Amber Archive May 2017 by thread
- Re: [AMBER] External electric fields on CUDA enabled PMEMD Charles Lin (Sun Apr 30 2017 - 19:32:00 PDT)
- [AMBER] Missing File: charmmlipid2amber.csv Alexander Adams (Sun Apr 30 2017 - 23:28:02 PDT)
- Re: [AMBER] Restraint in Steered MD/Jarzynski method Hannes Loeffler (Mon May 01 2017 - 00:11:42 PDT)
- Re: [AMBER] [SPAM] Re: consult about LEaP in amber 张壮壮 (Mon May 01 2017 - 07:28:07 PDT)
- Re: [AMBER] does not have a type Sowmya Indrakumar (Mon May 01 2017 - 07:56:14 PDT)
- Re: [AMBER] Too many iterations in routine! in RMSD calculation Daniel Roe (Mon May 01 2017 - 08:29:09 PDT)
- [AMBER] Find entropy from non-equilibrium free energy calculation Ramin Salimi (Mon May 01 2017 - 10:50:48 PDT)
- [AMBER] acdoctor: fatal error when reading carboxylates from .mol2 files Niel Henriksen (Mon May 01 2017 - 15:09:32 PDT)
- [AMBER] glycoprotein Neha Gandhi (Mon May 01 2017 - 23:49:10 PDT)
- [AMBER] MD under external electric field & GPUs parallel problem 吴萌 (Tue May 02 2017 - 02:28:29 PDT)
- [AMBER] Fwd: failed to generate parameter and topology file for protein-ligand complex containing zinc Sharon D. Morris (Tue May 02 2017 - 05:22:55 PDT)
- [AMBER] AddtoBox failure sylvester kisembo (Tue May 02 2017 - 07:21:22 PDT)
- Re: [AMBER] Error with 'surf' and acetonitrile-water solvent mixture Daniel Roe (Tue May 02 2017 - 10:45:28 PDT)
- [AMBER] Regarding amber-gaussian QM/MM problem Budhathoki, Dipesh (Tue May 02 2017 - 15:35:08 PDT)
- [AMBER] Ambertools coulomb constant Gard Nelson (Tue May 02 2017 - 16:55:28 PDT)
- [AMBER] ntx=5 and ntx=7 (Sanderinput) Johannes Kalliauer (Wed May 03 2017 - 00:16:49 PDT)
- [AMBER] Question on implementing igb=8, along with mbondi3 Ramin Salimi (Wed May 03 2017 - 00:26:23 PDT)
- Re: [AMBER] DNA Tutorial B1 - Temperature Drop Johannes Kalliauer (Wed May 03 2017 - 03:57:37 PDT)
- Re: [AMBER] AddToBox Failure David Case (Wed May 03 2017 - 10:20:16 PDT)
- [AMBER] LEaP failing after update to AmberTools17 Charles-Alexandre Mattelaer (Wed May 03 2017 - 10:35:19 PDT)
- [AMBER] The problem for image tool in AMBER 鲁俊波 (Wed May 03 2017 - 20:20:58 PDT)
- [AMBER] How to restart MD Garima Singh (Wed May 03 2017 - 23:48:32 PDT)
- [AMBER] GPUs parallel problem Meng Wu (Thu May 04 2017 - 01:26:20 PDT)
- [AMBER] aMD and cpH-MD Hofer, Florian (Thu May 04 2017 - 01:45:42 PDT)
- Re: [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber. Miguel Rivera (Thu May 04 2017 - 15:18:54 PDT)
- [AMBER] ff parameters Andrea Spitaleri (Fri May 05 2017 - 00:38:28 PDT)
- Re: [AMBER] intra-residue water bridge with cpptraj Joanna Sarzynska (Fri May 05 2017 - 01:17:20 PDT)
- [AMBER] Fast 3-point water residue error for coordinates generated with parmed Sadegh Faramarzi Ganjabad (Fri May 05 2017 - 11:32:46 PDT)
- [AMBER] Cellulose simulation luca maggi (Sun May 07 2017 - 07:37:18 PDT)
- [AMBER] Molecule with glyco - single amino acid linkage? yunshi11 . (Sun May 07 2017 - 20:25:23 PDT)
- [AMBER] Atom type assignment by Antechamber Matsuura, Azuma (Sun May 07 2017 - 22:13:13 PDT)
- Re: [AMBER] Fast 3-point water residue error for coordinates Sadegh Faramarzi Ganjabad (Sun May 07 2017 - 23:46:54 PDT)
- [AMBER] Parameterization Ligand Boron Pedro Fernandes (Mon May 08 2017 - 06:09:46 PDT)
- [AMBER] Cpptraj calculates only three PHI-PSI angles in a 18-residue long peptide Chetna Tyagi (Mon May 08 2017 - 08:07:34 PDT)
- [AMBER] tleap-incorpoarating .frcmod, .prep files for unnatural nucleotides p.kartheek (Mon May 08 2017 - 10:33:43 PDT)
- [AMBER] Possible bug in the GPU code Pratul K. Agarwal (Mon May 08 2017 - 15:35:44 PDT)
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphaelinger (Tue May 09 2017 - 01:00:06 PDT)
- [AMBER] Amber parameters for CPD and 6-4PP p.kartheek (Tue May 09 2017 - 02:50:28 PDT)
- [AMBER] Problem in splitting mdcrd file with cpptraj Manjula Saravanan (Tue May 09 2017 - 23:11:11 PDT)
- [AMBER] Two questions for GAFF Matsuura, Azuma (Wed May 10 2017 - 00:58:16 PDT)
- [AMBER] Distance regarding to interface between two solvents Habib Rozale (Wed May 10 2017 - 02:00:40 PDT)
- [AMBER] fcc_metals.lib is not a valid databae Sohag Biswas (Wed May 10 2017 - 04:58:24 PDT)
- [AMBER] how to draw Radial Distribution Functions? Yang Jinpeng (Wed May 10 2017 - 05:15:30 PDT)
- [AMBER] MG angle parameter Tommaso Biagini (Wed May 10 2017 - 05:37:58 PDT)
- [AMBER] question about commutation of sub-trajectories and frame aligning Gordon Richard Chalmers (Wed May 10 2017 - 05:56:42 PDT)
- [AMBER] CX1 missing connect0 atom._MCPB Thakur, Abhishek (Wed May 10 2017 - 12:24:55 PDT)
- [AMBER] ERROR: Could not read coords from .rst file Vishal Nemaysh (Thu May 11 2017 - 00:23:45 PDT)
- [AMBER] Water Analysis with SPAM julian.zachmann selvita.home.pl (Thu May 11 2017 - 07:29:58 PDT)
- [AMBER] Tip3p water box size for two different systems. Saman Yousuf ali (Thu May 11 2017 - 07:57:17 PDT)
- [AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na Thakur, Abhishek (Thu May 11 2017 - 09:10:52 PDT)
- [AMBER] How to use Amber in HPC Garima Singh (Fri May 12 2017 - 03:53:49 PDT)
- [AMBER] EEL and VDW Notification on minimization with sander/pmemd Charles Mariasoosai (Fri May 12 2017 - 09:57:53 PDT)
- [AMBER] Has Hessian printing been added? Eric Hansen (Fri May 12 2017 - 12:47:17 PDT)
- [AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin') Ramin Salimi (Sat May 13 2017 - 05:21:35 PDT)
- [AMBER] MCPB and Can not run MD simulation; some residue move out of protein kungking Hanpaibool (Sat May 13 2017 - 13:05:59 PDT)
- [AMBER] dimer rmsd issue. Saman Yousuf ali (Sun May 14 2017 - 10:13:54 PDT)
- [AMBER] Fwd: Request for troubleshoot in MAWS (igem software from Heidelberg) based on AMBER Abudhahir Buhari (Mon May 15 2017 - 01:24:23 PDT)
- [AMBER] Partial Mini error Nikita Devnarain (Mon May 15 2017 - 05:33:02 PDT)
- [AMBER] Ante_R.E.D script files. Vatsal Purohit (Mon May 15 2017 - 11:10:25 PDT)
- [AMBER] Reference structure for targeted MD Francesco Gentile (Mon May 15 2017 - 19:26:39 PDT)
- [AMBER] convergence question about xmin liu junjun (Tue May 16 2017 - 02:53:21 PDT)
- [AMBER] sander API data structure Brent Krueger (Tue May 16 2017 - 06:43:26 PDT)
- [AMBER] Building distributable executable D'Auria, Raffaella (Tue May 16 2017 - 12:24:09 PDT)
- [AMBER] addions doubt Mary Varughese (Wed May 17 2017 - 00:05:22 PDT)
- [AMBER] resp charges Jacopo Sgrignani (Wed May 17 2017 - 01:11:21 PDT)
- [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Ramin Salimi (Wed May 17 2017 - 01:24:54 PDT)
- [AMBER] Problem with parmed Qinghua Liao (Wed May 17 2017 - 03:00:42 PDT)
- [AMBER] early bird deadline extended Thomas Exner (Wed May 17 2017 - 08:56:52 PDT)
- [AMBER] Doubt about EVB/LES-PIMD Stregone (Wed May 17 2017 - 11:06:07 PDT)
- [AMBER] understanding results Carlos Romero (Wed May 17 2017 - 11:46:28 PDT)
- [AMBER] Implicit solvation method giving the error number of triangulated 3-point waters found: 0 Ramin Salimi (Wed May 17 2017 - 12:51:28 PDT)
- [AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" 冯国强 (Wed May 17 2017 - 23:18:10 PDT)
- [AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" 冯国强 (Wed May 17 2017 - 23:23:58 PDT)
- [AMBER] reference or custom GPUs? Hadházi Ádám (Thu May 18 2017 - 03:00:57 PDT)
- [AMBER] Could not find vdW (or other) parameters for type: Na+ Michael Shokhen (Thu May 18 2017 - 04:13:40 PDT)
- [AMBER] phosaa10 reference Jacopo Sgrignani (Thu May 18 2017 - 07:30:39 PDT)
- [AMBER] possible bug for reading &qmmm after &lmod liu junjun (Thu May 18 2017 - 09:00:01 PDT)
- [AMBER] cpptraj nastruct local helical vectors? Kenneth Huang (Thu May 18 2017 - 12:03:55 PDT)
- [AMBER] Help with PB simulations using MPI Jake (Thu May 18 2017 - 12:34:54 PDT)
- [AMBER] Amber Error Jerrano Bowleg (Thu May 18 2017 - 12:48:22 PDT)
- [AMBER] Unstable umbrella simulation with Amber16 in GTX1080 kurisaki (Thu May 18 2017 - 15:41:03 PDT)
- [AMBER] How to use Amber GAFF force field for methylated DNA MINGREN SHEN (Thu May 18 2017 - 20:03:15 PDT)
- [AMBER] calculation of the binding energy in amber 12 or 14 Saikat Pal (Thu May 18 2017 - 22:33:30 PDT)
- [AMBER] GAFF parameters in amber16 and amber14 Meiting Wang (Fri May 19 2017 - 00:14:19 PDT)
- [AMBER] Input case causing NaN in sander (and possibly pmemd) (Ambertools17) Åke Sandgren (Fri May 19 2017 - 00:32:43 PDT)
- [AMBER] mdgx configuration sampling CA gmail (Fri May 19 2017 - 04:55:05 PDT)
- [AMBER] Distance based mask and reference Marion, Antoine (Fri May 19 2017 - 09:15:21 PDT)
- [AMBER] A9 tutorial analyse.sh problem Robert Wohlhueter (Fri May 19 2017 - 17:37:18 PDT)
- [AMBER] NetCDF error: Invalid argument xu qingliang (Sat May 20 2017 - 06:03:18 PDT)
- Re: [AMBER] Query regarding energy calcuation using 3D-RISM Vertika Gautam (Sat May 20 2017 - 13:44:54 PDT)
- [AMBER] Unable to view the box coordinates in VMD Ramin Salimi (Sun May 21 2017 - 10:55:32 PDT)
- [AMBER] NetCDF error: Invalid argument xu qingliang (Sun May 21 2017 - 23:28:03 PDT)
- [AMBER] Minimisation of a complex Nikita Devnarain (Mon May 22 2017 - 00:54:09 PDT)
- [AMBER] Wrong Quotation marks in Manual in several examplecodes Johannes Kalliauer (Mon May 22 2017 - 01:59:09 PDT)
- [AMBER] Regarding Native Contacts Suchetana Gupta (Mon May 22 2017 - 03:28:01 PDT)
- [AMBER] Which Linux distro for Amber16? Hadházi Ádám (Mon May 22 2017 - 05:00:20 PDT)
- [AMBER] MD Simulation of chemical complex ruqaiya khalil (Mon May 22 2017 - 06:18:15 PDT)
- Re: [AMBER] AMBER Digest, Vol 1932, Issue 1 Garima Singh (Tue May 23 2017 - 00:17:18 PDT)
- [AMBER] Virial and Kinetic energy Iain Bethune (Tue May 23 2017 - 03:47:10 PDT)
- [AMBER] .prmtop file not saved Shafaq Muzammal (Tue May 23 2017 - 05:33:51 PDT)
- [AMBER] Installation of AMBER 16 Vidhya Srivatsan (Tue May 23 2017 - 06:26:15 PDT)
- [AMBER] Libgfortran error during amber tools install Van Rompaey Dries (Tue May 23 2017 - 10:57:43 PDT)
- [AMBER] . Re: NetCDF error: Invalid argument (David Case) xu qingliang (Wed May 24 2017 - 01:39:17 PDT)
- [AMBER] Translate the center of mass of the protein to the origin (0, 0, 0) Meng Wu (Wed May 24 2017 - 02:47:27 PDT)
- [AMBER] Error while upgrading to AmberTools 17 Chetna Tyagi (Wed May 24 2017 - 03:29:51 PDT)
- [AMBER] finding number of atoms within a radius Debodyuti Dutta (Wed May 24 2017 - 04:45:20 PDT)
- [AMBER] Reg residue selection in trajectory Vidhya Srivatsan (Wed May 24 2017 - 11:07:12 PDT)
- [AMBER] AMBER error Neha Gandhi (Wed May 24 2017 - 20:28:10 PDT)
- [AMBER] amino-cyclopropyl parameters Loris Moretti (Fri May 26 2017 - 00:32:30 PDT)
- [AMBER] add ligand parameters Loris Moretti (Fri May 26 2017 - 01:45:01 PDT)
- [AMBER] cpptraj GIST Gabriel Jara (Fri May 26 2017 - 10:49:54 PDT)
- [AMBER] random coil in the protein secondary structure analysis leila karami (Sat May 27 2017 - 09:04:03 PDT)
- [AMBER] Question about RMSD "jumps" Ly, Thu Ngoc Anh (Sat May 27 2017 - 16:26:55 PDT)
- [AMBER] Spherical flat bottom restraint M. Wong (Sat May 27 2017 - 20:41:16 PDT)
- [AMBER] Fwd: Error while preparing docked complex for minimization NADIA RAHMAH (Sun May 28 2017 - 03:59:59 PDT)
- [AMBER] MMGBSA energy decomposition per frame Thomas Evangelidis (Sun May 28 2017 - 06:29:19 PDT)
- [AMBER] Water Geometry in SPCBOX Inconsistent with Literatures Changhao Wang (Mon May 29 2017 - 00:30:23 PDT)
- [AMBER] RESP charge for protonated cytosine ribonucleotide xuzhh (Mon May 29 2017 - 03:42:02 PDT)
- [AMBER] KeyError: 'A' (MCPB.py) Sushi Shilpa (Mon May 29 2017 - 05:35:33 PDT)
- [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial Nikolay N. Kuzmich (Mon May 29 2017 - 06:08:32 PDT)
- [AMBER] Wrong quotation marks in manual David Case (Mon May 29 2017 - 09:07:50 PDT)
- Re: [AMBER] Amber16 configure: error: could not find mpi library for --enable-mpi Lucas (Mon May 29 2017 - 13:19:27 PDT)
- [AMBER] fcc_metals.lib not found Sohag Biswas (Mon May 29 2017 - 21:24:47 PDT)
- [AMBER] No Torsion terms sylvester kisembo (Tue May 30 2017 - 06:15:39 PDT)
- [AMBER] external electric field in Amber 16 michal biler (Tue May 30 2017 - 07:39:20 PDT)
- [AMBER] Citation for frcmod.parmbsc0, frcmod.ionsjc_tip3p Ramin Salimi (Tue May 30 2017 - 17:33:58 PDT)
- [AMBER] Antechamber can't transform Gaussian output file into *.mol2 Nikolay N. Kuzmich (Wed May 31 2017 - 05:06:28 PDT)
- [AMBER] High pressure fluctuation in isothermal-isobaric ensemble Ramin Salimi (Wed May 31 2017 - 09:12:03 PDT)
- [AMBER] Input case causing NaN in sander David Case (Wed May 31 2017 - 19:10:34 PDT)
- Last message date: Wed May 31 2017 - 19:30:03 PDT
- Archived on: Fri Nov 15 2024 - 05:55:34 PST
