Amber Archive Feb 2023: by date

Tuesday, 31 January 2023
- [AMBER] Distance calculation using cpptraj Dulal Mondal via AMBER
- Re: [AMBER] CPPTRAJ, PCA, Effect of Mutation Elvis Martis via AMBER
- [AMBER] How restart md simulation with amber22 ABDELATIF MESSAOUDI via AMBER
Wednesday, 1 February 2023
- [AMBER] A query on using a non-standard solvent devendra.prajapat.cys19--- via AMBER
- Re: [AMBER] A query on using a non-standard solvent Steinbrecher, Thomas via AMBER
- [AMBER] Failures inamber test Freddy Bernal via AMBER
- Re: [AMBER] How restart md simulation with amber22 Carlos Simmerling via AMBER
- [AMBER] Announcement: Release of DOCK 6.10 Scott Brozell via AMBER
- Re: [AMBER] Failures inamber test Scott Brozell via AMBER
- [AMBER] Problem with MMGBSA Suchetana Gupta via AMBER
- [AMBER] GLH with HE1 He, Amy via AMBER
- Re: [AMBER] GLH with HE1 He, Amy via AMBER
- Re: [AMBER] Problem with MMGBSA Suchetana Gupta via AMBER
- Re: [AMBER] Problem with MMGBSA Suchetana Gupta via AMBER
- Re: [AMBER] Problem with MMGBSA Suchetana Gupta via AMBER
- Re: [AMBER] GLH with HE1 Carlos Simmerling via AMBER
- [AMBER] D-glucosamine GLYCAM parameters Michael Owen via AMBER
Thursday, 2 February 2023
- [AMBER] CPPTRAJ, Salt Bridge Matthew Guberman-Pfeffer via AMBER
- [AMBER] Opening for a PLUMED developer position Giovanni Bussi via AMBER
Friday, 3 February 2023
- [AMBER] PCA porjection & representative structure Hocine EL KHAOUDI ENYOURY via AMBER
- [AMBER] RTX4070TI Benchmarks Ross Walker via AMBER
- [AMBER] Amber2020 and Amber2022 comparability issue: alchemical free energy calc Michael T Kim via AMBER
Saturday, 4 February 2023
- [AMBER] Conference Announcement: 35th MMWS in Erlangen, Germany Dr. Anselm Horn via AMBER
Sunday, 5 February 2023
- Re: [AMBER] Amber2020 and Amber2022 comparability issue: alchemical free energy calc David A Case via AMBER
- Re: [AMBER] AMBER simulation heating step David A Case via AMBER
- [AMBER] GPU memory error during ABMD run Owen O'Reilly via AMBER
- [AMBER] Installation Error: miniconda issue Sumra Abbasi via AMBER
- [AMBER] RMSF calculation descrepancy of dimeric systems Prathit Chatterjee via AMBER
Monday, 6 February 2023
- [AMBER] Error in tests for pmemd.cuda.MPI Freddy Bernal via AMBER
- Re: [AMBER] CPPTRAJ, PCA, Effect of Mutation Daniel Roe via AMBER
- Re: [AMBER] Distance calculation using cpptraj Daniel Roe via AMBER
- Re: [AMBER] CPPTRAJ, Salt Bridge Daniel Roe via AMBER
- Re: [AMBER] GPU memory error during ABMD run David A Case via AMBER
- Re: [AMBER] Installation Error: miniconda issue Sumra Abbasi via AMBER
- Re: [AMBER] PCA porjection & representative structure Daniel Roe via AMBER
- Re: [AMBER] PCA porjection & representative structure Hocine EL KHAOUDI ENYOURY via AMBER
- [AMBER] Fortran runtime error: Bad real number in item 1 of list input Nishad Ankita Rudal via AMBER
- Re: [AMBER] GPU memory error during ABMD run Owen O'Reilly via AMBER
- Re: [AMBER] Fortran runtime error: Bad real number in item 1 of list input Dr. Anselm Horn via AMBER
- Re: [AMBER] Fortran runtime error: Bad real number in item 1 of list input David Case via AMBER
- [AMBER] Density distribution angad sharma via AMBER
- Re: [AMBER] Fortran runtime error: Bad real number in item 1 of list input Nishad Ankita Rudal via AMBER
- Re: [AMBER] Fortran runtime error: Bad real number in item 1 of list input Nishad Ankita Rudal via AMBER
- Re: [AMBER] Nucleic acid simulation error Prithviraj Nandigrami via AMBER
- Re: [AMBER] Amber2020 and Amber2022 comparability issue: alchemical free energy calc Michael T Kim via AMBER
- Re: [AMBER] Fortran runtime error: Bad real number in item 1 of list input David A Case via AMBER
- Re: [AMBER] Error in tests for pmemd.cuda.MPI Hector A. Baldoni via AMBER
Tuesday, 7 February 2023
- [AMBER] FW: Bad atom type: i Zachariah Schuurs via AMBER
- [AMBER] load amber trj using vmd automatically laura zhang via AMBER
- Re: [AMBER] load amber trj using vmd automatically Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] load amber trj using vmd automatically Daniel Roe via AMBER
Wednesday, 8 February 2023
- Re: [AMBER] Error in tests for pmemd.cuda.MPI Freddy Bernal via AMBER
- Re: [AMBER] Error in tests for pmemd.cuda.MPI Freddy Bernal via AMBER
- Re: [AMBER] Nucleic acid simulation error Carlos Simmerling via AMBER
- Re: [AMBER] Nucleic acid simulation error Carlos Simmerling via AMBER
- [AMBER] Suspicious pKas from CpHMD Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Suspicious pKas from CpHMD Vinicius Wilian Cruzeiro via AMBER
- Re: [AMBER] Suspicious pKas from CpHMD Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Suspicious pKas from CpHMD Vinicius Wilian Cruzeiro via AMBER
Thursday, 9 February 2023
- Re: [AMBER] Nucleic acid simulation error Carlos Simmerling via AMBER
- Re: [AMBER] Suspicious pKas from CpHMD Adrian Roitberg via AMBER
- Re: [AMBER] Nucleic acid simulation error Carlos Simmerling via AMBER
- Re: [AMBER] {SPAM?} Re: Suspicious pKas from CpHMD Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] {SPAM?} Re: Suspicious pKas from CpHMD Matthew Guberman-Pfeffer via AMBER
Friday, 10 February 2023
- [AMBER] Warning in MMPBSA calculation with glycoprotein 王霂生 via AMBER
- [AMBER] H bonding Dulal Mondal via AMBER
- Re: [AMBER] {SPAM?} Re: Suspicious pKas from CpHMD brian.radak--- via AMBER
- Re: [AMBER] {SPAM?} Re: Suspicious pKas from CpHMD Adrian Roitberg via AMBER
Sunday, 12 February 2023
- [AMBER] NMR refinement of G-Quadruplex DNA by AMBER22 Anirban Ghosh via AMBER
- [AMBER] scalpha and scbeta defaults are not right for TI calculations with smoothstep gti_lam_sch=1? Skanda Sastry via AMBER
Monday, 13 February 2023
- Re: [AMBER] Error in tests for pmemd.cuda.MPI Freddy Bernal via AMBER
- [AMBER] How to protonate ligand manually ? Enrico Martinez via AMBER
- [AMBER] Calculating Electrostatic energy between 2 atoms angad sharma via AMBER
- Re: [AMBER] NMR refinement of G-Quadruplex DNA by AMBER22 David A Case via AMBER
- [AMBER] Removing rotational-transnational movements in dimmer protein Enrico Martinez via AMBER
- [AMBER] tleap ion naming issues Gonzalo R. Vazquez-Jimenez via AMBER
- Re: [AMBER] [Sender Not Verified] tleap ion naming issues Steinbrecher, Thomas via AMBER
Tuesday, 14 February 2023
- [AMBER] Electrostatic calculation angad sharma via AMBER
- [AMBER] Warning tells me to report Bryan Cox via AMBER
Wednesday, 15 February 2023
- Re: [AMBER] Warning tells me to report David A Case via AMBER
- [AMBER] Net charge of ligand Enrico Martinez via AMBER
- [AMBER] CIC Annual Meeting during WiFo 2023, Sep 4-6 in Leipzig – Call for Papers Guessregen, Stefan /DE via AMBER
- [AMBER] amber20 installation failed on ubuntu Renato Freitas via AMBER
- [AMBER] benchmarking Amber 22 with WSL2 on Windows 11 Martin Juhás via AMBER
- Re: [AMBER] benchmarking Amber 22 with WSL2 on Windows 11 Martin Juhás via AMBER
- [AMBER] SHAKE failed for hydrogens that interact with soft-core and/or no-SHAKE atoms He, Amy via AMBER
- [AMBER] drug including B atom laura zhang via AMBER
- Re: [AMBER] [Sender Not Verified] drug including B atom Steinbrecher, Thomas via AMBER
Thursday, 16 February 2023
- [AMBER] Antechamber Error Rana Rehan Khalid via AMBER
- [AMBER] amber20 installation failed on ubuntu Renato Freitas via AMBER
- Re: [AMBER] amber20 installation failed on ubuntu Gert Kruger via AMBER
- Re: [AMBER] amber20 installation failed on ubuntu David A Case via AMBER
- Re: [AMBER] drug including B atom David A Case via AMBER
- [AMBER] Error in parmstrip Enrico Martinez via AMBER
- [AMBER] Ambertools on M2 pro mohamed marzouk via AMBER
- Re: [AMBER] [Sender Not Verified] Net charge of ligand Enrico Martinez via AMBER
- Re: [AMBER] [Sender Not Verified] drug including B atom laura zhang via AMBER
- [AMBER] parallel pysander? liu junjun via AMBER
- Re: [AMBER] Where to install Amber on an Ubuntu Server David A Case via AMBER
- Re: [AMBER] amber20 installation failed on ubuntu Renato Freitas via AMBER
- Re: [AMBER] [Sender Not Verified] drug including B atom David A Case via AMBER
- Re: [AMBER] amber20 installation failed on ubuntu David A Case via AMBER
Friday, 17 February 2023
- [AMBER] sander seeks for the .skf integral file for a single-empty atomtype Maciej Spiegel via AMBER
- [AMBER] Method (SHAKE/SETTLE, HMR) to conditionally constrain waters He, Amy via AMBER
- [AMBER] Comparison of TIP3P vs AMOEBA water models Umesh Roy via AMBER
- Re: [AMBER] Method (SHAKE/SETTLE, HMR) to conditionally constrain waters Carlos Simmerling via AMBER
- Re: [AMBER] Method (SHAKE/SETTLE, HMR) to conditionally constrain waters Carlos Simmerling via AMBER
- Re: [AMBER] Method (SHAKE/SETTLE, HMR) to conditionally constrain waters Brian Radak via AMBER
- [AMBER] Using amber19sb forcefield to simulate cyclic peptide Ho, Minh via AMBER
- Re: [AMBER] Using amber19sb forcefield to simulate cyclic peptide Carlos Simmerling via AMBER
Saturday, 18 February 2023
- Re: [AMBER] sander seeks for the .skf integral file for a single-empty atomtype David A Case via AMBER
Sunday, 19 February 2023
- [AMBER] [Amber20] QM region of QM/MM computations cannot converge Maciej Spiegel via AMBER
Monday, 20 February 2023
- Re: [AMBER] [Amber20] QM region of QM/MM computations cannot converge David A Case via AMBER
- Re: [AMBER] [Amber20] QM region of QM/MM computations cannot converge Maciej Spiegel via AMBER
- Re: [AMBER] [Amber20] QM region of QM/MM computations cannot converge Adrian Roitberg via AMBER
- Re: [AMBER] [External] Re: Using amber19sb forcefield to simulate cyclic peptide Carlos Simmerling via AMBER
- [AMBER] Error - Amber 22 Installation with Cuda ABDELATIF MESSAOUDI via AMBER
- Re: [AMBER] Error - Amber 22 Installation with Cuda Osadchey Brown, Reilly via AMBER
- [AMBER] Error similation with cuda ABDELATIF MESSAOUDI via AMBER
- Re: [AMBER] Error similation with cuda David A Case via AMBER
- Re: [AMBER] Error - Amber 22 Installation with Cuda David A Case via AMBER
Tuesday, 21 February 2023
- [AMBER] How to do analysis on specific frames in cpptraj? XP Chen via AMBER
- Re: [AMBER] [Sender Not Verified] How to do analysis on specific frames in cpptraj? Steinbrecher, Thomas via AMBER
- Re: [AMBER] How to do analysis on specific frames in cpptraj? Daniel Roe via AMBER
- [AMBER] tleap error Prithviraj Nandigrami via AMBER
Wednesday, 22 February 2023
- [AMBER] Terminal phosphates with RNA Piia Bartos via AMBER
- Re: [AMBER] Terminal phosphates with RNA David A Case via AMBER
- Re: [AMBER] Terminal phosphates with RNA Piia Bartos via AMBER
Thursday, 23 February 2023
- [AMBER] problem with pmemd.cuda and RTX4090 Martin Zacharias via AMBER
- [AMBER] Query regarding Acceptance ratio file Munazzah Fatima Ansari via AMBER
- [AMBER] pysander for gas energy with belly? liu junjun via AMBER
- Re: [AMBER] Query regarding Acceptance ratio file Carlos Simmerling via AMBER
- Re: [AMBER] Amber2020 and Amber2022 comparability issue: alchemical free energy calc Michael T Kim via AMBER
- [AMBER] pmemd.cuda test possible failure Freddy Bernal via AMBER
Friday, 24 February 2023
- [AMBER] MMPBSA problem Jurica Novak via AMBER
- Re: [AMBER] pysander for gas energy with belly? liu junjun via AMBER
- Re: [AMBER] Terminal phosphates with RNA Piia Bartos via AMBER
- [AMBER] pmemd.cuda: error while loading shared libraries ABDELATIF MESSAOUDI via AMBER
- [AMBER] cudaGetDeviceCount failed no CUDA-capable device is detected ABDELATIF MESSAOUDI via AMBER
- Re: [AMBER] pmemd.cuda: error while loading shared libraries Markowska
Saturday, 25 February 2023
- [AMBER] Regarding the visualization of the nmd file after pca in VMD Sruthi Sudhakar via AMBER
Sunday, 26 February 2023
- [AMBER] How to set water molecule without EPW dummy atom? Maciej Spiegel via AMBER
- Re: [AMBER] How to set water molecule without EPW dummy atom? Vinicius Wilian Cruzeiro via AMBER
- Re: [AMBER] How to set water molecule without EPW dummy atom? Maciej Spiegel via AMBER
Monday, 27 February 2023
- Re: [AMBER] How to set water molecule without EPW dummy atom? Carlos Simmerling via AMBER
- [AMBER] explanation of extra TI control variables Michael T Kim via AMBER
Tuesday, 28 February 2023
- Re: [AMBER] pmemd.cuda test possible failure David A Case via AMBER
- Re: [AMBER] MMPBSA problem David A Case via AMBER
- Re: [AMBER] pmemd.cuda: error while loading shared libraries David A Case via AMBER
- Re: [AMBER] cudaGetDeviceCount failed no CUDA-capable device is detected David A Case via AMBER
- [AMBER] amber install error Tang, Jun via AMBER
- Re: [AMBER] MMPBSA problem Jurica Novak via AMBER
- Re: [AMBER] MMPBSA problem Bill Miller III via AMBER
- [AMBER] RTX 2080 vs RTX 3060 TI Renato Freitas via AMBER
- Re: [AMBER] amber install error David A Case via AMBER
- Re: [AMBER] pmemd.cuda: error while loading shared libraries ABDELATIF MESSAOUDI via AMBER
- Re: [AMBER] amber install error Tang, Jun via AMBER
- Re: [AMBER] amber install error Daniel Roe via AMBER

Last message date: Tue Feb 28 2023 - 16:30:02 PST
Archived on: Fri Apr 19 2024 - 05:56:00 PDT

Amber Archive Feb 2023 by date