Amber Archive Dec 2021 by thread
- [AMBER] A bug in phishi Amber20? 余青芬 (Wed Dec 01 2021 - 02:04:07 PST)
- [AMBER] bond equilibrium achieved with sander but not with pmemd, Amber 20 Qinghua Liao (Wed Dec 01 2021 - 03:03:31 PST)
- Re: [AMBER] Problems with RMSD of different proteins. Daniel Roe (Wed Dec 01 2021 - 05:26:17 PST)
- Re: [AMBER] How to interpret clustering Daniel Roe (Wed Dec 01 2021 - 05:39:23 PST)
- Re: [AMBER] closest ions radiation distribution Daniel Roe (Wed Dec 01 2021 - 05:43:11 PST)
- Re: [AMBER] Equilibrate and Production Run Membrane-protein complex Daniel Roe (Wed Dec 01 2021 - 05:46:36 PST)
- Re: [AMBER] Protein in mixed of solvents Daniel Roe (Wed Dec 01 2021 - 05:47:19 PST)
- Re: [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)
- Re: [AMBER] Dynamic cross correlation matrices in AMBER20 Daniel Roe (Wed Dec 01 2021 - 05:52:19 PST)
- Re: [AMBER] GIST: Entropy calculations Daniel Roe (Wed Dec 01 2021 - 08:07:39 PST)
- Re: [AMBER] How to generate mol2 file with topology and crd file? Daniel Roe (Wed Dec 01 2021 - 08:10:34 PST)
- Re: [AMBER] water box corrupted by minimization Daniel Roe (Wed Dec 01 2021 - 08:14:28 PST)
- Re: [AMBER] Amber calculate RMSF Daniel Roe (Wed Dec 01 2021 - 08:19:54 PST)
- Re: [AMBER] Reg: Cpptraj-Hierarchical Agglomerative Reference paper for methodology and result analysis Daniel Roe (Wed Dec 01 2021 - 08:21:03 PST)
- Re: [AMBER] How is correlation computed in cpptraj Daniel Roe (Wed Dec 01 2021 - 08:24:44 PST)
- Re: [AMBER] RMSD of residues within 3A of ligand Daniel Roe (Wed Dec 01 2021 - 08:30:24 PST)
- [AMBER] size (info) difference in traj file format: nc vs mdcrd King Wu (Wed Dec 01 2021 - 10:25:47 PST)
- Re: [AMBER] open mpi compiler error Ayesha Fatima (Wed Dec 01 2021 - 11:00:44 PST)
- [AMBER] TiMergeError: Cannot have dihedral cross through softcore region. Saikat Pal (Wed Dec 01 2021 - 11:09:11 PST)
- Re: [AMBER] Some errors for the membrane system Monsurat M. Lawal (Wed Dec 01 2021 - 11:43:13 PST)
- [AMBER] Missing DNA base pair in cpptraj analysis Abhilash J (Wed Dec 01 2021 - 13:23:22 PST)
- Re: [AMBER] installation error amber 18 in ubuntu 20.04 David A Case (Wed Dec 01 2021 - 14:16:25 PST)
- [AMBER] Non-periodic boundry condition simulation Nagar, Hemant (Wed Dec 01 2021 - 15:27:43 PST)
- [AMBER] Installation error amber 20 in ubuntu 20.04 Joanna Michelle E. Chua (Wed Dec 01 2021 - 19:43:29 PST)
- [AMBER] Fortran runtime error during 1D-RISM analysis to generate .xvv file Alexis Azucena (Thu Dec 02 2021 - 02:02:15 PST)
- [AMBER] Zn ion coordination Aravind R (Thu Dec 02 2021 - 05:04:38 PST)
- [AMBER] TiMergeError: Cannot have dihedral cross through softcore region. Saikat Pal (Thu Dec 02 2021 - 07:07:12 PST)
- [AMBER] Amber Installation Error Suguna Sakkiah (Thu Dec 02 2021 - 11:26:26 PST)
- [AMBER] numpy error with pdb4amber on cluster Vaibhav Dixit (Thu Dec 02 2021 - 19:51:01 PST)
- [AMBER] problem loading the trajectory files in vmd ankita mehta (Fri Dec 03 2021 - 02:51:09 PST)
- [AMBER] Problem loading crd file in vmd ankita mehta (Fri Dec 03 2021 - 03:58:26 PST)
- [AMBER] Error during 1D-RISM run Alexis Azucena (Sat Dec 04 2021 - 02:08:42 PST)
- [AMBER] Mmpbsa inp=1 or inp=2 Fabian Glaser (Sat Dec 04 2021 - 02:39:40 PST)
- [AMBER] What if MM Energy > QM Energy Even Vn=0 Erdem Yeler (Sat Dec 04 2021 - 06:56:43 PST)
- [AMBER] run_cmake error for installing the GPU version of Amber20 jinfeng liu (Sat Dec 04 2021 - 22:52:06 PST)
- [AMBER] Meaning of "Multiple 'e' in NUMBER-like thing" Matthew Guberman-Pfeffer (Sun Dec 05 2021 - 14:57:44 PST)
- [AMBER] about RAMD 田佳琪 (Sun Dec 05 2021 - 23:00:11 PST)
- [AMBER] Error with MMPBSA Kehinde Idowu (Mon Dec 06 2021 - 18:06:28 PST)
- [AMBER] Error for installing the GPU version of Amber20 jinfeng liu (Tue Dec 07 2021 - 19:54:24 PST)
- [AMBER] GAFF2 "ho" atoms have non-bonded 0 Stefan Doerr (Wed Dec 08 2021 - 02:47:54 PST)
- [AMBER] install error for GPU version of Amber20 on A100 GPU card jinfeng liu (Fri Dec 10 2021 - 04:30:46 PST)
- [AMBER] Electrostatic energy in TI at lambda=1 for a toy system Ali Morshedi (Sat Dec 11 2021 - 00:04:27 PST)
- [AMBER] Error with Zn ion Coordination Aravind R (Sat Dec 11 2021 - 02:21:02 PST)
- [AMBER] README script from CHARMM-GUI to run PMEDE.CUDA King Wu (Sat Dec 11 2021 - 06:31:33 PST)
- [AMBER] permission error installing amber20 Vaibhav Dixit (Sun Dec 12 2021 - 20:33:35 PST)
- Re: [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] Neutralizing a protein with unknown charge? Gustavo Seabra (Mon Dec 13 2021 - 12:55:47 PST)
- [AMBER] Q-Chem and GPU use James Kress (Mon Dec 13 2021 - 12:57:48 PST)
- [AMBER] Peptide's charge is not 0 when getting parm7 and rst7 files Yen Nguyen (Mon Dec 13 2021 - 14:13:17 PST)
- [AMBER] Thermodynamic integration in tutorial 9 鱼翔 (Mon Dec 13 2021 - 16:29:03 PST)
- [AMBER] CHAMBER prmtops cannot be used with NMODE 周丽萍 (Mon Dec 13 2021 - 23:01:24 PST)
- [AMBER] Old Amber Force Fields Niransha Kumarachchi (Tue Dec 14 2021 - 08:35:27 PST)
- [AMBER] Question about build Amber20 with Intel compiler 2019 Chen, Guoquan (Tue Dec 14 2021 - 12:26:05 PST)
- [AMBER] Parallel test stuck at Run.dhfr.noboxinfo Yu Chen (Tue Dec 14 2021 - 12:48:23 PST)
- [AMBER] loadpdb and SSBOND Alan (Wed Dec 15 2021 - 00:03:04 PST)
- [AMBER] tleap: tab complete, highlight, cmd history etc. Alan (Wed Dec 15 2021 - 00:06:06 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] amber pmemd.cuda for implicit solvent simulations Prithviraj Nandigrami (Wed Dec 15 2021 - 11:45:11 PST)
- [AMBER] Non periodic system in Amber Nagar, Hemant (Wed Dec 15 2021 - 16:04:04 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] How to restart a MMPBSA job Sadaf Rani (Thu Dec 16 2021 - 13:13:40 PST)
- [AMBER] Help parameterizing iron citrate Matthew Guberman-Pfeffer (Thu Dec 16 2021 - 23:29:00 PST)
- [AMBER] second structure Sepideh Jafari (Fri Dec 17 2021 - 19:12:35 PST)
- [AMBER] Amber20 installation error on Centos 7 Suguna Sakkiah (Fri Dec 17 2021 - 10:04:58 PST)
- Re: [AMBER] Amber -log4J impact ? David A Case (Fri Dec 17 2021 - 17:52:11 PST)
- [AMBER] Adding atom types to gaff.dat Sam Walsworth (Researcher) (Fri Dec 17 2021 - 21:50:00 PST)
- [AMBER] Atom types and atom order of lib files and pdb files Sam Walsworth (Researcher) (Sun Dec 19 2021 - 15:28:39 PST)
- [AMBER] Hydrogen Bonding Analysis Huimin Tian (Mon Dec 20 2021 - 01:27:40 PST)
- [AMBER] Constant PH simulations Sruthi Sudhakar (Mon Dec 20 2021 - 09:38:00 PST)
- [AMBER] CPPTRAJ Segmentation Fault with modified topology file Chris Lee (Mon Dec 20 2021 - 10:58:25 PST)
- [AMBER] Amber20 installation error - Centos 7 Suguna Sakkiah (Mon Dec 20 2021 - 12:56:46 PST)
- [AMBER] Error running TI with pmemd.cuda: "Error: an illegal memory access was encountered launching kernel kClearTIKinEnergy_kernel" Ali Morshedi (Mon Dec 20 2021 - 13:50:56 PST)
- Re: [AMBER] amber20 - test suite picks up the wrong libgfortran Mark Dixon (Tue Dec 21 2021 - 07:55:30 PST)
- [AMBER] Amber installation error on Centos 7 Suguna Sakkiah (Tue Dec 21 2021 - 11:00:58 PST)
- [AMBER] Amber20 installation error on Centos 7 Suguna Sakkiah (Tue Dec 21 2021 - 11:33:11 PST)
- [AMBER] Problems with mdgx - torsional parameters fitting Casalini Tommaso (Tue Dec 21 2021 - 11:35:33 PST)
- [AMBER] Creating library files - optimised or docked structure? Sam Walsworth (Researcher) (Tue Dec 21 2021 - 16:45:09 PST)
- [AMBER] Thermodynamic integration in tutorial 9 鱼翔 (Tue Dec 21 2021 - 17:46:39 PST)
- [AMBER] Issue with defining angle parameters in frcmod files Sam Walsworth (Researcher) (Wed Dec 22 2021 - 11:21:46 PST)
- [AMBER] Query regarding minimization in AMBER 20 Arooma Maryam (Wed Dec 22 2021 - 13:08:57 PST)
- [AMBER] prmtop file generated with CLOSEST in cpptraj James Kress (Wed Dec 22 2021 - 16:04:41 PST)
- [AMBER] Problems about quasi-harmonic 周丽萍 (Wed Dec 22 2021 - 18:02:40 PST)
- [AMBER] Parameters for Boron nitride Rituparna Roy (Wed Dec 22 2021 - 21:44:56 PST)
- [AMBER] Handling new atom types - bonded Sam Walsworth (Researcher) (Thu Dec 23 2021 - 07:49:58 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] Frequency unit used for Oscillating electric field Surajit Kalita (Thu Dec 23 2021 - 09:43:04 PST)
- [AMBER] Adjust system in certain axis mohamed marzouk (Thu Dec 23 2021 - 16:31:01 PST)
- [AMBER] Amber20 CUDA installation error Centos 7 Suguna Sakkiah (Fri Dec 24 2021 - 15:52:51 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] Non-standard residue parameterization quesitons Matthew Guberman-Pfeffer (Sat Dec 25 2021 - 16:24:21 PST)
- [AMBER] MCPB, how to treat protein-attached Ru-dye Matthew Guberman-Pfeffer (Sat Dec 25 2021 - 21:05:28 PST)
- [AMBER] Extending constant pH to additional titratable groups 王金玉 (Sun Dec 26 2021 - 06:44:58 PST)
- [AMBER] CUDA installation error - CENTOS 7 Suguna Sakkiah (Sun Dec 26 2021 - 12:30:16 PST)
- Re: [AMBER] scientific issue Alexander Izvorski (Sun Dec 26 2021 - 13:29:53 PST)
- [AMBER] DE Shaw RNA parameters error Alexander Izvorski (Sun Dec 26 2021 - 14:30:53 PST)
- [AMBER] TIP4PD water box error Alexander Izvorski (Sun Dec 26 2021 - 14:47:53 PST)
- [AMBER] Ligand problem in system preparation Ch Bilal (Tue Dec 28 2021 - 01:17:56 PST)
- [AMBER] Problem in installation Guodong (Tue Dec 28 2021 - 04:28:23 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] what is origin in DX from 3DRISM angad sharma (Tue Dec 28 2021 - 05:32:21 PST)
- [AMBER] Li salt parameterisation issue Damiano Spadoni (Tue Dec 28 2021 - 07:26:29 PST)
- [AMBER] 【Error on testing benz_water_md.reaxff and openMPI】 Shang-Wei Li (TMU) (Tue Dec 28 2021 - 17:31:01 PST)
- [AMBER] Non-standard residue parameterization questions Matthew Guberman-Pfeffer (Tue Dec 28 2021 - 20:54:10 PST)
- [AMBER] amber docker container Fabian Glaser (Wed Dec 29 2021 - 02:07:56 PST)
- [AMBER] Advice on Simulated Annealing Matthew Guberman-Pfeffer (Wed Dec 29 2021 - 10:39:23 PST)
- [AMBER] A10 cards Fabian Glaser (Thu Dec 30 2021 - 06:36:11 PST)
- [AMBER] MCPB, how to treat protein-attached Ru-dye Matthew Guberman-Pfeffer (Thu Dec 30 2021 - 09:48:49 PST)
- [AMBER] Dihedral restraint on a C=N double bond Liao (Thu Dec 30 2021 - 12:11:54 PST)
- [AMBER] sqm performance: does it run in parallel? Alan (Thu Dec 30 2021 - 22:47:20 PST)
- Last message date: Fri Dec 31 2021 - 05:30:02 PST
- Archived on: Fri Dec 20 2024 - 05:56:10 PST
