Amber Archive Jan 2020: by author

Abdullah Bin Faheem
- Re: [AMBER] Wanting to get synchronized trajectory files (Wed Jan 22 2020 - 10:58:14 PST)
- Re: [AMBER] Wanting to get synchronized trajectory files (Wed Jan 22 2020 - 08:06:01 PST)
- Re: [AMBER] Wanting to get synchronized trajectory files (Wed Jan 22 2020 - 07:05:28 PST)
- [AMBER] Wanting to get synchronized trajectory files (Wed Jan 22 2020 - 02:53:50 PST)
Abdullah Faheem
- [AMBER] Semi-empirical QMMD on all molecules (Thu Jan 02 2020 - 23:43:39 PST)
Adrian Roitberg
- [AMBER] saxs (Tue Jan 07 2020 - 12:41:25 PST)
Agata Sowińska I34
- [AMBER] Autoimage problem (Fri Jan 24 2020 - 08:41:14 PST)
Airy Sanjeev
- [AMBER] Calculation of mask for TI input (Mon Jan 27 2020 - 20:22:34 PST)
Akshay Prabhakant
- [AMBER] parameters for Si3N4 (Mon Jan 13 2020 - 08:38:24 PST)
ALAMGIR KHAN
- Re: [AMBER] kindly guide me (Wed Jan 29 2020 - 01:43:08 PST)
- [AMBER] kindly guide me (Tue Jan 28 2020 - 21:00:54 PST)
- Re: [AMBER] installing amber on wsl (Sun Jan 12 2020 - 20:04:17 PST)
amirhossein taghavi
- [AMBER] Shaw DE RNA ff in Amber format (Thu Jan 23 2020 - 13:59:17 PST)
An Ta
- [AMBER] Cpptraj - Density Action Command Units (Thu Jan 09 2020 - 13:11:53 PST)
ankita mehta
- Re: [AMBER] hiiiii (Sun Jan 05 2020 - 23:43:51 PST)
- Re: [AMBER] hiiiii (Sun Jan 05 2020 - 20:02:52 PST)
- Re: [AMBER] hiiiii (Sun Jan 05 2020 - 07:37:54 PST)
- Re: [AMBER] hiiiii (Sun Jan 05 2020 - 07:20:44 PST)
- [AMBER] hiiiii (Sun Jan 05 2020 - 06:18:43 PST)
- [AMBER] hiiiii (Sat Jan 04 2020 - 23:01:39 PST)
- [AMBER] hiiiiii (Sat Jan 04 2020 - 07:17:42 PST)
- [AMBER] hiii (Sat Jan 04 2020 - 05:54:40 PST)
- Re: [AMBER] query (Fri Jan 03 2020 - 02:50:20 PST)
- [AMBER] Query (Fri Jan 03 2020 - 02:42:39 PST)
- [AMBER] query (Thu Jan 02 2020 - 08:45:08 PST)
Annachiara TINIVELLA
- [AMBER] sulfonamide parameters for correct geometry (Wed Jan 29 2020 - 04:31:25 PST)
Anthony Bogetti
- [AMBER] sqm calculation with external charges not working (Mon Jan 20 2020 - 07:53:08 PST)
Anthony Cruz-Balberdy
- Re: [AMBER] Does anyone here use a99SB-disp force field and how did you obtain it? (Thu Jan 23 2020 - 04:56:36 PST)
Antonio Bauzá
- [AMBER] compatible graphics card (Sun Jan 12 2020 - 09:01:29 PST)
Ayesha Fatima
- Re: [AMBER] installing amber on wsl (Mon Jan 13 2020 - 06:59:49 PST)
- Re: [AMBER] installing amber on wsl (Sun Jan 12 2020 - 22:54:28 PST)
- [AMBER] installing amber on wsl (Sun Jan 12 2020 - 05:29:26 PST)
- [AMBER] parmed issue (Sat Jan 04 2020 - 05:50:11 PST)
Baker, Joseph
- [AMBER] steered MD question (Thu Jan 23 2020 - 12:10:50 PST)
- Re: [AMBER] Generating parameters for iron-sulfur protein (Tue Jan 14 2020 - 20:51:28 PST)
Bhat Zahoor
- Re: [AMBER] Periodic box problem when simulating Membrane system (Mon Jan 13 2020 - 07:09:40 PST)
- Re: [AMBER] Lipid bilayer imaging problem (Thu Jan 09 2020 - 04:59:41 PST)
- [AMBER] Lipid bilayer imaging problem (Thu Jan 09 2020 - 03:58:07 PST)
- [AMBER] Adjacent cell molecules appear in the trajectory after autoimaging in cpptraj [ DOPC lipid bilayer simulation with lipid14 force field] (Wed Jan 08 2020 - 01:46:26 PST)
- [AMBER] DOPC lipid bilayer deformation in Implicit MD simulation using Lipid14 force field in Amber18 (Mon Jan 06 2020 - 23:16:55 PST)
Billiot, Eugene
- [AMBER] MMPBSA run failure (Sat Jan 18 2020 - 04:45:31 PST)
- Re: [AMBER] Amber 18 installation error (Tue Jan 07 2020 - 09:19:04 PST)
- [AMBER] Amber 18 installation error (Mon Jan 06 2020 - 14:29:11 PST)
Buteler,Maria del Pilar
- [AMBER] saxs_md (Wed Jan 08 2020 - 08:49:02 PST)
Carlos Simmerling
- Re: [AMBER] Several alpha-helices stitched together - how would you stress-test it with MD? (Tue Jan 28 2020 - 02:52:49 PST)
- Re: [AMBER] Calculation of mask for TI input (Tue Jan 28 2020 - 02:40:09 PST)
- Re: [AMBER] Wanting to get synchronized trajectory files (Wed Jan 22 2020 - 09:10:16 PST)
- Re: [AMBER] Wanting to get synchronized trajectory files (Wed Jan 22 2020 - 07:43:43 PST)
- Re: [AMBER] NEB Simulations in Amber (Mon Jan 20 2020 - 13:55:31 PST)
- Re: [AMBER] Is there any sense in even trying to model large conformational dynamics with molecular dynamics? (Mon Jan 20 2020 - 11:59:07 PST)
- Re: [AMBER] ligand split (Fri Jan 17 2020 - 07:24:07 PST)
- Re: [AMBER] How to use polarizable water model in Amber 18? (Wed Jan 15 2020 - 10:23:48 PST)
- Re: [AMBER] ligand split (Wed Jan 15 2020 - 10:22:33 PST)
- Re: [AMBER] ligand split (Wed Jan 15 2020 - 03:07:00 PST)
- Re: [AMBER] ligand split (Wed Jan 15 2020 - 02:31:48 PST)
- Re: [AMBER] Is error bar necessary for umbrella sampling? (Tue Jan 14 2020 - 03:30:35 PST)
- Re: [AMBER] Is error bar necessary for umbrella sampling? (Mon Jan 13 2020 - 06:42:49 PST)
- Re: [AMBER] Generalized Born and entropy (Mon Jan 13 2020 - 05:04:43 PST)
- Re: [AMBER] Tracking ligand position throughout equilibration stages (Mon Jan 13 2020 - 02:29:32 PST)
- Re: [AMBER] ff99SBnmr2 Force field implemented in AMBER18 (Fri Jan 10 2020 - 17:58:30 PST)
- Re: [AMBER] [ prmtop ] SOLVENT_POINTERS (Fri Jan 10 2020 - 03:31:25 PST)
- Re: [AMBER] weights for the lambda values (Fri Jan 10 2020 - 03:30:35 PST)
- Re: [AMBER] hiiiii (Sun Jan 05 2020 - 07:28:38 PST)
- Re: [AMBER] hiiiii (Sun Jan 05 2020 - 06:32:56 PST)
- Re: [AMBER] Drug parameter generation (Fri Jan 03 2020 - 10:22:19 PST)
- Re: [AMBER] Regarding clustering using mmtsb toolkit (Thu Jan 02 2020 - 04:58:17 PST)
Casalini Tommaso
- Re: [AMBER] Does anyone here use a99SB-disp force field and how did you obtain it? (Thu Jan 23 2020 - 07:05:43 PST)
- Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer (Fri Jan 17 2020 - 01:24:23 PST)
- Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer (Thu Jan 16 2020 - 04:37:26 PST)
- [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer (Thu Jan 16 2020 - 01:30:58 PST)
Charles Lin
- Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer (Tue Jan 21 2020 - 06:30:36 PST)
Chetna Tyagi
- Re: [AMBER] Lipid bilayer imaging problem (Thu Jan 09 2020 - 03:48:47 PST)
Christina Bergonzo
- Re: [AMBER] saxs_md (Wed Jan 08 2020 - 09:25:11 PST)
- Re: [AMBER] NMR distance restrained MD (Thu Jan 02 2020 - 05:45:30 PST)
Cory Ayres
- Re: [AMBER] hiiiii (Mon Jan 06 2020 - 03:19:12 PST)
cpimenta
- [AMBER] Membrane simulation with PSM (Wed Jan 15 2020 - 11:09:24 PST)
Cruzeiro,Vinicius Wilian D
- Re: [AMBER] convergence of Ref energies in cpHMD (Thu Jan 23 2020 - 14:38:23 PST)
- Re: [AMBER] convergence of Ref energies in cpHMD (Tue Jan 21 2020 - 23:43:35 PST)
- Re: [AMBER] convergence of Ref energies in cpHMD (Mon Jan 20 2020 - 14:27:11 PST)
- Re: [AMBER] convergence of Ref energies in cpHMD (Mon Jan 20 2020 - 12:15:54 PST)
- Re: [AMBER] empty cein file redox potential calculations (Thu Jan 09 2020 - 07:01:11 PST)
Daniel Roe
- Re: [AMBER] RDF: corrupted trajectory (Tue Jan 21 2020 - 11:00:46 PST)
- Re: [AMBER] RDF: corrupted trajectory (Fri Jan 17 2020 - 10:47:57 PST)
- Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ (Fri Jan 17 2020 - 07:35:57 PST)
- Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ (Fri Jan 17 2020 - 06:41:09 PST)
- Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ (Fri Jan 17 2020 - 06:37:12 PST)
- Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ (Fri Jan 17 2020 - 06:34:12 PST)
- Re: [AMBER] Reg. Centering of Molecule and Periodic Boundary Conditions (Thu Jan 16 2020 - 12:26:02 PST)
- Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ (Tue Jan 14 2020 - 07:46:30 PST)
- Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ (Mon Jan 13 2020 - 16:20:42 PST)
- Re: [AMBER] CPPTRAJ-Hbonds (Mon Jan 13 2020 - 09:08:01 PST)
David Case
- Re: [AMBER] how does one reply to a thread in a mailing list (Wed Jan 29 2020 - 11:08:18 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error (Thu Jan 23 2020 - 06:39:31 PST)
- Re: [AMBER] Wanting to get synchronized trajectory files (Wed Jan 22 2020 - 05:09:18 PST)
- Re: [AMBER] generating g-quadruplex DNA structures from a sequence (Wed Jan 22 2020 - 05:05:18 PST)
- Re: [AMBER] Reg. working of Periodic Boundary Conditions (Tue Jan 21 2020 - 09:38:10 PST)
- Re: [AMBER] Problem regarding umbrella sampling (Mon Jan 20 2020 - 05:44:45 PST)
- Re: [AMBER] How to use polarizable water model in Amber 18? (Sun Jan 19 2020 - 17:46:57 PST)
- Re: [AMBER] rror: an illegal memory access was encountered launching kernel kNLSkinTest (Sat Jan 18 2020 - 05:31:36 PST)
- Re: [AMBER] Problem in Amber update (Sat Jan 18 2020 - 05:27:10 PST)
- [AMBER] defining a progress variable to be the z-component of some atom or group of atoms? (Sat Jan 18 2020 - 05:14:29 PST)
- Re: [AMBER] vanilla Nose-Hoover thermostat availability (Fri Jan 17 2020 - 06:43:07 PST)
- Re: [AMBER] ValueError: could not convert string to float: ********* Error occured on rank 0. Exiting. All files have been retained. (Thu Jan 16 2020 - 05:36:00 PST)
- Re: [AMBER] modeling a Schiff base with GAFF atom types (Wed Jan 15 2020 - 05:54:42 PST)
- Re: [AMBER] ligand split (Tue Jan 14 2020 - 11:25:48 PST)
- Re: [AMBER] [ MD Failure ] (Mon Jan 13 2020 - 06:27:42 PST)
- Re: [AMBER] installing amber on wsl (Sun Jan 12 2020 - 11:56:35 PST)
- Re: [AMBER] MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest (Fri Jan 10 2020 - 12:54:26 PST)
- Re: [AMBER] [ Error with MD ] Energetics of the system (Fri Jan 10 2020 - 05:43:39 PST)
- Re: [AMBER] Question about addtobox (Thu Jan 09 2020 - 10:03:14 PST)
- Re: [AMBER] MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest (Thu Jan 09 2020 - 10:01:48 PST)
- Re: [AMBER] Resolving overlapping atoms. (Thu Jan 09 2020 - 06:23:04 PST)
- Re: [AMBER] Generalized Born and entropy (Wed Jan 08 2020 - 07:30:25 PST)
- Re: [AMBER] Question about addtobox (Wed Jan 08 2020 - 07:22:21 PST)
- Re: [AMBER] AMBER 18 cuda installation (Tue Jan 07 2020 - 18:47:26 PST)
- Re: [AMBER] P2 correlation functions questions (Tue Jan 07 2020 - 18:29:27 PST)
- Re: [AMBER] Amber 18 installation error (Tue Jan 07 2020 - 06:09:08 PST)
- Re: [AMBER] Any help on the error (Tue Jan 07 2020 - 05:59:45 PST)
- Re: [AMBER] Molecule is wrapped out of the cell. (Mon Jan 06 2020 - 07:07:43 PST)
- Re: [AMBER] printing charges in pdb (Mon Jan 06 2020 - 07:04:07 PST)
- Re: [AMBER] Fwd: Problems using groups to provide centre for solvent caps in tLeap (Mon Jan 06 2020 - 06:34:20 PST)
- Re: [AMBER] gaff with and without gaff atom types (Sun Jan 05 2020 - 10:42:28 PST)
- Re: [AMBER] hiiiii (Sun Jan 05 2020 - 10:32:44 PST)
- Re: [AMBER] hiiiii (Sun Jan 05 2020 - 05:47:26 PST)
- Re: [AMBER] hiii (Sat Jan 04 2020 - 14:18:12 PST)
- Re: [AMBER] parmed issue (Sat Jan 04 2020 - 14:16:27 PST)
- Re: [AMBER] query (Thu Jan 02 2020 - 12:13:55 PST)
- Re: [AMBER] NMR distance restrained MD (Thu Jan 02 2020 - 05:41:00 PST)
- Re: [AMBER] Regarding clustering using mmtsb toolkit (Thu Jan 02 2020 - 05:35:57 PST)
- Re: [AMBER] Tleap naming problem (Thu Jan 02 2020 - 05:30:41 PST)
David Cerutti
- Re: [AMBER] Question about addtobox (Thu Jan 09 2020 - 06:52:13 PST)
- Re: [AMBER] [ Polymer with Extra Points ] (Thu Jan 09 2020 - 00:02:47 PST)
- Re: [AMBER] [ Polymer ] Parameter Modification (Wed Jan 08 2020 - 21:56:12 PST)
- Re: [AMBER] [ Polymer with Extra Points ] (Mon Jan 06 2020 - 23:56:54 PST)
David Wright
- Re: [AMBER] Fwd: Problems using groups to provide centre for solvent caps in tLeap (Tue Jan 07 2020 - 03:41:40 PST)
- [AMBER] Fwd: Problems using groups to provide centre for solvent caps in tLeap (Mon Jan 06 2020 - 03:37:59 PST)
- [AMBER] Problems using groups to provide centre for solvent caps in tLeap (Sat Jan 04 2020 - 05:10:03 PST)
Debarati DasGupta
- [AMBER] Tracking ligand position throughout equilibration stages (Sat Jan 11 2020 - 07:21:37 PST)
- [AMBER] weights for the lambda values (Thu Jan 09 2020 - 11:30:49 PST)
- [AMBER] FW: NPT density equilibration (Wed Jan 08 2020 - 12:44:41 PST)
- [AMBER] NPT density equilibration (Wed Jan 08 2020 - 12:43:00 PST)
- [AMBER] TI data collection of DU/Dlambda at constant volume (Tue Jan 07 2020 - 09:00:20 PST)
- [AMBER] Any help on the error (Mon Jan 06 2020 - 12:22:52 PST)
DHEERAJ CHITARA
- [AMBER] Reg. working of Periodic Boundary Conditions (Tue Jan 21 2020 - 06:25:23 PST)
- [AMBER] Reg. Centering of Molecule and Periodic Boundary Conditions (Thu Jan 16 2020 - 00:46:32 PST)
dilrajl.bii.a-star.edu.sg
- [AMBER] Error in installing parallel version of AMBER18 (Thu Jan 30 2020 - 06:51:57 PST)
Divya Rai
- [AMBER] Normal mode analysis using trajectory files (Wed Jan 22 2020 - 22:26:31 PST)
Dr. Anselm Horn
- Re: [AMBER] Tracking ligand position throughout equilibration stages (Mon Jan 13 2020 - 01:34:40 PST)
Elvis Martis
- Re: [AMBER] About utilities to convert Amber input files for MD into the Tinker, NAMD, Genesis, or Desmond input files (Tue Jan 28 2020 - 20:17:49 PST)
- Re: [AMBER] Amber on windows 10 (Tue Jan 28 2020 - 07:22:22 PST)
- Re: [AMBER] Amber on windows 10 (Tue Jan 28 2020 - 04:19:42 PST)
- Re: [AMBER] pmemd.cuda.MPI run error (Mon Jan 27 2020 - 03:58:28 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error (Sat Jan 25 2020 - 18:45:45 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error (Fri Jan 24 2020 - 03:51:15 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error (Thu Jan 23 2020 - 07:38:03 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error (Thu Jan 23 2020 - 05:15:11 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error (Thu Jan 23 2020 - 01:33:20 PST)
- Re: [AMBER] Normal mode analysis using trajectory files (Thu Jan 23 2020 - 00:08:52 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error (Thu Jan 23 2020 - 00:06:36 PST)
- Re: [AMBER] RESP fitting (Wed Jan 15 2020 - 04:53:12 PST)
emanuele falbo
- Re: [AMBER] RDF: corrupted trajectory (Wed Jan 22 2020 - 01:40:51 PST)
- Re: [AMBER] RDF: corrupted trajectory (Mon Jan 20 2020 - 02:24:06 PST)
- [AMBER] RDF: corrupted trajectory (Fri Jan 17 2020 - 08:02:09 PST)
Erdem Yeler
- Re: [AMBER] gaff with and without gaff atom types (Tue Jan 07 2020 - 00:27:24 PST)
- [AMBER] gaff with and without gaff atom types (Sun Jan 05 2020 - 08:32:08 PST)
erik zuiderweg
- [AMBER] P2 correlation functions questions (Tue Jan 07 2020 - 09:08:28 PST)
Feng Pan
- Re: [AMBER] defining a progress variable to be the z-component of some atom or group of atoms? (Sun Jan 19 2020 - 08:31:08 PST)
Gerardo Zerbetto De Palma
- Re: [AMBER] pmemd.cuda.MPI run error (Mon Jan 27 2020 - 04:31:08 PST)
- Re: [AMBER] pmemd.cuda.MPI run error (Mon Jan 27 2020 - 03:52:05 PST)
- Re: [AMBER] Is there any sense in even trying to model large conformational dynamics with molecular dynamics? (Mon Jan 20 2020 - 11:24:30 PST)
- Re: [AMBER] defining a progress variable to be the z-component of some atom or group of atoms? (Sat Jan 18 2020 - 18:26:19 PST)
Goetz, Andreas
- Re: [AMBER] sqm calculation with external charges not working (Tue Jan 21 2020 - 21:58:43 PST)
- Re: [AMBER] defining a progress variable to be the z-component of some atom or group of atoms? (Sat Jan 18 2020 - 18:01:59 PST)
- Re: [AMBER] Semi-empirical QMMD on all molecules (Fri Jan 03 2020 - 03:36:43 PST)
Gould, Ian R
- Re: [AMBER] DOPC lipid bilayer deformation in Implicit MD simulation using Lipid14 force field in Amber18 (Tue Jan 07 2020 - 00:37:25 PST)
Gustaf Olsson
- Re: [AMBER] kindly guide me (Tue Jan 28 2020 - 22:42:49 PST)
- Re: [AMBER] Amber on windows 10 (Tue Jan 28 2020 - 07:08:14 PST)
- Re: [AMBER] Amber on windows 10 (Tue Jan 28 2020 - 05:21:47 PST)
- Re: [AMBER] Amber on windows 10 (Tue Jan 28 2020 - 04:22:32 PST)
- Re: [AMBER] Wanting to get synchronized trajectory files (Wed Jan 22 2020 - 05:47:36 PST)
- Re: [AMBER] Periodic box problem when simulating Membrane system (Mon Jan 13 2020 - 06:44:36 PST)
- Re: [AMBER] [ inpcrd file ] (Thu Jan 09 2020 - 03:40:35 PST)
- Re: [AMBER] error (Wed Jan 08 2020 - 22:54:22 PST)
Gustavo Seabra
- [AMBER] Help building a model of a 2F-2S protein with MDPB.py (Wed Jan 29 2020 - 10:57:18 PST)
Homeo Morphism
- [AMBER] how does one reply to a thread in a mailing list (Wed Jan 29 2020 - 07:26:57 PST)
- [AMBER] Several alpha-helices stitched together - how would you stress-test it with MD? (Tue Jan 28 2020 - 02:48:35 PST)
- [AMBER] Does anyone here use a99SB-disp force field and how did you obtain it? (Thu Jan 23 2020 - 02:44:52 PST)
- [AMBER] Is there any sense in even trying to model large conformational dynamics with molecular dynamics? (Mon Jan 20 2020 - 11:15:52 PST)
Jiri Sponer
- [AMBER] postdoc DNA/RNA simulations (Thu Jan 30 2020 - 09:36:31 PST)
ke.gohda.camm-kansai.org
- Re: [AMBER] GPU-AMBER18 installation on RTX2080Ti (Mon Jan 20 2020 - 03:30:38 PST)
- [AMBER] GPU-AMBER18 installation on RTX2080Ti (Sat Jan 18 2020 - 02:29:48 PST)
Kolattukudy P. Santo
- Re: [AMBER] convergence of Ref energies in cpHMD (Wed Jan 22 2020 - 06:37:44 PST)
- Re: [AMBER] convergence of Ref energies in cpHMD (Tue Jan 21 2020 - 06:13:47 PST)
- Re: [AMBER] convergence of Ref energies in cpHMD (Mon Jan 20 2020 - 12:41:18 PST)
- [AMBER] convergence of Ref energies in cpHMD (Mon Jan 20 2020 - 10:43:20 PST)
Kshatresh Dutta Dubey
- Re: [AMBER] Problem in Amber update (Sun Jan 19 2020 - 05:14:27 PST)
- [AMBER] Problem in Amber update (Sat Jan 18 2020 - 00:07:50 PST)
Lachele Foley
- Re: [AMBER] Glycosylation issue: Atom xx was assigned a lower molecule # than previous atom. (Fri Jan 03 2020 - 15:49:35 PST)
- Re: [AMBER] Glycosylation issue: Atom xx was assigned a lower molecule # than previous atom. (Fri Jan 03 2020 - 14:44:14 PST)
Lambach, Lauren
- [AMBER] usefrcascoords calculations (Thu Jan 30 2020 - 14:25:28 PST)
Liao
- Re: [AMBER] pdb to mol2 conversion via antechamber (Fri Jan 17 2020 - 00:20:02 PST)
- Re: [AMBER] pmemd.cuda:command not found (Sat Jan 04 2020 - 23:56:35 PST)
Lod King
- [AMBER] cpptraj_clucster (Tue Jan 21 2020 - 19:16:44 PST)
- [AMBER] ff99SBnmr2 Force field implemented in AMBER18 (Fri Jan 10 2020 - 17:41:14 PST)
Madhur Aggarwal
- [AMBER] Drug parameter generation (Fri Jan 03 2020 - 10:09:16 PST)
Makay Murray
- [AMBER] Custom language module(s) for AMBER file types for common text editors? (Sat Jan 11 2020 - 18:17:06 PST)
Manisha Yadav
- [AMBER] Long syntax error on complex molecule (Fri Jan 17 2020 - 20:00:20 PST)
Markowska
- Re: [AMBER] How to use polarizable water model in Amber 18? (Sat Jan 18 2020 - 10:01:14 PST)
- Re: [AMBER] How to use polarizable water model in Amber 18? (Fri Jan 17 2020 - 00:22:11 PST)
- [AMBER] How to use polarizable water model in Amber 18? (Wed Jan 15 2020 - 05:39:39 PST)
- Re: [AMBER] charting Ligand's movement in the binding pocket (Thu Jan 09 2020 - 12:02:08 PST)
Martin Rosellen
- [AMBER] Generalized Born and entropy (Wed Jan 08 2020 - 06:03:51 PST)
- [AMBER] Umbrella sampling sufficient overlap test (Mon Jan 06 2020 - 04:20:06 PST)
Matias Machado
- Re: [AMBER] Custom language module(s) for AMBER file types for common text editors? (Wed Jan 15 2020 - 12:23:52 PST)
- Re: [AMBER] How to use polarizable water model in Amber 18? (Wed Jan 15 2020 - 08:46:11 PST)
- [AMBER] Harmless bug in Lipid11-17 residue libraries causing tleap to split fragments in saved PDB (Wed Jan 15 2020 - 08:32:38 PST)
maya nair
- Re: [AMBER] NMR distance restrained MD (Tue Jan 28 2020 - 23:44:59 PST)
- Re: [AMBER] NMR distance restrained MD (Mon Jan 06 2020 - 04:21:57 PST)
- Re: [AMBER] NMR distance restrained MD (Mon Jan 06 2020 - 04:17:14 PST)
- [AMBER] NMR distance restrained MD (Wed Jan 01 2020 - 23:56:32 PST)
MENDOZA Cesar
- Re: [AMBER] Help building a model of a 2F-2S protein with MDPB.py (Wed Jan 29 2020 - 12:27:36 PST)
- Re: [AMBER] Help building a model of a 2F-2S protein with MDPB.py (Wed Jan 29 2020 - 12:25:47 PST)
- [AMBER] About ferrocene (Mon Jan 27 2020 - 08:54:45 PST)
- Re: [AMBER] About ions coordinated to Zinc (Fri Jan 24 2020 - 15:18:38 PST)
- Re: [AMBER] About ions coordinated to Zinc (Thu Jan 23 2020 - 07:23:05 PST)
- [AMBER] About ions coordinated to Zinc (Mon Jan 20 2020 - 06:45:22 PST)
MYRIAN TORRES RICO
- [AMBER] gnuplot (Wed Jan 29 2020 - 02:18:56 PST)
- [AMBER] gnuplot (Wed Jan 29 2020 - 02:17:48 PST)
- Re: [AMBER] ligand split (Fri Jan 17 2020 - 07:32:27 PST)
- Re: [AMBER] ligand split (Fri Jan 17 2020 - 07:15:52 PST)
- Re: [AMBER] ligand split (Wed Jan 15 2020 - 04:52:20 PST)
- Re: [AMBER] ligand split (Wed Jan 15 2020 - 02:44:40 PST)
- Re: [AMBER] ligand split (Wed Jan 15 2020 - 02:26:22 PST)
- [AMBER] ligand split (Tue Jan 14 2020 - 09:07:35 PST)
- Re: [AMBER] error (Wed Jan 08 2020 - 07:07:38 PST)
Neha Gandhi
- [AMBER] ValueError: could not convert string to float: ********* Error occured on rank 0. Exiting. All files have been retained. (Wed Jan 15 2020 - 20:35:09 PST)
- [AMBER] ligand clustering (Wed Jan 01 2020 - 21:47:51 PST)
Nicolas Feldman
- Re: [AMBER] postdoc DNA/RNA simulations (Thu Jan 30 2020 - 10:14:06 PST)
- Re: [AMBER] Amber on windows 10 (Tue Jan 28 2020 - 07:13:37 PST)
- Re: [AMBER] Amber on windows 10 (Tue Jan 28 2020 - 04:33:33 PST)
- Re: [AMBER] Amber on windows 10 (Tue Jan 28 2020 - 04:27:06 PST)
- [AMBER] Amber on windows 10 (Tue Jan 28 2020 - 04:14:39 PST)
Pengfei Li
- Re: [AMBER] Generating parameters for iron-sulfur protein (Sat Jan 18 2020 - 16:39:57 PST)
Petro
- Re: [AMBER] Resolving overlapping atoms. (Thu Jan 09 2020 - 10:19:36 PST)
- [AMBER] Resolving overlapping atoms. (Thu Jan 09 2020 - 01:54:12 PST)
- Re: [AMBER] Question about addtobox (Wed Jan 08 2020 - 15:19:41 PST)
- [AMBER] Question about addtobox (Tue Jan 07 2020 - 22:28:09 PST)
- Re: [AMBER] Molecule is wrapped out of the cell. (Tue Jan 07 2020 - 09:32:41 PST)
- [AMBER] Molecule is wrapped out of the cell. (Mon Jan 06 2020 - 02:44:51 PST)
Prasanth G, Research Scholar
- [AMBER] charting Ligand's movement in the binding pocket (Thu Jan 09 2020 - 02:58:01 PST)
Qing Lv
- Re: [AMBER] Is error bar necessary for umbrella sampling? (Mon Jan 13 2020 - 18:48:06 PST)
- [AMBER] Is error bar necessary for umbrella sampling? (Mon Jan 13 2020 - 06:36:15 PST)
- [AMBER] Is NPT ensemble necessary for the protein-water system? (Fri Jan 10 2020 - 07:55:57 PST)
- [AMBER] Is minimization and equilibration needed in umbrella sampling? (Fri Jan 10 2020 - 07:46:29 PST)
Rana Rehan Khalid
- [AMBER] Fwd: CalcError: /truba/sw/centos6.4/app/amber/amber14/bin/sander failed with prmtop gas.complex.prmtop! (Mon Jan 27 2020 - 08:51:02 PST)
Ray Luo
- Re: [AMBER] MMPBSA standard deviation (Geng Dong) (Sun Jan 05 2020 - 07:46:29 PST)
- Re: [AMBER] MMPBSA error (Sat Jan 04 2020 - 17:41:50 PST)
- Re: [AMBER] MMPBSA error (Fri Jan 03 2020 - 12:05:06 PST)
- Re: [AMBER] MMPBSA error (Thu Jan 02 2020 - 22:15:58 PST)
- Re: [AMBER] MMPBSA error (Thu Jan 02 2020 - 16:37:15 PST)
Rituparna Roy
- [AMBER] Problem regarding umbrella sampling (Sun Jan 19 2020 - 20:31:13 PST)
roomno sixtysix
- [AMBER] Problem regarding umbrella sampling (Sun Jan 19 2020 - 06:45:41 PST)
Rosellen, Martin
- Re: [AMBER] Generalized Born and entropy (Mon Jan 13 2020 - 04:48:19 PST)
Ross Walker
- Re: [AMBER] GPU-AMBER18 installation on RTX2080Ti (Sat Jan 18 2020 - 11:32:13 PST)
Rui Chen
- [AMBER] CPPTRAJ-Hbonds (Mon Jan 13 2020 - 07:49:11 PST)
- [AMBER] esp charge (Fri Jan 03 2020 - 16:49:52 PST)
- Re: [AMBER] MMPBSA error (Fri Jan 03 2020 - 12:59:10 PST)
- Re: [AMBER] MMPBSA error (Fri Jan 03 2020 - 08:58:42 PST)
- Re: [AMBER] MMPBSA error (Thu Jan 02 2020 - 21:37:14 PST)
- [AMBER] MMPBSA error (Thu Jan 02 2020 - 16:27:54 PST)
- Re: [AMBER] Tleap naming problem (Wed Jan 01 2020 - 13:19:00 PST)
Sally Pias
- Re: [AMBER] vanilla Nose-Hoover thermostat availability (Wed Jan 22 2020 - 17:41:00 PST)
- [AMBER] vanilla Nose-Hoover thermostat availability (Thu Jan 16 2020 - 14:19:39 PST)
- [AMBER] modeling a Schiff base with GAFF atom types (Tue Jan 14 2020 - 15:16:57 PST)
Santiago Movilla
- [AMBER] DUMPAVE digits (Mon Jan 20 2020 - 14:29:33 PST)
Satyaseelan C
- Re: [AMBER] generating g-quadruplex DNA structures from a sequence (Thu Jan 23 2020 - 00:53:24 PST)
Scott Brozell
- Re: [AMBER] Error in installing parallel version of AMBER18 (Thu Jan 30 2020 - 11:55:53 PST)
SHAUNAK BADANI
- [AMBER] Doubt regarding Collision frequency during NEB simulations (Fri Jan 31 2020 - 11:37:03 PST)
- [AMBER] NEB Simulations in Amber (Mon Jan 20 2020 - 12:25:26 PST)
Sruthi Sudhakar
- Re: [AMBER] pmemd.cuda.MPI run error (Mon Jan 27 2020 - 05:11:08 PST)
- Re: [AMBER] pmemd.cuda.MPI run error (Mon Jan 27 2020 - 04:55:00 PST)
- Re: [AMBER] pmemd.cuda.MPI run error (Mon Jan 27 2020 - 04:49:12 PST)
- [AMBER] pmemd.cuda.MPI run error (Mon Jan 27 2020 - 04:21:04 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error (Fri Jan 24 2020 - 22:25:09 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error (Fri Jan 24 2020 - 20:48:14 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error (Fri Jan 24 2020 - 02:13:20 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error (Thu Jan 23 2020 - 07:53:41 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error (Thu Jan 23 2020 - 07:24:01 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error (Thu Jan 23 2020 - 03:39:54 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error (Thu Jan 23 2020 - 02:10:05 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error (Thu Jan 23 2020 - 02:08:46 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error (Thu Jan 23 2020 - 00:17:11 PST)
- [AMBER] Multiple GPU imstallation of AMBER 18 error (Wed Jan 22 2020 - 22:54:08 PST)
- [AMBER] rror: an illegal memory access was encountered launching kernel kNLSkinTest (Sat Jan 18 2020 - 04:30:58 PST)
- [AMBER] pdb to mol2 conversion via antechamber (Thu Jan 16 2020 - 22:54:51 PST)
- [AMBER] RESP fitting (Wed Jan 15 2020 - 04:58:56 PST)
- [AMBER] pmemd.cuda:command not found (Sat Jan 04 2020 - 23:28:32 PST)
- [AMBER] Regarding clustering using mmtsb toolkit (Wed Jan 01 2020 - 22:37:22 PST)
Stephan Schott
- Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer (Mon Jan 20 2020 - 07:01:36 PST)
- Re: [AMBER] defining a progress variable to be the z-component of some atom or group of atoms? (Mon Jan 20 2020 - 07:12:55 PST)
- Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer (Thu Jan 16 2020 - 14:37:43 PST)
- Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer (Thu Jan 16 2020 - 04:13:59 PST)
Thayer, Kelly
- Re: [AMBER] cpptraj_clucster (Wed Jan 29 2020 - 07:13:49 PST)
Thomas Cheatham
- Re: [AMBER] Long syntax error on complex molecule (Fri Jan 17 2020 - 20:11:19 PST)
Tiejun Wei
- [AMBER] Fwd: Periodic box problem when simulating Membrane system (Mon Jan 13 2020 - 06:26:41 PST)
Vaibhav Dixit
- Re: [AMBER] generating g-quadruplex DNA structures from a sequence (Wed Jan 22 2020 - 21:09:14 PST)
- [AMBER] generating g-quadruplex DNA structures from a sequence (Tue Jan 21 2020 - 22:51:39 PST)
- Re: [AMBER] printing charges in pdb (Mon Jan 06 2020 - 09:04:05 PST)
- [AMBER] printing charges in pdb (Mon Jan 06 2020 - 01:44:53 PST)
- Re: [AMBER] empty cein file redox potential calculations (Mon Jan 06 2020 - 00:59:37 PST)
Vishal Reddy
- [AMBER] Parameter Files for Nanopore made of Si3N4(Silicon Nitride) (Thu Jan 23 2020 - 02:05:25 PST)
Vlad
- [AMBER] About utilities to convert Amber input files for MD into the Tinker, NAMD, Genesis, or Desmond input files (Tue Jan 28 2020 - 20:00:19 PST)
Vlad Cojocaru
- [AMBER] Workshop on Free Energy calculations in Muenster March 11-13 2020 (Fri Jan 17 2020 - 01:32:27 PST)
Yinglong Miao
- Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ (Fri Jan 17 2020 - 07:45:10 PST)
- Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ (Fri Jan 17 2020 - 07:09:34 PST)
- Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ (Tue Jan 14 2020 - 08:05:11 PST)
- Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ (Mon Jan 13 2020 - 17:10:04 PST)
yinglong.miao.gmail.com
- Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ (Tue Jan 14 2020 - 09:34:22 PST)
- [AMBER] Error with using dpeaks clustering in CPPTRAJ (Mon Jan 13 2020 - 15:50:49 PST)
zizhang sheng
- Re: [AMBER] MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest (Fri Jan 10 2020 - 13:43:01 PST)
- Re: [AMBER] MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest (Fri Jan 10 2020 - 09:29:32 PST)
- [AMBER] MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest (Thu Jan 09 2020 - 06:18:32 PST)
- [AMBER] Glycoprotein MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest (Tue Jan 07 2020 - 07:47:45 PST)
- [AMBER] Glycosylation issue: Atom xx was assigned a lower molecule # than previous atom. (Fri Jan 03 2020 - 13:44:04 PST)
zz sheng
- Re: [AMBER] Glycosylation issue: Atom xx was assigned a lower molecule # than previous atom. (Fri Jan 03 2020 - 15:43:14 PST)
东庚
- [AMBER] MMPBSA standard deviation (Geng Dong) (Sun Jan 05 2020 - 03:30:01 PST)
조준범
- [AMBER] [ MD Failure ] (Sun Jan 12 2020 - 08:19:33 PST)
- [AMBER] [ Error with MD ] Energetics of the system (Thu Jan 09 2020 - 23:35:38 PST)
- Re: [AMBER] [ Polymer with Extra Points ] (Thu Jan 09 2020 - 21:29:10 PST)
- [AMBER] [ prmtop ] SOLVENT_POINTERS (Thu Jan 09 2020 - 21:15:18 PST)
- [AMBER] [ inpcrd file ] (Thu Jan 09 2020 - 03:09:29 PST)
- [AMBER] [ Polymer ] Parameter Modification (Wed Jan 08 2020 - 21:17:32 PST)
- Re: [AMBER] [ Polymer with Extra Points ] (Tue Jan 07 2020 - 01:04:40 PST)
- [AMBER] [ Polymer with Extra Points ] (Mon Jan 06 2020 - 22:40:38 PST)
- [AMBER] [ Lone pair electron & Polymer ] (Mon Jan 06 2020 - 22:06:13 PST)

Amber Archive Jan 2020 by author