Amber Archive Dec 2021: by subject

[AMBER] A bug in phishi Amber20?
- Daniel Roe (Wed Dec 01 2021 - 05:20:15 PST)
- 余青芬 (Wed Dec 01 2021 - 02:04:07 PST)
[AMBER] A10 cards
- Jason Hogrefe (Thu Dec 30 2021 - 06:52:08 PST)
- Fabian Glaser (Thu Dec 30 2021 - 06:36:11 PST)
[AMBER] about RAMD
- Charles Lin (Tue Dec 07 2021 - 17:28:26 PST)
- 田佳琪 (Tue Dec 07 2021 - 00:54:35 PST)
- Charles Lin (Mon Dec 06 2021 - 08:51:37 PST)
- 田佳琪 (Sun Dec 05 2021 - 23:00:11 PST)
[AMBER] Addendum on problems about finding CUDA
- David A Case (Sun Dec 05 2021 - 05:56:30 PST)
[AMBER] Adding atom types to gaff.dat
- Pengfei Li (Tue Dec 21 2021 - 07:59:29 PST)
- David A Case (Sat Dec 18 2021 - 07:09:00 PST)
- Sam Walsworth (Researcher) (Fri Dec 17 2021 - 21:50:00 PST)
[AMBER] Adjust system in certain axis
- mohamed marzouk (Thu Dec 23 2021 - 16:31:01 PST)
[AMBER] Advice on Simulated Annealing
- Matthew Guberman-Pfeffer (Thu Dec 30 2021 - 09:45:46 PST)
- Hector A. Baldoni (Thu Dec 30 2021 - 08:50:38 PST)
- Matthew Guberman-Pfeffer (Thu Dec 30 2021 - 08:00:57 PST)
- David A Case (Wed Dec 29 2021 - 18:59:09 PST)
- Carlos Simmerling (Wed Dec 29 2021 - 11:48:19 PST)
- Matthew Guberman-Pfeffer (Wed Dec 29 2021 - 10:39:23 PST)
[AMBER] Amber -log4J impact ?
- David A Case (Fri Dec 17 2021 - 17:52:11 PST)
[AMBER] Amber calculate RMSF
- Daniel Roe (Wed Dec 01 2021 - 08:19:54 PST)
[AMBER] amber docker container
- Carlos Simmerling (Wed Dec 29 2021 - 05:29:40 PST)
- Fabian Glaser (Wed Dec 29 2021 - 02:07:56 PST)
[AMBER] Amber Installation Error
- David A Case (Thu Dec 02 2021 - 13:29:38 PST)
- Suguna Sakkiah (Thu Dec 02 2021 - 11:26:26 PST)
[AMBER] Amber installation error on Centos 7
- David A Case (Tue Dec 21 2021 - 11:13:11 PST)
- Suguna Sakkiah (Tue Dec 21 2021 - 11:00:58 PST)
[AMBER] amber pmemd.cuda for implicit solvent simulations
- Prithviraj Nandigrami (Wed Dec 15 2021 - 11:45:11 PST)
[AMBER] amber20 - test suite picks up the wrong libgfortran
- Mark Dixon (Tue Dec 21 2021 - 07:55:30 PST)
[AMBER] Amber20 CUDA installation error Centos 7
- David A Case (Fri Dec 24 2021 - 18:30:29 PST)
- Suguna Sakkiah (Fri Dec 24 2021 - 15:52:51 PST)
[AMBER] Amber20 installation error - Centos 7
- David A Case (Mon Dec 20 2021 - 18:26:36 PST)
- Suguna Sakkiah (Mon Dec 20 2021 - 12:56:46 PST)
[AMBER] Amber20 installation error on Centos 7
- Suguna Sakkiah (Fri Dec 24 2021 - 15:35:48 PST)
- David A Case (Fri Dec 24 2021 - 06:16:25 PST)
- Suguna Sakkiah (Thu Dec 23 2021 - 11:01:22 PST)
- David A Case (Wed Dec 22 2021 - 17:55:31 PST)
- Suguna Sakkiah (Wed Dec 22 2021 - 07:42:42 PST)
- David A Case (Tue Dec 21 2021 - 20:32:16 PST)
- Suguna Sakkiah (Tue Dec 21 2021 - 11:33:11 PST)
- David A Case (Mon Dec 20 2021 - 09:25:19 PST)
- Suguna Sakkiah (Fri Dec 17 2021 - 10:04:58 PST)
[AMBER] Atom types and atom order of lib files and pdb files
- Carlos Simmerling (Tue Dec 21 2021 - 04:14:47 PST)
- Sam Walsworth (Researcher) (Mon Dec 20 2021 - 05:23:27 PST)
- Carlos Simmerling (Mon Dec 20 2021 - 02:22:49 PST)
- Sam Walsworth (Researcher) (Sun Dec 19 2021 - 15:28:39 PST)
[AMBER] bond equilibrium achieved with sander but not with pmemd, Amber 20
- Qinghua Liao (Wed Dec 01 2021 - 03:03:31 PST)
[AMBER] Call for papers - 17th German Conference on Cheminformatics and EuroSAMPL Satellite Workshop, May 8 -12, 2022 in Garmisch-Partenkirchen/Germany
- Guessregen, Stefan /DE (Thu Dec 23 2021 - 09:23:05 PST)
[AMBER] CHAMBER prmtops cannot be used with NMODE
- 周丽萍 (Mon Dec 13 2021 - 23:01:24 PST)
[AMBER] closest ions radiation distribution
- Daniel Roe (Wed Dec 01 2021 - 05:43:11 PST)
[AMBER] Constant PH simulations
- Carlos Simmerling (Mon Dec 20 2021 - 09:41:42 PST)
- Sruthi Sudhakar (Mon Dec 20 2021 - 09:38:00 PST)
[AMBER] CPPTRAJ Segmentation Fault with modified topology file
- Daniel Roe (Mon Dec 20 2021 - 13:52:25 PST)
- Chris Lee (Mon Dec 20 2021 - 13:40:20 PST)
- Daniel Roe (Mon Dec 20 2021 - 11:06:25 PST)
- Chris Lee (Mon Dec 20 2021 - 10:58:25 PST)
[AMBER] Creating library files - optimised or docked structure?
- Sam Walsworth (Researcher) (Tue Dec 21 2021 - 16:45:09 PST)
[AMBER] CUDA installation error - CENTOS 7
- David A Case (Sun Dec 26 2021 - 13:22:45 PST)
- Suguna Sakkiah (Sun Dec 26 2021 - 12:30:16 PST)
[AMBER] DE Shaw RNA parameters error
- Alexander Izvorski (Sun Dec 26 2021 - 14:30:53 PST)
[AMBER] Dihedral restraint on a C=N double bond
- Liao (Thu Dec 30 2021 - 17:55:31 PST)
- Carlos Simmerling (Thu Dec 30 2021 - 13:30:15 PST)
- Liao (Thu Dec 30 2021 - 12:11:54 PST)
[AMBER] Dynamic cross correlation matrices in AMBER20
- Debarati DasGupta (Wed Dec 01 2021 - 06:11:21 PST)
- Daniel Roe (Wed Dec 01 2021 - 05:52:19 PST)
[AMBER] Electrostatic energy in TI at lambda=1 for a toy system
- Ali Morshedi (Sat Dec 11 2021 - 00:04:27 PST)
[AMBER] Equilibrate and Production Run Membrane-protein complex
- Dickson, Callum (Wed Dec 01 2021 - 11:46:40 PST)
- King Wu (Wed Dec 01 2021 - 10:21:40 PST)
- Daniel Roe (Wed Dec 01 2021 - 05:46:36 PST)
[AMBER] Error during 1D-RISM run
- David A Case (Sun Dec 05 2021 - 06:12:16 PST)
- Alexis Azucena (Sat Dec 04 2021 - 02:08:42 PST)
[AMBER] Error for installing the GPU version of Amber20
- Joanna Michelle E. Chua (Tue Dec 14 2021 - 20:18:27 PST)
- David A Case (Wed Dec 08 2021 - 05:50:33 PST)
- jinfeng liu (Tue Dec 07 2021 - 19:54:24 PST)
[AMBER] Error running TI with pmemd.cuda: "Error: an illegal memory access was encountered launching kernel kClearTIKinEnergy_kernel"
- Ali Morshedi (Tue Dec 21 2021 - 00:09:53 PST)
- Rafał Madaj (Mon Dec 20 2021 - 23:56:42 PST)
- Ali Morshedi (Mon Dec 20 2021 - 13:50:56 PST)
[AMBER] Error with MMPBSA
- Monsurat M. Lawal (Wed Dec 08 2021 - 05:36:30 PST)
- Kehinde Idowu (Tue Dec 07 2021 - 08:59:54 PST)
- Debarati DasGupta (Tue Dec 07 2021 - 07:44:30 PST)
- Monsurat M. Lawal (Tue Dec 07 2021 - 04:51:33 PST)
- David A Case (Tue Dec 07 2021 - 04:50:35 PST)
- Kehinde Idowu (Mon Dec 06 2021 - 18:06:28 PST)
[AMBER] Error with Zn ion Coordination
- Maria Nagan (Sun Dec 12 2021 - 17:06:50 PST)
- Aravind R (Sat Dec 11 2021 - 02:21:02 PST)
[AMBER] Extending constant pH to additional titratable groups
- 王金玉 (Sun Dec 26 2021 - 06:44:58 PST)
[AMBER] Fortran runtime error during 1D-RISM analysis to generate .xvv file
- Alexis Azucena (Thu Dec 02 2021 - 17:31:22 PST)
- tluchko (Thu Dec 02 2021 - 10:01:10 PST)
- David A Case (Thu Dec 02 2021 - 05:17:21 PST)
- Alexis Azucena (Thu Dec 02 2021 - 02:02:15 PST)
[AMBER] Frequency unit used for Oscillating electric field
- Surajit Kalita (Thu Dec 23 2021 - 09:43:04 PST)
[AMBER] GAFF2 "ho" atoms have non-bonded 0
- Stefan Doerr (Mon Dec 13 2021 - 07:13:41 PST)
- David A Case (Wed Dec 08 2021 - 05:23:17 PST)
- Stefan Doerr (Wed Dec 08 2021 - 02:47:54 PST)
[AMBER] GIST: Entropy calculations
- Daniel Roe (Wed Dec 01 2021 - 08:07:39 PST)
[AMBER] Handling new atom types - bonded
- Sam Walsworth (Researcher) (Thu Dec 23 2021 - 07:49:58 PST)
[AMBER] Help parameterizing iron citrate
- Matthew Guberman-Pfeffer (Thu Dec 16 2021 - 23:29:00 PST)
[AMBER] How is correlation computed in cpptraj
- Daniel Roe (Wed Dec 01 2021 - 08:24:44 PST)
[AMBER] How to add an amidated residue at the C-terminal in AMBER tleap ?
- Yen Nguyen (Mon Dec 13 2021 - 10:35:24 PST)
[AMBER] How to build one metal ions surrounding with two ligands by MCPB.py
- ning (Fri Dec 24 2021 - 19:35:38 PST)
[AMBER] How to generate coordinate and parameter files for OXY bind with copper ions in the protein structure
- 辛志宏 (Tue Dec 28 2021 - 04:37:09 PST)
[AMBER] How to generate mol2 file with topology and crd file?
- Daniel Roe (Wed Dec 01 2021 - 08:10:34 PST)
[AMBER] How to interpret clustering
- Daniel Roe (Wed Dec 01 2021 - 05:39:23 PST)
[AMBER] How to restart a MMPBSA job
- Sadaf Rani (Thu Dec 16 2021 - 13:13:40 PST)
[AMBER] Hydrogen Bonding Analysis
- Daniel Roe (Mon Dec 20 2021 - 06:56:28 PST)
- Huimin Tian (Mon Dec 20 2021 - 01:27:40 PST)
[AMBER] Improving our options for pre-compiled AmberTools?
- Matias Machado (Fri Dec 17 2021 - 10:42:12 PST)
- David A Case (Fri Dec 17 2021 - 07:01:49 PST)
[AMBER] Inquiry about an error message when I constructing the frcmod file for my organometallic complex
- Yi Ren (Wed Dec 15 2021 - 17:22:43 PST)
[AMBER] install error for GPU version of Amber20 on A100 GPU card
- jinfeng liu (Fri Dec 10 2021 - 07:52:01 PST)
- David A Case (Fri Dec 10 2021 - 06:35:53 PST)
- jinfeng liu (Fri Dec 10 2021 - 04:30:46 PST)
[AMBER] installation error amber 18 in ubuntu 20.04
- David A Case (Wed Dec 01 2021 - 14:16:25 PST)
[AMBER] Installation error amber 20 in ubuntu 20.04
- David A Case (Thu Dec 02 2021 - 05:10:26 PST)
- Joanna Michelle E. Chua (Wed Dec 01 2021 - 19:43:29 PST)
[AMBER] ISSUE About Abmer prep file can not recoganized by TAO package
- 辛志宏 (Wed Dec 15 2021 - 00:44:18 PST)
[AMBER] Issue with defining angle parameters in frcmod files
- Sam Walsworth (Researcher) (Wed Dec 22 2021 - 17:03:46 PST)
- Carlos Simmerling (Wed Dec 22 2021 - 12:19:28 PST)
- Sam Walsworth (Researcher) (Wed Dec 22 2021 - 11:21:46 PST)
[AMBER] Li salt parameterisation issue
- Damiano Spadoni (Tue Dec 28 2021 - 07:26:29 PST)
[AMBER] Ligand problem in system preparation
- David A Case (Tue Dec 28 2021 - 06:34:43 PST)
- Ch Bilal (Tue Dec 28 2021 - 01:17:56 PST)
[AMBER] loadpdb and SSBOND
- David A Case (Thu Dec 16 2021 - 06:14:33 PST)
- Alan (Wed Dec 15 2021 - 00:03:04 PST)
[AMBER] MCPB, how to treat protein-attached Ru-dye
- Matthew Guberman-Pfeffer (Thu Dec 30 2021 - 09:48:49 PST)
- Matthew Guberman-Pfeffer (Sat Dec 25 2021 - 21:05:28 PST)
[AMBER] Meaning of "Multiple 'e' in NUMBER-like thing"
- Matthew Guberman-Pfeffer (Sun Dec 05 2021 - 14:57:44 PST)
[AMBER] Missing DNA base pair in cpptraj analysis
- Abhilash J (Wed Dec 01 2021 - 16:51:18 PST)
- Abhilash J (Wed Dec 01 2021 - 13:23:22 PST)
[AMBER] Mmpbsa inp=1 or inp=2
- Fabian Glaser (Wed Dec 08 2021 - 05:56:21 PST)
- Fabian Glaser (Tue Dec 07 2021 - 03:55:07 PST)
- David A Case (Sun Dec 05 2021 - 06:04:44 PST)
- Fabian Glaser (Sat Dec 04 2021 - 05:23:04 PST)
- Fabian Glaser (Sat Dec 04 2021 - 02:39:40 PST)
[AMBER] Neutralizing a protein with unknown charge?
- Gustavo Seabra (Mon Dec 13 2021 - 14:15:13 PST)
- Matias Machado (Mon Dec 13 2021 - 13:20:10 PST)
- Debarati DasGupta (Mon Dec 13 2021 - 13:19:15 PST)
- Carlos Simmerling (Mon Dec 13 2021 - 13:12:36 PST)
- Gustavo Seabra (Mon Dec 13 2021 - 12:55:47 PST)
[AMBER] Non periodic system in Amber
- Nagar, Hemant (Wed Dec 15 2021 - 16:04:04 PST)
[AMBER] Non-periodic boundry condition simulation
- Nagar, Hemant (Wed Dec 01 2021 - 15:27:43 PST)
[AMBER] Non-standard residue parameterization quesitons
- Matthew Guberman-Pfeffer (Sat Dec 25 2021 - 16:24:21 PST)
[AMBER] Non-standard residue parameterization questions
- Matthew Guberman-Pfeffer (Wed Dec 29 2021 - 10:26:27 PST)
- Dr. Anselm Horn (Wed Dec 29 2021 - 01:57:17 PST)
- Matthew Guberman-Pfeffer (Tue Dec 28 2021 - 20:54:10 PST)
[AMBER] numpy error with pdb4amber on cluster
- Vaibhav Dixit (Thu Dec 16 2021 - 20:18:45 PST)
- David A Case (Thu Dec 16 2021 - 05:49:07 PST)
- Vaibhav Dixit (Thu Dec 16 2021 - 05:04:07 PST)
- David A Case (Mon Dec 13 2021 - 06:44:29 PST)
- Vaibhav Dixit (Sat Dec 11 2021 - 21:34:04 PST)
- David A Case (Fri Dec 03 2021 - 05:01:53 PST)
- Vaibhav Dixit (Thu Dec 02 2021 - 19:51:01 PST)
[AMBER] Old Amber Force Fields
- Carlos Simmerling (Tue Dec 14 2021 - 09:04:13 PST)
- Niransha Kumarachchi (Tue Dec 14 2021 - 08:35:27 PST)
[AMBER] open mpi compiler error
- Ayesha Fatima (Wed Dec 01 2021 - 11:00:44 PST)
[AMBER] Parallel test stuck at Run.dhfr.noboxinfo
- Yu Chen (Wed Dec 15 2021 - 06:57:18 PST)
- David A Case (Wed Dec 15 2021 - 05:45:03 PST)
- Yu Chen (Tue Dec 14 2021 - 12:48:23 PST)
[AMBER] Parameters for Boron nitride
- Rituparna Roy (Wed Dec 22 2021 - 21:44:56 PST)
[AMBER] Peptide's charge is not 0 when getting parm7 and rst7 files
- Yen Nguyen (Mon Dec 13 2021 - 14:40:29 PST)
- Carlos Simmerling (Mon Dec 13 2021 - 14:31:15 PST)
- Yen Nguyen (Mon Dec 13 2021 - 14:25:06 PST)
- Carlos Simmerling (Mon Dec 13 2021 - 14:15:34 PST)
- Carlos Simmerling (Mon Dec 13 2021 - 14:14:26 PST)
- Yen Nguyen (Mon Dec 13 2021 - 14:13:17 PST)
[AMBER] permission error installing amber20
- Vaibhav Dixit (Sun Dec 12 2021 - 20:33:35 PST)
[AMBER] prmtop file generated with CLOSEST in cpptraj
- James Kress (Thu Dec 23 2021 - 11:09:59 PST)
- Daniel Roe (Thu Dec 23 2021 - 06:22:38 PST)
- James Kress (Wed Dec 22 2021 - 16:04:41 PST)
[AMBER] Problem in installation
- David A Case (Tue Dec 28 2021 - 06:47:39 PST)
- Guodong (Tue Dec 28 2021 - 04:28:23 PST)
[AMBER] Problem loading crd file in vmd
- ankita mehta (Fri Dec 03 2021 - 03:58:26 PST)
[AMBER] problem loading the trajectory files in vmd
- Matias Machado (Mon Dec 06 2021 - 13:55:07 PST)
- Carlos Simmerling (Mon Dec 06 2021 - 04:32:44 PST)
- ankita mehta (Mon Dec 06 2021 - 03:16:58 PST)
- Daniel Roe (Fri Dec 03 2021 - 08:20:01 PST)
- Carlos Simmerling (Fri Dec 03 2021 - 06:19:58 PST)
- Mohamed Aboelnga (Fri Dec 03 2021 - 04:37:51 PST)
- Mohamed Aboelnga (Fri Dec 03 2021 - 04:24:42 PST)
- Priya Dey (Fri Dec 03 2021 - 03:58:20 PST)
- ankita mehta (Fri Dec 03 2021 - 02:51:09 PST)
[AMBER] Problems about quasi-harmonic
- 周丽萍 (Wed Dec 22 2021 - 18:02:40 PST)
[AMBER] Problems with mdgx - torsional parameters fitting
- Casalini Tommaso (Tue Dec 21 2021 - 11:35:33 PST)
[AMBER] Problems with RMSD of different proteins.
- Daniel Roe (Wed Dec 01 2021 - 05:26:17 PST)
[AMBER] Protein in mixed of solvents
- Daniel Roe (Wed Dec 01 2021 - 05:47:19 PST)
[AMBER] Q-Chem and GPU use
- James Kress (Mon Dec 13 2021 - 12:57:48 PST)
[AMBER] Query regarding minimization in AMBER 20
- Carlos Simmerling (Wed Dec 22 2021 - 14:15:45 PST)
- Arooma Maryam (Wed Dec 22 2021 - 13:08:57 PST)
[AMBER] Question about build Amber20 with Intel compiler 2019
- David A Case (Fri Dec 17 2021 - 07:17:36 PST)
- Chen, Guoquan (Tue Dec 14 2021 - 12:26:05 PST)
[AMBER] README script from CHARMM-GUI to run PMEDE.CUDA
- David A Case (Sat Dec 11 2021 - 18:42:51 PST)
- King Wu (Sat Dec 11 2021 - 06:31:33 PST)
[AMBER] Reg: Cpptraj-Hierarchical Agglomerative Reference paper for methodology and result analysis
- Daniel Roe (Wed Dec 01 2021 - 08:21:03 PST)
[AMBER] RMSD of residues within 3A of ligand
- Daniel Roe (Wed Dec 01 2021 - 08:30:24 PST)
[AMBER] run_cmake error for installing the GPU version of Amber20
- Tru Huynh (Mon Dec 06 2021 - 00:23:59 PST)
- jinfeng liu (Sun Dec 05 2021 - 19:02:07 PST)
- David A Case (Sun Dec 05 2021 - 05:35:24 PST)
- jinfeng liu (Sat Dec 04 2021 - 22:52:06 PST)
[AMBER] scientific issue
- Alexander Izvorski (Sun Dec 26 2021 - 13:29:53 PST)
[AMBER] second structure
- Carlos Simmerling (Fri Dec 17 2021 - 10:13:01 PST)
- Sepideh Jafari (Fri Dec 17 2021 - 19:12:35 PST)
[AMBER] size (info) difference in traj file format: nc vs mdcrd
- Thomas Cheatham (Wed Dec 01 2021 - 10:56:32 PST)
- King Wu (Wed Dec 01 2021 - 10:25:47 PST)
[AMBER] Some errors for the membrane system
- Monsurat M. Lawal (Wed Dec 01 2021 - 11:43:13 PST)
[AMBER] sqm performance: does it run in parallel?
- David A Case (Fri Dec 31 2021 - 05:07:53 PST)
- Alan (Thu Dec 30 2021 - 22:47:20 PST)
[AMBER] Summit compile and "Attempted to read inpcrd as a NetCDF restart file, but failed"
- Daniel Roe (Wed Dec 01 2021 - 05:50:38 PST)
[AMBER] Thermodynamic integration in tutorial 9
- 鱼翔 (Tue Dec 21 2021 - 17:46:39 PST)
- 鱼翔 (Mon Dec 13 2021 - 16:29:03 PST)
[AMBER] TiMergeError: Cannot have dihedral cross through softcore region.
- Saikat Pal (Thu Dec 02 2021 - 07:53:57 PST)
- Carlos Simmerling (Thu Dec 02 2021 - 07:24:54 PST)
- Saikat Pal (Thu Dec 02 2021 - 07:07:12 PST)
- Saikat Pal (Wed Dec 01 2021 - 11:09:11 PST)
[AMBER] TIP4PD water box error
- Alexander Izvorski (Sun Dec 26 2021 - 14:47:53 PST)
[AMBER] tleap: tab complete, highlight, cmd history etc.
- Alan (Wed Dec 15 2021 - 00:06:06 PST)
[AMBER] water box corrupted by minimization
- Daniel Roe (Wed Dec 01 2021 - 08:14:28 PST)
[AMBER] What if MM Energy > QM Energy Even Vn=0
- David Cerutti (Mon Dec 13 2021 - 08:06:46 PST)
- David A Case (Sat Dec 04 2021 - 08:40:35 PST)
- Erdem Yeler (Sat Dec 04 2021 - 06:56:43 PST)
[AMBER] what is origin in DX from 3DRISM
- tluchko (Thu Dec 30 2021 - 10:44:41 PST)
- angad sharma (Tue Dec 28 2021 - 05:32:21 PST)
[AMBER] Zn ion coordination
- Pengfei Li (Fri Dec 17 2021 - 17:04:48 PST)
- Aravind R (Tue Dec 07 2021 - 05:38:31 PST)
- Aravind R (Thu Dec 02 2021 - 05:04:38 PST)
[AMBER] 【Error on testing benz_water_md.reaxff and openMPI】
- David A Case (Wed Dec 29 2021 - 18:43:09 PST)
- David A Case (Wed Dec 29 2021 - 06:58:44 PST)
- Shang-Wei Li (TMU) (Tue Dec 28 2021 - 17:31:01 PST)

Amber Archive Dec 2021 by subject