Amber Archive Aug 2024: by subject

[AMBER] [Sender Not Verified] Cutoff value significantly impacts the electrostatic energy in PME
- Ge Song via AMBER (Fri Aug 23 2024 - 08:34:21 PDT)
- Timothy Giese via AMBER (Fri Aug 23 2024 - 08:14:22 PDT)
- David A Case via AMBER (Thu Aug 22 2024 - 09:32:20 PDT)
- Ge Song via AMBER (Wed Aug 21 2024 - 07:31:00 PDT)
- Ge Song via AMBER (Tue Aug 20 2024 - 11:03:58 PDT)
- Steinbrecher, Thomas via AMBER (Tue Aug 20 2024 - 08:05:39 PDT)
[AMBER] About making Amber code a more standard
- Vlad via AMBER (Thu Aug 29 2024 - 16:37:41 PDT)
[AMBER] Amber 24 encounters freezed jobs
- Carlos Simmerling via AMBER (Sun Aug 11 2024 - 14:39:40 PDT)
- Morad Mustafa via AMBER (Sun Aug 11 2024 - 08:19:24 PDT)
[AMBER] Amber to Lammps; velocities conversion
- David A Case via AMBER (Tue Aug 27 2024 - 20:37:04 PDT)
- Meyer, Olivia \(meyerok\) via AMBER (Tue Aug 27 2024 - 07:59:31 PDT)
[AMBER] Amber/AmberTools24 installation Apple M2
- Elvis Martis via AMBER (Tue Aug 06 2024 - 08:38:22 PDT)
- Elvis Martis via AMBER (Tue Aug 06 2024 - 07:43:51 PDT)
- Elvis Martis via AMBER (Tue Aug 06 2024 - 07:23:31 PDT)
- Elvis Martis via AMBER (Tue Aug 06 2024 - 05:38:17 PDT)
- Elvis Martis via AMBER (Tue Aug 06 2024 - 02:49:36 PDT)
- Xavier Brazzolotto via AMBER (Tue Aug 06 2024 - 01:24:43 PDT)
[AMBER] amber19 installation error
- David A Case via AMBER (Tue Aug 20 2024 - 09:23:52 PDT)
- Dulal Mondal via AMBER (Mon Aug 19 2024 - 13:28:50 PDT)
[AMBER] Amber22 cudaGetDeviceCount failed unknown error
- Gustavo Seabra via AMBER (Fri Aug 16 2024 - 12:17:27 PDT)
- Gustavo Seabra via AMBER (Fri Aug 16 2024 - 08:39:03 PDT)
[AMBER] Amber22_Error: an illegal memory access was encountered launching kernel kNLSkinTest
- Carlos Simmerling via AMBER (Wed Aug 28 2024 - 03:17:47 PDT)
- ABDELATIF MESSAOUDI via AMBER (Wed Aug 28 2024 - 00:52:09 PDT)
[AMBER] Amber24 Cuda installation
- Pertschy, Florian via AMBER (Thu Aug 08 2024 - 08:07:41 PDT)
[AMBER] AmberMDPrep.sh finishes after final.1.in step
- Daniel Roe via AMBER (Mon Aug 19 2024 - 14:45:13 PDT)
- Daniel Roe via AMBER (Mon Aug 19 2024 - 12:36:13 PDT)
- Daniel Roe via AMBER (Mon Aug 19 2024 - 06:01:23 PDT)
- Daniel Roe via AMBER (Mon Aug 19 2024 - 05:41:08 PDT)
- Daniel Roe via AMBER (Sun Aug 18 2024 - 15:38:14 PDT)
- Daniel Roe via AMBER (Sat Aug 17 2024 - 15:28:22 PDT)
- Maciej Spiegel via AMBER (Sat Aug 17 2024 - 13:57:06 PDT)
[AMBER] Assigning GPUs with pHREMD
- Guberman-Pfeffer, Matthew via AMBER (Fri Aug 23 2024 - 05:14:43 PDT)
[AMBER] Assistance Needed with PCA at Different Temperatures in AMBER
- Carlos Simmerling via AMBER (Mon Aug 12 2024 - 15:07:34 PDT)
- Carlos Simmerling via AMBER (Mon Aug 12 2024 - 14:29:28 PDT)
- ABDELATIF MESSAOUDI via AMBER (Mon Aug 12 2024 - 11:37:22 PDT)
[AMBER] Atom type of DU does not exist in PARMCHK.DAT
- Abdelrahman, Noureen via AMBER (Thu Aug 01 2024 - 12:58:01 PDT)
[AMBER] CHARMM-GUI-provided scripts
- Masoud Keramati via AMBER (Mon Aug 05 2024 - 12:18:41 PDT)
- HAFIDAH ZAKI AL QUDAH via AMBER (Mon Aug 05 2024 - 12:09:57 PDT)
[AMBER] Cmake unable to find Mpich
- Nil Mu via AMBER (Tue Aug 06 2024 - 13:20:30 PDT)
- Pertschy, Florian via AMBER (Tue Aug 06 2024 - 08:46:47 PDT)
[AMBER] combining the results of nab nmode and mmpbsa
- David A Case via AMBER (Tue Aug 27 2024 - 20:27:27 PDT)
- Siavoush Dastmalchi via AMBER (Sun Aug 25 2024 - 03:38:03 PDT)
[AMBER] Compiling CUDA - gpu compatability
- Daniel Roe via AMBER (Mon Aug 19 2024 - 10:21:44 PDT)
- Daniel Roe via AMBER (Sat Aug 17 2024 - 13:45:18 PDT)
- Alexander Hung Lee via AMBER (Thu Aug 15 2024 - 11:49:42 PDT)
[AMBER] Computing free energy of binding from advanced TI calculation:
- Timothy Giese via AMBER (Thu Aug 29 2024 - 06:59:13 PDT)
- Kankana Bhattacharjee via AMBER (Wed Aug 28 2024 - 22:27:45 PDT)
[AMBER] Continuous constant pH MD with pH replica exchange
- Nancy Zhu via AMBER (Mon Aug 26 2024 - 15:13:27 PDT)
[AMBER] Convergence checking in Advanced TI calculation:
- Kankana Bhattacharjee via AMBER (Thu Aug 22 2024 - 02:16:22 PDT)
- Kankana Bhattacharjee via AMBER (Wed Aug 21 2024 - 20:57:51 PDT)
[AMBER] cphstats processing of pH-REMD 'chunks'
- Nitin Kulhar via AMBER (Mon Aug 26 2024 - 20:20:42 PDT)
- He, Amy via AMBER (Mon Aug 12 2024 - 20:47:04 PDT)
- Nitin Kulhar via AMBER (Sun Aug 11 2024 - 22:41:06 PDT)
- He, Amy via AMBER (Tue Aug 06 2024 - 12:54:42 PDT)
- Nitin Kulhar via AMBER (Tue Aug 06 2024 - 09:36:50 PDT)
- He, Amy via AMBER (Sun Aug 04 2024 - 16:05:31 PDT)
[AMBER] Custom AA residue missing parameters
- Daniel Roe via AMBER (Mon Aug 19 2024 - 12:47:06 PDT)
- Javier O Sanlley-hernandez via AMBER (Mon Aug 19 2024 - 12:39:45 PDT)
[AMBER] Cutoff value significantly impacts the electrostatic energy in PME
- Ge Song via AMBER (Tue Aug 20 2024 - 06:44:12 PDT)
[AMBER] different pH conditions for membrane protein simulations
- Prithviraj Nandigrami via AMBER (Mon Aug 12 2024 - 10:12:18 PDT)
- Prithviraj Nandigrami via AMBER (Tue Aug 06 2024 - 12:34:58 PDT)
[AMBER] Effective Born Radius
- David A Case via AMBER (Sat Aug 03 2024 - 06:44:42 PDT)
- Jaime Rubio Martinez via AMBER (Sat Aug 03 2024 - 04:30:38 PDT)
[AMBER] Error in ligand paramterisation in tleap
- David A Case via AMBER (Tue Aug 20 2024 - 09:28:35 PDT)
- Simran Modi via AMBER (Tue Aug 20 2024 - 01:33:56 PDT)
- Dr. Anselm Horn via AMBER (Fri Aug 09 2024 - 04:43:18 PDT)
- Simran Modi via AMBER (Fri Aug 09 2024 - 03:23:13 PDT)
[AMBER] Error message : "unsigned long long of length = 42Failed an illegal memory access was encountered"
- Ryan Snyder via AMBER (Fri Aug 30 2024 - 08:01:37 PDT)
- Anna Herz via AMBER (Fri Aug 30 2024 - 07:43:10 PDT)
[AMBER] Error to run constant pH replica exchange in explicit solvent in amber18
- Dulal Mondal via AMBER (Mon Aug 26 2024 - 23:13:38 PDT)
- Vinicius Cruzeiro via AMBER (Mon Aug 26 2024 - 23:04:13 PDT)
- Dulal Mondal via AMBER (Mon Aug 26 2024 - 20:39:23 PDT)
- Dulal Mondal via AMBER (Mon Aug 26 2024 - 20:09:47 PDT)
- Vinicius Cruzeiro via AMBER (Mon Aug 26 2024 - 17:20:29 PDT)
- Dulal Mondal via AMBER (Mon Aug 26 2024 - 14:37:02 PDT)
- Dulal Mondal via AMBER (Mon Aug 26 2024 - 10:16:34 PDT)
[AMBER] Evaluate change in affinity due to mutation
- Abhilash J via AMBER (Tue Aug 06 2024 - 12:11:50 PDT)
[AMBER] Executing absolute binding free energy calculations in Amber
- Amara Jabeen via AMBER (Tue Aug 13 2024 - 00:59:56 PDT)
[AMBER] Extracting every 10th frame from *.nc file
- Carlos Simmerling via AMBER (Fri Aug 23 2024 - 08:46:38 PDT)
- Timothy Giese via AMBER (Fri Aug 23 2024 - 08:24:05 PDT)
- Maciej Spiegel via AMBER (Fri Aug 23 2024 - 08:15:27 PDT)
[AMBER] FETookit analysis issue:
- Shi Zhang via AMBER (Fri Aug 16 2024 - 08:51:21 PDT)
- Kankana Bhattacharjee via AMBER (Fri Aug 16 2024 - 08:17:11 PDT)
- Shi Zhang via AMBER (Fri Aug 16 2024 - 07:25:50 PDT)
- Timothy Giese via AMBER (Fri Aug 16 2024 - 07:03:24 PDT)
- Kankana Bhattacharjee via AMBER (Fri Aug 16 2024 - 00:10:21 PDT)
[AMBER] ff99 and ff14SB - Slight Atom Type Differences
- Carlos Simmerling via AMBER (Thu Aug 01 2024 - 08:42:16 PDT)
[AMBER] finddgref.py error with manually added titratable ligand
- Vinicius Cruzeiro via AMBER (Mon Aug 12 2024 - 10:21:36 PDT)
- Nitin Kulhar via AMBER (Mon Aug 12 2024 - 08:59:24 PDT)
- Vinicius Cruzeiro via AMBER (Mon Aug 12 2024 - 08:40:40 PDT)
- Nitin Kulhar via AMBER (Sun Aug 11 2024 - 21:30:33 PDT)
[AMBER] Free energy calculation of complex with covalent bond
- David A Case via AMBER (Tue Aug 20 2024 - 09:35:20 PDT)
- SUBHASMITA MAHAPATRA MAHAPATRA via AMBER (Tue Aug 20 2024 - 03:11:02 PDT)
[AMBER] Fwd: modifying colvars
- Gard Nelson via AMBER (Fri Aug 16 2024 - 15:30:18 PDT)
[AMBER] Fwd: Regarding Advanced Thermodynamic Integration:
- Carlos Simmerling via AMBER (Thu Aug 08 2024 - 12:19:48 PDT)
- Kankana Bhattacharjee via AMBER (Thu Aug 08 2024 - 11:53:48 PDT)
[AMBER] Fwd: TI calculation using pmemd
- Darrin York via AMBER (Fri Aug 30 2024 - 07:11:45 PDT)
- David A Case via AMBER (Thu Aug 29 2024 - 12:27:59 PDT)
- Timothy Giese via AMBER (Thu Aug 29 2024 - 06:55:17 PDT)
- Tamalika Ash via AMBER (Wed Aug 28 2024 - 08:55:12 PDT)
[AMBER] How to build own system
- Sepideh Jafari via AMBER (Thu Aug 08 2024 - 09:51:14 PDT)
[AMBER] illegal memory access
- Alois Zdrha via AMBER (Tue Aug 13 2024 - 05:01:55 PDT)
[AMBER] issue using pemed.cuda of AMBER 24
- Abhilash J via AMBER (Fri Aug 23 2024 - 10:38:05 PDT)
[AMBER] Issues with the Glycoprotein builder on the glycamm website
- Carlos Simmerling via AMBER (Mon Aug 05 2024 - 15:24:49 PDT)
- Natesan Mani via AMBER (Mon Aug 05 2024 - 14:37:02 PDT)
[AMBER] Lone pair treatment AMBER24
- Juraj Dobias via AMBER (Tue Aug 27 2024 - 02:46:39 PDT)
- Sorin Draga via AMBER (Tue Aug 27 2024 - 02:21:03 PDT)
[AMBER] MCPB.py keyerror
- Li, Zhen via AMBER (Mon Aug 05 2024 - 08:51:41 PDT)
[AMBER] MD simulations for 100 ns and PCA
- Thomas Cheatham via AMBER (Thu Aug 01 2024 - 23:20:02 PDT)
[AMBER] Missing angle parameter between unconnected atoms
- Peng Zhang via AMBER (Sun Aug 18 2024 - 14:25:32 PDT)
[AMBER] MMGBSA Calculation Python --version
- Carlos Simmerling via AMBER (Mon Aug 26 2024 - 04:00:08 PDT)
- 王世玉 via AMBER (Mon Aug 26 2024 - 02:28:59 PDT)
- ABDELATIF MESSAOUDI via AMBER (Mon Aug 26 2024 - 02:03:49 PDT)
[AMBER] Modeling and simulating a cyclic depsipeptide
- David A Case via AMBER (Tue Aug 27 2024 - 20:30:09 PDT)
- Carlos Simmerling via AMBER (Sun Aug 25 2024 - 11:11:29 PDT)
- Baker, Joseph via AMBER (Sun Aug 25 2024 - 08:02:04 PDT)
[AMBER] Modification of MMPBSA electrostatic energy
- Bill Miller III via AMBER (Thu Aug 29 2024 - 16:47:10 PDT)
- Anupaul Baruah via AMBER (Thu Aug 29 2024 - 03:10:46 PDT)
[AMBER] MPI installation failing.
- David A Case via AMBER (Tue Aug 06 2024 - 13:34:27 PDT)
- Timothy Giese via AMBER (Tue Aug 06 2024 - 12:44:30 PDT)
- Pertschy, Florian via AMBER (Tue Aug 06 2024 - 09:18:42 PDT)
[AMBER] Multiple Replicas per GPU?
- Guberman-Pfeffer, Matthew via AMBER (Sun Aug 18 2024 - 12:02:04 PDT)
- Guberman-Pfeffer, Matthew via AMBER (Sun Aug 18 2024 - 00:18:53 PDT)
[AMBER] No QM parameter for a Sulfur atom
- David A Case via AMBER (Tue Aug 06 2024 - 13:24:28 PDT)
- Martin Juhás via AMBER (Mon Aug 05 2024 - 01:07:57 PDT)
- Sunanda Samanta via AMBER (Sun Aug 04 2024 - 23:03:28 PDT)
[AMBER] packmol-memgen: issue with the parametrization of gpcr-ligand system
- Enrico Martinez via AMBER (Fri Aug 23 2024 - 04:49:18 PDT)
- Enrico Martinez via AMBER (Fri Aug 23 2024 - 01:56:34 PDT)
[AMBER] parameterize a non-standard residue
- Peng Zhang via AMBER (Wed Aug 07 2024 - 09:12:40 PDT)
[AMBER] parm10 and PARMCHK.DAT Atom Types
- Warren, Kyle Benjamin via AMBER (Sat Aug 10 2024 - 06:30:52 PDT)
- Pye, Aaron Wesley via AMBER (Sat Aug 10 2024 - 05:40:04 PDT)
[AMBER] PCA on Unmodified and Modified Nucleobases within RNA: Different Ribose Atom Ordering
- Warren, Kyle Benjamin via AMBER (Tue Aug 27 2024 - 10:12:03 PDT)
[AMBER] Per residue energy decomposition
- Carlos Simmerling via AMBER (Wed Aug 21 2024 - 03:38:36 PDT)
- RAMPRAKASH YADAV via AMBER (Tue Aug 20 2024 - 22:30:31 PDT)
[AMBER] production run mdin file
- Dulal Mondal via AMBER (Thu Aug 01 2024 - 05:10:51 PDT)
[AMBER] Protein RNA complex simulation best standards in the field.
- Jiri Sponer via AMBER (Wed Aug 28 2024 - 05:45:18 PDT)
- Reza Khayat via AMBER (Wed Aug 28 2024 - 05:00:29 PDT)
- Guberman-Pfeffer, Matthew via AMBER (Tue Aug 27 2024 - 19:19:49 PDT)
- Debarati DasGupta via AMBER (Tue Aug 27 2024 - 16:16:40 PDT)
[AMBER] QM/MM Energy Decomposition
- Timothy Giese via AMBER (Wed Aug 14 2024 - 07:09:07 PDT)
- Ge Song via AMBER (Tue Aug 13 2024 - 12:28:16 PDT)
[AMBER] QM/MM produces no error but doesn't run successfully
- Timothy Giese via AMBER (Mon Aug 12 2024 - 08:57:47 PDT)
[AMBER] Query about continuous constant pH in amber24 (chapter 28)
- Carlos Simmerling via AMBER (Fri Aug 09 2024 - 03:36:00 PDT)
- Dulal Mondal via AMBER (Thu Aug 08 2024 - 21:20:52 PDT)
- Dulal Mondal via AMBER (Wed Aug 07 2024 - 20:44:43 PDT)
[AMBER] query about scaling of nonbonded interactions.
- Prof. Mark Wilson via AMBER (Fri Aug 16 2024 - 06:32:11 PDT)
- Carlos Simmerling via AMBER (Fri Aug 16 2024 - 04:45:32 PDT)
- Prof. Mark Wilson via AMBER (Fri Aug 16 2024 - 02:10:10 PDT)
[AMBER] Regarding Advanced Thermodynamic Integration:
- He, Amy via AMBER (Thu Aug 08 2024 - 15:36:04 PDT)
[AMBER] Regarding an issue with Thermodynamic Integration calculation
- Timothy Giese via AMBER (Wed Aug 21 2024 - 12:55:26 PDT)
- Weerawarna Kurukulasooriy, Sandaruwani Tharaka \[CHEM\] via AMBER (Wed Aug 21 2024 - 10:53:03 PDT)
[AMBER] Regarding placement of periodic box
- David A Case via AMBER (Sat Aug 24 2024 - 18:44:04 PDT)
- Natesan Mani via AMBER (Sat Aug 24 2024 - 10:59:28 PDT)
[AMBER] Regarding REUS simulations
- miyagi bunkutu via AMBER (Thu Aug 29 2024 - 12:06:37 PDT)
[AMBER] remlog in cpptraj for pH-REMD
- Daniel Roe via AMBER (Sun Aug 18 2024 - 16:04:31 PDT)
- Daniel Roe via AMBER (Sun Aug 18 2024 - 15:39:51 PDT)
- Guberman-Pfeffer, Matthew via AMBER (Sun Aug 18 2024 - 10:55:56 PDT)
[AMBER] Requesting help with Amber TI calculation
- Carlos Simmerling via AMBER (Thu Aug 08 2024 - 09:25:22 PDT)
- Weerawarna Kurukulasooriy, Sandaruwani Tharaka \[CHEM\] via AMBER (Thu Aug 08 2024 - 08:48:07 PDT)
[AMBER] run errorn in sander.MPI for constant pH replica exchange in amber18
- Dulal Mondal via AMBER (Sun Aug 25 2024 - 23:03:21 PDT)
[AMBER] SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f> in QUICK
- Kriti Shukla via AMBER (Tue Aug 06 2024 - 07:05:39 PDT)
- Timothy Giese via AMBER (Tue Aug 06 2024 - 06:57:57 PDT)
- Goetz, Andreas via AMBER (Mon Aug 05 2024 - 23:48:41 PDT)
[AMBER] Surface area of one protein to another
- King Wang via AMBER (Thu Aug 08 2024 - 13:17:57 PDT)
[AMBER] Tleap error
- Prabir Khatua via AMBER (Thu Aug 08 2024 - 23:15:46 PDT)
- FyD via AMBER (Thu Aug 08 2024 - 07:19:37 PDT)
- Carlos Simmerling via AMBER (Wed Aug 07 2024 - 06:43:20 PDT)
- Prabir Khatua via AMBER (Wed Aug 07 2024 - 00:23:03 PDT)
[AMBER] Torsion Term Error
- Carlos Simmerling via AMBER (Tue Aug 06 2024 - 12:47:37 PDT)
- Cinar, Sena via AMBER (Tue Aug 06 2024 - 11:55:31 PDT)
[AMBER] Trouble Calculating Nucleic Pseudo-Torsions Eta and Theta (η-θ) w/ CPPTRAJ
- Daniel Roe via AMBER (Mon Aug 19 2024 - 08:00:47 PDT)
- Daniel Roe via AMBER (Fri Aug 16 2024 - 12:51:27 PDT)
- Warren, Kyle Benjamin via AMBER (Fri Aug 16 2024 - 07:52:43 PDT)
[AMBER] Unclear cphstats warning
- Guberman-Pfeffer, Matthew via AMBER (Mon Aug 19 2024 - 14:56:02 PDT)
- He, Amy via AMBER (Mon Aug 19 2024 - 14:46:49 PDT)
- Guberman-Pfeffer, Matthew via AMBER (Sun Aug 18 2024 - 21:17:01 PDT)
- He, Amy via AMBER (Sun Aug 18 2024 - 20:28:41 PDT)
- Guberman-Pfeffer, Matthew via AMBER (Sun Aug 18 2024 - 12:02:31 PDT)
[AMBER] 回复: Custom AA residue missing parameters
- Huang ZiJian via AMBER (Fri Aug 30 2024 - 00:59:08 PDT)
- Huang ZiJian via AMBER (Mon Aug 19 2024 - 21:38:55 PDT)
combining the results of nab nmode and mmpbsa
- Siavoush Dastmalchi via AMBER (Tue Aug 27 2024 - 22:58:21 PDT)
Requesting help with Amber TI calculation
- Steinbrecher, Thomas via AMBER (Tue Aug 13 2024 - 23:16:53 PDT)

Amber Archive Aug 2024 by subject