Amber Archive Feb 2018 by thread
- [AMBER] distance restrain for group of residues ARMIN HODAEI (Wed Jan 31 2018 - 15:19:56 PST)
- [AMBER] Query on thermodynamic integration of complexes involving metal ions muthu kumaran (Wed Jan 31 2018 - 21:33:20 PST)
- [AMBER] by MM-PBSA binding energy at 310K? Michael Shokhen (Thu Feb 01 2018 - 00:00:16 PST)
- [AMBER] Regarding vdW (or other) parameters for type: Pb Garima Singh (Thu Feb 01 2018 - 02:03:48 PST)
- [AMBER] CPPTRAJ ERROR-Reg. Manjula Saravanan (Thu Feb 01 2018 - 02:26:52 PST)
- Re: [AMBER] AMBER16 and intel 2017, possible to compile? David A Case (Thu Feb 01 2018 - 04:24:40 PST)
- [AMBER] printcharges not working when imin=5 and maxcyc=0 David Sáez (Thu Feb 01 2018 - 05:48:36 PST)
- Re: [AMBER] CPPTRAJ HBond analysis Segmentation fault (core dumped) Daniel Roe (Thu Feb 01 2018 - 05:58:10 PST)
- Re: [AMBER] Reorienting the protein during simulation Daniel Roe (Thu Feb 01 2018 - 05:59:19 PST)
- Re: [AMBER] Extract Velocity (and Force) from Gromacs .trr trajectory using cpptraj Daniel Roe (Thu Feb 01 2018 - 06:03:48 PST)
- Re: [AMBER] hbond analysis on DNA-protein complex Daniel Roe (Thu Feb 01 2018 - 06:05:41 PST)
- Re: [AMBER] Use amber output velocity for different system Daniel Roe (Thu Feb 01 2018 - 06:06:48 PST)
- Re: [AMBER] Compressing trajectory file Daniel Roe (Thu Feb 01 2018 - 06:10:06 PST)
- Re: [AMBER] CPPTRAJ: How to project trajectories of one simulation onto principal components (PCs) of another simulation? Daniel Roe (Thu Feb 01 2018 - 06:20:05 PST)
- Re: [AMBER] PCA scree plots Daniel Roe (Thu Feb 01 2018 - 06:26:10 PST)
- [AMBER] is that possible to change the size of the box in one direction in simulation? Parviz Seifpanahi Shabane (Thu Feb 01 2018 - 08:55:23 PST)
- [AMBER] BASIC information for AMBER Vikram Dalal (Thu Feb 01 2018 - 10:35:13 PST)
- [AMBER] Thermodynamic Integration query Sowmya Indrakumar (Fri Feb 02 2018 - 02:15:48 PST)
- [AMBER] path_mode variable in SMD David Sáez (Fri Feb 02 2018 - 06:29:46 PST)
- [AMBER] setbox for octahedral Andrew Schaub (Fri Feb 02 2018 - 10:07:57 PST)
- [AMBER] amb2gmx roja rahmani (Fri Feb 02 2018 - 23:15:46 PST)
- [AMBER] Units used in ff14sb Siddhartha Jain (Sun Feb 04 2018 - 14:16:41 PST)
- [AMBER] amber workshop reminder Fabian Glaser (Mon Feb 05 2018 - 02:02:59 PST)
- [AMBER] adding ions Krystyna Zakrzewska (Mon Feb 05 2018 - 02:15:38 PST)
- [AMBER] Extracting lowest energy snapshot from trajectory MOHD HOMAIDUR RAHMAN (Mon Feb 05 2018 - 08:28:04 PST)
- [AMBER] Jobs and Evens in CHARMM-GUI Jumin Lee (Mon Feb 05 2018 - 14:00:04 PST)
- [AMBER] EULA/NVIDIA Adrian Roitberg (Mon Feb 05 2018 - 14:31:20 PST)
- [AMBER] Quasi-harmonic analysis Chetna Tyagi (Tue Feb 06 2018 - 06:50:52 PST)
- [AMBER] how to run/install leap Mike Mazanetz (Tue Feb 06 2018 - 08:39:54 PST)
- Re: [AMBER] how to run/install leap - help needed Mike Mazanetz (Tue Feb 06 2018 - 11:04:12 PST)
- Re: [AMBER] how to run/install leap - solved Mike Mazanetz (Tue Feb 06 2018 - 12:04:30 PST)
- [AMBER] gist analysis Sofia Vasilakaki (Tue Feb 06 2018 - 16:14:58 PST)
- [AMBER] Constant Redox potential MD simulations Tarsis (Tue Feb 06 2018 - 16:19:00 PST)
- [AMBER] Problem in installing Amber16 Tasneem Kausar (Wed Feb 07 2018 - 00:43:25 PST)
- [AMBER] Certain statistics from the trajectory Nikolay N. Kuzmich (Wed Feb 07 2018 - 03:54:56 PST)
- [AMBER] Paramfit WRITE_ENERGY CA gmail (Wed Feb 07 2018 - 05:35:25 PST)
- [AMBER] solvatebox iso error Ahmed Mashaly (Wed Feb 07 2018 - 10:10:21 PST)
- [AMBER] lipidorder in cpptraj Chitrak Gupta (Wed Feb 07 2018 - 16:13:59 PST)
- [AMBER] Regarding termination of pmemd.cuda Rajarshi Roy (Thu Feb 08 2018 - 00:41:25 PST)
- [AMBER] Ion dissociation computed by umbrella sampling Veronika Jurásková (Thu Feb 08 2018 - 02:21:52 PST)
- [AMBER] Ph.D. and Post-doc positions in molecular simulations and structural bioinformatics Jan Brezovsky (Thu Feb 08 2018 - 05:16:42 PST)
- [AMBER] Adding divalent ions in LEaP Nikolay N. Kuzmich (Thu Feb 08 2018 - 06:19:36 PST)
- [AMBER] Forcefield for methylated and acetylated amino acids Shahryar Alavi (Thu Feb 08 2018 - 07:55:27 PST)
- [AMBER] SMD using Orca for QM region unknown atom specifier Ruth Helena Tichauer (Thu Feb 08 2018 - 12:37:28 PST)
- [AMBER] Trajectory processing Ming Tang (Thu Feb 08 2018 - 16:39:51 PST)
- [AMBER] AMBER on AWS - Beta testers wanted. Mike Mazanetz (Thu Feb 08 2018 - 17:10:36 PST)
- [AMBER] B-factor Values Mac Kevin Braza (Thu Feb 08 2018 - 23:12:34 PST)
- [AMBER] Strong Na+-ASP interactions Rui, Huan (Fri Feb 09 2018 - 06:57:14 PST)
- [AMBER] RMSD with cpptraj Rui, Huan (Fri Feb 09 2018 - 11:38:32 PST)
- [AMBER] Information required about the potential of Amber software. Ubaid Ullah (Fri Feb 09 2018 - 20:10:56 PST)
- [AMBER] MPI error in running a multi-sander job for TI calculation Ahsan Mohd (Sat Feb 10 2018 - 11:27:42 PST)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C Morrow,John Kenneth (Sun Feb 11 2018 - 14:08:57 PST)
- [AMBER] STSM sample files Szymon Żaczek (Mon Feb 12 2018 - 00:48:31 PST)
- [AMBER] Regarding error in frcmod file Aashish Bhatt (Mon Feb 12 2018 - 05:46:53 PST)
- [AMBER] Question about how to compute kinetic energy from velocity trajectory Lee-Ping Wang (Mon Feb 12 2018 - 12:04:21 PST)
- [AMBER] Problem calculating energies using cpptraj and sander API Lee-Ping Wang (Mon Feb 12 2018 - 14:16:27 PST)
- [AMBER] some programs do not appear Ibrahim Said (Mon Feb 12 2018 - 14:50:09 PST)
- [AMBER] ff15ipq and divalent ions Neha Gandhi (Mon Feb 12 2018 - 22:05:15 PST)
- [AMBER] Problem with Atomtype of ligand in protein-ligand complex Sivasudhan R (Mon Feb 12 2018 - 23:22:33 PST)
- [AMBER] PatchingError: No changes made from this patch Elisa Pieri (Tue Feb 13 2018 - 01:27:26 PST)
- [AMBER] Make install Error Elisa Pieri (Tue Feb 13 2018 - 01:46:05 PST)
- [AMBER] Question about proper usage of pysander Lee-Ping Wang (Tue Feb 13 2018 - 07:31:06 PST)
- [AMBER] AMBER disk usage on CPU or GPU nodes Lenz, Stefan (Tue Feb 13 2018 - 09:27:53 PST)
- [AMBER] Dendrogram from cpptraj clustering? Gustavo Seabra (Thu Feb 15 2018 - 06:51:00 PST)
- [AMBER] Torsion angle frequency Lizelle Lubbe (Thu Feb 15 2018 - 23:56:30 PST)
- [AMBER] 3 GPUs and replica exchange MD Nikolay N. Kuzmich (Fri Feb 16 2018 - 01:27:01 PST)
- [AMBER] MD simulation of a protein at pH 3.0 Rakesh Srivastava (Fri Feb 16 2018 - 04:15:48 PST)
- [AMBER] sander API does not support EP with igb 6 Lee-Ping Wang (Fri Feb 16 2018 - 05:44:16 PST)
- [AMBER] Amber16 pmemd.cuda on Tesla M2075 Richard Smith (Fri Feb 16 2018 - 08:46:59 PST)
- [AMBER] "Issue" with hbond Núbia Prates (Fri Feb 16 2018 - 13:57:29 PST)
- [AMBER] Updated Website James Kress (Mon Feb 05 2018 - 11:47:42 PST)
- [AMBER] Problem with using Monte Carlo Barostat algorithm in pmemd cuda Roma Mukhopadhyay (Fri Feb 16 2018 - 20:07:06 PST)
- [AMBER] eChemInfo 2018 workshop on drug design in Milano Thomas Exner (Sat Feb 17 2018 - 02:51:15 PST)
- [AMBER] 3D-RISM calculation at pH 3.0 Rakesh Srivastava (Sun Feb 18 2018 - 21:55:12 PST)
- [AMBER] "The unperturbed charge of the unit is not integral": really nothing to care about? Nikolay N. Kuzmich (Mon Feb 19 2018 - 01:09:32 PST)
- [AMBER] add vertical lines for initial and final angle Rosellen, Martin (Mon Feb 19 2018 - 04:41:27 PST)
- [AMBER] Scaling QM energy/forces Raimon Fabregat (Mon Feb 19 2018 - 06:50:16 PST)
- [AMBER] workshop amber Technion Israel Fabian Glaser (Mon Feb 19 2018 - 23:41:38 PST)
- [AMBER] OL15 (leaprc.DNA.OL15) vs bsc1 (leaprc.DNA.bsc1). Saikat Pal (Tue Feb 20 2018 - 04:41:06 PST)
- [AMBER] Mask building problems James Kress (Tue Feb 20 2018 - 16:14:44 PST)
- [AMBER] visualization of long simulation data with out downloading .mdcrd file Rana Rehan Khalid (Wed Feb 21 2018 - 05:23:27 PST)
- [AMBER] Amber16/AmberTools17 CUDA version Baker D.J. (Wed Feb 21 2018 - 08:28:09 PST)
- [AMBER] Combining coordinate files + Renumbering residues Jag Silwal (Wed Feb 21 2018 - 12:07:05 PST)
- [AMBER] Amber16/AmberTools17 CUDA version Baker D.J. (Wed Feb 21 2018 - 12:53:42 PST)
- [AMBER] Is there a bug in how Amber16 handles qmmask and WAT? James Kress (Wed Feb 21 2018 - 13:25:25 PST)
- [AMBER] amber coordinates in VMD Stefano Guglielmo (Wed Feb 21 2018 - 16:17:54 PST)
- [AMBER] Enquiry on ntt Ming Tang (Thu Feb 22 2018 - 03:22:08 PST)
- Re: [AMBER] The unperturbed charge of the unit is not integral": really nothing to care about? Nikolay N. Kuzmich (Thu Feb 22 2018 - 08:18:49 PST)
- [AMBER] Using solvatebox with a SO2 molecule - difficulties in adding duplicate oxygen atoms in .pdb M Conte (Thu Feb 22 2018 - 08:52:48 PST)
- [AMBER] Is there a bug in how Amber16 handles qmmask and WAT? James Kress (Thu Feb 22 2018 - 11:58:54 PST)
- [AMBER] selection of the type of box in molecular dynamics in AMBER Vikram Dalal (Thu Feb 22 2018 - 13:22:38 PST)
- [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large NITTER, NIT, LL and J are 0 1 151 KRIPI TOMAR (Thu Feb 22 2018 - 23:24:35 PST)
- [AMBER] Simulation does not restart from restart file written in previous step. Abhilash J (Fri Feb 23 2018 - 04:49:29 PST)
- Re: [AMBER] The unperturbed charge of the unit is not integral: really nothing to care about? Nikolay N. Kuzmich (Fri Feb 23 2018 - 09:33:07 PST)
- [AMBER] RDF Marcelo Andrade Chagas (Fri Feb 23 2018 - 10:39:06 PST)
- [AMBER] trouble with pdb4amber Jennifer L. Muzyka (Sun Feb 25 2018 - 09:18:12 PST)
- [AMBER] Placing ions within a maximum distance from the solute Nikolay N. Kuzmich (Mon Feb 26 2018 - 00:14:24 PST)
- [AMBER] AMBER/ORCA for QM/MM minyuan.mail.ustc.edu.cn (Mon Feb 26 2018 - 06:24:29 PST)
- [AMBER] How to generate parameters for two MG 2+ ions ---GTP Rana Rehan Khalid (Mon Feb 26 2018 - 08:02:02 PST)
- Re: [AMBER] Problem with parallel install Maria Clelia Milletti (Mon Feb 26 2018 - 14:04:25 PST)
- [AMBER] Interface with DFTB+ Raimon Fabregat (Tue Feb 27 2018 - 02:26:55 PST)
- [AMBER] "refc" file Armin Hodaei (Tue Feb 27 2018 - 02:45:29 PST)
- [AMBER] Has anyone determined a fix for QM_CHECK_PERIODIC or inability to include solvent in qmmask error James Kress (Tue Feb 27 2018 - 12:02:30 PST)
- [AMBER] Adding a new atom type - ATTN, no polarizability parameter Henrik Hariman (Tue Feb 27 2018 - 12:21:59 PST)
- [AMBER] Can I include Mg ions in receptor mask when using MMPBSA.py Jie Zhu (Tue Feb 27 2018 - 14:19:04 PST)
- [AMBER] leap (UNKNOWN ATOM TYPE: O3) Ruth Helena Tichauer (Wed Feb 28 2018 - 04:46:59 PST)
- [AMBER] Question about using cpptraj - Script Marcelo Andrade Chagas (Wed Feb 28 2018 - 11:28:02 PST)
- Re: [AMBER] ABMD write error to MDOUT Feng Pan (Wed Feb 28 2018 - 20:45:24 PST)
- Last message date: Wed Feb 28 2018 - 21:00:03 PST
- Archived on: Mon Dec 30 2024 - 05:55:34 PST
