Amber Archive Aug 2025 by date

75 messages: Starting Thu Jul 31 2025 - 12:00:03 PDT, Ending Sat Aug 30 2025 - 06:30:02 PDT
This period: Most recent messages
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Thursday, 31 July 2025
- [AMBER] To calculate the volume of an octahedral box MAMTA YADAV via AMBER
Friday, 1 August 2025
- [AMBER] Previous versions of Amber Adam Huffman via AMBER
- Re: [AMBER] Help with optimizing the time of calculation Christina Bergonzo via AMBER
- [AMBER] MCPB.py Error at Step 2: TypeError with numpy.complex128 in angle parameter generation maciej.spiegel via AMBER
- Re: [AMBER] MCPB.py Error at Step 2: TypeError with numpy.complex128 in angle parameter generation Jeffrey Wagner via AMBER
- [AMBER] ASMD simulation of protein-protein complex Prithviraj Nandigrami via AMBER
- [AMBER] CCYM missing Simona Saporiti via AMBER
- [AMBER] Line minimizer abort while doing mmpbsa and Normal mode analysis Priyasha Majee via AMBER
- Re: [AMBER] MCPB.py Error at Step 2: TypeError with numpy.complex128 in angle parameter generation Li, Zhen via AMBER
- Re: [AMBER] [Potencjalny SPAM] Re: MCPB.py Error at Step 2: TypeError with numpy.complex128 in angle parameter generation maciej.spiegel via AMBER
- Re: [AMBER] Line minimizer abort while doing mmpbsa and Normal mode analysis Priyasha Majee via AMBER
Saturday, 2 August 2025
- [AMBER] Numerical Instability in Umbrella Sampling Sudipti Priyadarsinee via AMBER
- [AMBER] Segmentation fault when running on GPU, working fine on CPU Markowska
- Re: [AMBER] MD simulations running slowly David A Case via AMBER
- Re: [AMBER] Problems with MMPB/MMGBSA David A Case via AMBER
- Re: [AMBER] Previous versions of Amber David A Case via AMBER
- Re: [AMBER] CCYM missing David A Case via AMBER
- Re: [AMBER] Line minimizer abort while doing mmpbsa and Normal mode analysis David A Case via AMBER
- Re: [AMBER] Numerical Instability in Umbrella Sampling David A Case via AMBER
Sunday, 3 August 2025
- Re: [AMBER] CCYM missing Carlos Simmerling via AMBER
Monday, 4 August 2025
- [AMBER] Compilation with MVAPICH2-GDR Yasser Almeida via AMBER
Tuesday, 5 August 2025
- Re: [AMBER] Compilation with MVAPICH2-GDR Scott Brozell via AMBER
Wednesday, 6 August 2025
- Re: [AMBER] Problem of water breaking in coordinate file. YASHIKA . via AMBER
- Re: [AMBER] Problem of water breaking in coordinate file. Timothy Giese via AMBER
- Re: [AMBER] Problems with MMPB/MMGBSA Carmi, Jason R via AMBER
- [AMBER] findgrep.py error Dulal Mondal via AMBER
Thursday, 7 August 2025
- Re: [AMBER] Problem of water breaking in coordinate file. Timothy Giese via AMBER
Friday, 8 August 2025
- Re: [AMBER] findgrep.py error Dulal Mondal via AMBER
- Re: [AMBER] findgrep.py error Dulal Mondal via AMBER
- [AMBER] How to define pseudodihedral angle in the DISANG file for Umbrella Sampling Simulation in AMBER? Gourav Das via AMBER
- Re: [AMBER] How to define pseudodihedral angle in the DISANG file for Umbrella Sampling Simulation in AMBER? Carlos Simmerling via AMBER
- Re: [AMBER] Segmentation fault when running on GPU, working fine on CPU Markowska
- Re: [AMBER] How to define pseudodihedral angle in the DISANG file for Umbrella Sampling Simulation in AMBER? Carlos Simmerling via AMBER
- Re: [AMBER] findgrep.py error Vinicius Cruzeiro via AMBER
- Re: [AMBER] findgrep.py error Dulal Mondal via AMBER
- Re: [AMBER] findgrep.py error Vinicius Cruzeiro via AMBER
- [AMBER] .rst file not generated during heating step, simulation stops YASHIKA . via AMBER
Saturday, 9 August 2025
- Re: [AMBER] findgrep.py error Dulal Mondal via AMBER
- Re: [AMBER] findgrep.py error Vinicius Cruzeiro via AMBER
- Re: [AMBER] findgrep.py error Dulal Mondal via AMBER
- Re: [AMBER] .rst file not generated during heating step, simulation stops David A Case via AMBER
- Re: [AMBER] findgrep.py error Vinicius Cruzeiro via AMBER
Monday, 11 August 2025
- Re: [AMBER] Segmentation fault when running on GPU, working fine on CPU Markowska
- [AMBER] Error: Incompatible CUDA and GNU versions when trying to install Amber Cherry, Kendall via AMBER
- [AMBER] LEaP inconsistent peripheral improper atom ordering Evan Pretti via AMBER
Tuesday, 12 August 2025
- Re: [AMBER] LEaP inconsistent peripheral improper atom ordering Daniel Roe via AMBER
- Re: [AMBER] Error: Incompatible CUDA and GNU versions when trying to install Amber Li, Zhen via AMBER
- Re: [AMBER] Error: Incompatible CUDA and GNU versions when trying to install Amber David A Case via AMBER
Wednesday, 13 August 2025
- [AMBER] Parameterizing cisplatin with MCPB.py Stefan Ivanov via AMBER
- Re: [AMBER] Parameterizing cisplatin with MCPB.py Charo del Genio via AMBER
- [AMBER] Bug in PMEMD Plumed Compilation in Amber24 Zihao Bai via AMBER
Thursday, 14 August 2025
- [AMBER] TI Problem Beierlein, Frank via AMBER
- [AMBER] segmentation fault error YASHIKA . via AMBER
Friday, 15 August 2025
- Re: [AMBER] TI Problem David A Case via AMBER
- Re: [AMBER] segmentation fault error David A Case via AMBER
- [AMBER] Bug Report: ABFQMMM with DFTBPLUS Zihao Bai via AMBER
Monday, 18 August 2025
- Re: [AMBER] Bug Report: ABFQMMM with DFTBPLUS Timothy Giese via AMBER
- Re: [AMBER] Bug Report: ABFQMMM with DFTBPLUS Zihao Bai via AMBER
Monday, 25 August 2025
- [AMBER] Hamiltonian REMD using CUDA Vaibhav Bhatt via AMBER
- [AMBER] conda TOS error during cmake Charles-Alexandre Mattelaer via AMBER
- [AMBER] Error in sander.quick.cuda Kriti Shukla via AMBER
- Re: [AMBER] Hamiltonian REMD using CUDA Adrian Roitberg via AMBER
- Re: [AMBER] Error in sander.quick.cuda Goetz, Andreas via AMBER
Tuesday, 26 August 2025
- [AMBER] mmpbsa-py error Carlos via AMBER
Thursday, 28 August 2025
- [AMBER] mm_pbsa.pl setup for dimer receptor with non-continuous atom numbering Patil Pranita Uttamrao via AMBER
- Re: [AMBER] mm_pbsa.pl setup for dimer receptor with non-continuous atom numbering Elvis Martis via AMBER
Friday, 29 August 2025
- [AMBER] On the idea of a frcmod file containing all possible bond terms 491439532 via AMBER
- Re: [AMBER] On the idea of a frcmod file containing all possible bond terms Arun Srikanth via AMBER
- [AMBER] pKa through TI calculation Dulal Mondal via AMBER
- Re: [AMBER] pKa through TI calculation Erika McCarthy via AMBER
- Re: [AMBER] pKa through TI calculation Dulal Mondal via AMBER
- Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? Li, Zhen via AMBER
- Re: [AMBER] Problem with ZAFF Modeling Tutorial Center ID 4 Li, Zhen via AMBER
Saturday, 30 August 2025
- [AMBER] R: Problem with ZAFF Modeling Tutorial Center ID 4 saverio lemme via AMBER
- [AMBER] MMPBSA.py "bad atom type" error with custom Fe(IV) ion 徐文波 via AMBER

Last message date: Sat Aug 30 2025 - 06:30:02 PDT
Archived on: Fri Sep 05 2025 - 05:56:26 PDT