25 2024 - 05:55:10 PST
