Amber Archive Feb 2023 by thread
- [AMBER] Distance calculation using cpptraj Dulal Mondal via AMBER (Tue Jan 31 2023 - 10:44:30 PST)
- Re: [AMBER] CPPTRAJ, PCA, Effect of Mutation Elvis Martis via AMBER (Tue Jan 31 2023 - 18:30:54 PST)
- [AMBER] How restart md simulation with amber22 ABDELATIF MESSAOUDI via AMBER (Tue Jan 31 2023 - 23:42:01 PST)
- [AMBER] A query on using a non-standard solvent devendra.prajapat.cys19--- via AMBER (Wed Feb 01 2023 - 00:49:02 PST)
- [AMBER] Failures inamber test Freddy Bernal via AMBER (Wed Feb 01 2023 - 02:00:22 PST)
- [AMBER] Announcement: Release of DOCK 6.10 Scott Brozell via AMBER (Wed Feb 01 2023 - 10:47:02 PST)
- [AMBER] Problem with MMGBSA Suchetana Gupta via AMBER (Wed Feb 01 2023 - 14:50:00 PST)
- [AMBER] GLH with HE1 He, Amy via AMBER (Wed Feb 01 2023 - 15:23:58 PST)
- [AMBER] D-glucosamine GLYCAM parameters Michael Owen via AMBER (Wed Feb 01 2023 - 23:20:58 PST)
- [AMBER] CPPTRAJ, Salt Bridge Matthew Guberman-Pfeffer via AMBER (Thu Feb 02 2023 - 07:55:27 PST)
- [AMBER] Opening for a PLUMED developer position Giovanni Bussi via AMBER (Thu Feb 02 2023 - 12:52:53 PST)
- [AMBER] PCA porjection & representative structure Hocine EL KHAOUDI ENYOURY via AMBER (Fri Feb 03 2023 - 01:40:50 PST)
- [AMBER] RTX4070TI Benchmarks Ross Walker via AMBER (Fri Feb 03 2023 - 06:31:14 PST)
- [AMBER] Amber2020 and Amber2022 comparability issue: alchemical free energy calc Michael T Kim via AMBER (Fri Feb 03 2023 - 18:01:14 PST)
- Re: [AMBER] AMBER simulation heating step David A Case via AMBER (Sun Feb 05 2023 - 09:04:45 PST)
- [AMBER] GPU memory error during ABMD run Owen O'Reilly via AMBER (Sun Feb 05 2023 - 15:33:39 PST)
- [AMBER] Installation Error: miniconda issue Sumra Abbasi via AMBER (Sun Feb 05 2023 - 21:13:34 PST)
- [AMBER] RMSF calculation descrepancy of dimeric systems Prathit Chatterjee via AMBER (Sun Feb 05 2023 - 21:32:49 PST)
- [AMBER] Error in tests for pmemd.cuda.MPI Freddy Bernal via AMBER (Mon Feb 06 2023 - 01:36:26 PST)
- [AMBER] Fortran runtime error: Bad real number in item 1 of list input Nishad Ankita Rudal via AMBER (Mon Feb 06 2023 - 07:10:24 PST)
- [AMBER] Density distribution angad sharma via AMBER (Mon Feb 06 2023 - 09:58:12 PST)
- Re: [AMBER] Nucleic acid simulation error Prithviraj Nandigrami via AMBER (Mon Feb 06 2023 - 12:26:19 PST)
- [AMBER] FW: Bad atom type: i Zachariah Schuurs via AMBER (Tue Feb 07 2023 - 00:02:19 PST)
- [AMBER] load amber trj using vmd automatically laura zhang via AMBER (Tue Feb 07 2023 - 12:17:02 PST)
- [AMBER] Suspicious pKas from CpHMD Matthew Guberman-Pfeffer via AMBER (Wed Feb 08 2023 - 21:08:35 PST)
- [AMBER] Warning in MMPBSA calculation with glycoprotein 王 霂生 via AMBER (Fri Feb 10 2023 - 02:03:16 PST)
- [AMBER] H bonding Dulal Mondal via AMBER (Fri Feb 10 2023 - 03:51:29 PST)
- [AMBER] NMR refinement of G-Quadruplex DNA by AMBER22 Anirban Ghosh via AMBER (Sun Feb 12 2023 - 12:13:52 PST)
- [AMBER] scalpha and scbeta defaults are not right for TI calculations with smoothstep gti_lam_sch=1? Skanda Sastry via AMBER (Sun Feb 12 2023 - 23:47:36 PST)
- [AMBER] How to protonate ligand manually ? Enrico Martinez via AMBER (Mon Feb 13 2023 - 02:03:27 PST)
- [AMBER] Calculating Electrostatic energy between 2 atoms angad sharma via AMBER (Mon Feb 13 2023 - 04:39:10 PST)
- [AMBER] Removing rotational-transnational movements in dimmer protein Enrico Martinez via AMBER (Mon Feb 13 2023 - 06:07:42 PST)
- [AMBER] tleap ion naming issues Gonzalo R. Vazquez-Jimenez via AMBER (Mon Feb 13 2023 - 11:41:08 PST)
- [AMBER] Electrostatic calculation angad sharma via AMBER (Tue Feb 14 2023 - 06:03:38 PST)
- [AMBER] Warning tells me to report Bryan Cox via AMBER (Tue Feb 14 2023 - 12:19:16 PST)
- [AMBER] Net charge of ligand Enrico Martinez via AMBER (Wed Feb 15 2023 - 08:03:46 PST)
- [AMBER] CIC Annual Meeting during WiFo 2023, Sep 4-6 in Leipzig – Call for Papers Guessregen, Stefan /DE via AMBER (Wed Feb 15 2023 - 11:51:54 PST)
- [AMBER] amber20 installation failed on ubuntu Renato Freitas via AMBER (Wed Feb 15 2023 - 13:07:13 PST)
- [AMBER] benchmarking Amber 22 with WSL2 on Windows 11 Martin Juhás via AMBER (Wed Feb 15 2023 - 13:13:46 PST)
- [AMBER] SHAKE failed for hydrogens that interact with soft-core and/or no-SHAKE atoms He, Amy via AMBER (Wed Feb 15 2023 - 14:17:14 PST)
- [AMBER] drug including B atom laura zhang via AMBER (Wed Feb 15 2023 - 18:49:31 PST)
- [AMBER] Antechamber Error Rana Rehan Khalid via AMBER (Thu Feb 16 2023 - 00:35:10 PST)
- [AMBER] amber20 installation failed on ubuntu Renato Freitas via AMBER (Thu Feb 16 2023 - 04:55:13 PST)
- [AMBER] Error in parmstrip Enrico Martinez via AMBER (Thu Feb 16 2023 - 06:26:22 PST)
- [AMBER] Ambertools on M2 pro mohamed marzouk via AMBER (Thu Feb 16 2023 - 06:28:41 PST)
- Re: [AMBER] [Sender Not Verified] Net charge of ligand Enrico Martinez via AMBER (Thu Feb 16 2023 - 06:28:33 PST)
- [AMBER] parallel pysander? liu junjun via AMBER (Thu Feb 16 2023 - 08:37:28 PST)
- Re: [AMBER] Where to install Amber on an Ubuntu Server David A Case via AMBER (Thu Feb 16 2023 - 10:06:57 PST)
- [AMBER] sander seeks for the .skf integral file for a single-empty atomtype Maciej Spiegel via AMBER (Fri Feb 17 2023 - 00:41:05 PST)
- [AMBER] Method (SHAKE/SETTLE, HMR) to conditionally constrain waters He, Amy via AMBER (Fri Feb 17 2023 - 09:36:39 PST)
- [AMBER] Comparison of TIP3P vs AMOEBA water models Umesh Roy via AMBER (Fri Feb 17 2023 - 09:50:11 PST)
- [AMBER] Using amber19sb forcefield to simulate cyclic peptide Ho, Minh via AMBER (Fri Feb 17 2023 - 14:56:18 PST)
- [AMBER] [Amber20] QM region of QM/MM computations cannot converge Maciej Spiegel via AMBER (Sun Feb 19 2023 - 08:42:37 PST)
- Re: [AMBER] [External] Re: Using amber19sb forcefield to simulate cyclic peptide Carlos Simmerling via AMBER (Mon Feb 20 2023 - 08:06:21 PST)
- [AMBER] Error - Amber 22 Installation with Cuda ABDELATIF MESSAOUDI via AMBER (Mon Feb 20 2023 - 11:37:18 PST)
- [AMBER] Error similation with cuda ABDELATIF MESSAOUDI via AMBER (Mon Feb 20 2023 - 16:14:40 PST)
- [AMBER] How to do analysis on specific frames in cpptraj? XP Chen via AMBER (Tue Feb 21 2023 - 04:02:45 PST)
- [AMBER] tleap error Prithviraj Nandigrami via AMBER (Tue Feb 21 2023 - 13:45:09 PST)
- [AMBER] Terminal phosphates with RNA Piia Bartos via AMBER (Wed Feb 22 2023 - 01:39:48 PST)
- [AMBER] problem with pmemd.cuda and RTX4090 Martin Zacharias via AMBER (Thu Feb 23 2023 - 01:36:50 PST)
- [AMBER] Query regarding Acceptance ratio file Munazzah Fatima Ansari via AMBER (Thu Feb 23 2023 - 03:16:08 PST)
- [AMBER] pysander for gas energy with belly? liu junjun via AMBER (Thu Feb 23 2023 - 08:15:34 PST)
- [AMBER] pmemd.cuda test possible failure Freddy Bernal via AMBER (Thu Feb 23 2023 - 11:46:04 PST)
- [AMBER] MMPBSA problem Jurica Novak via AMBER (Fri Feb 24 2023 - 01:32:13 PST)
- [AMBER] pmemd.cuda: error while loading shared libraries ABDELATIF MESSAOUDI via AMBER (Fri Feb 24 2023 - 14:49:40 PST)
- [AMBER] cudaGetDeviceCount failed no CUDA-capable device is detected ABDELATIF MESSAOUDI via AMBER (Fri Feb 24 2023 - 15:07:13 PST)
- [AMBER] Regarding the visualization of the nmd file after pca in VMD Sruthi Sudhakar via AMBER (Sat Feb 25 2023 - 05:55:49 PST)
- [AMBER] How to set water molecule without EPW dummy atom? Maciej Spiegel via AMBER (Sun Feb 26 2023 - 22:14:30 PST)
- [AMBER] explanation of extra TI control variables Michael T Kim via AMBER (Mon Feb 27 2023 - 16:21:57 PST)
- [AMBER] amber install error Tang, Jun via AMBER (Tue Feb 28 2023 - 06:17:13 PST)
- [AMBER] RTX 2080 vs RTX 3060 TI Renato Freitas via AMBER (Tue Feb 28 2023 - 13:06:00 PST)
- Last message date: Tue Feb 28 2023 - 16:30:02 PST
- Archived on: Wed Apr 24 2024 - 05:56:12 PDT
