Amber Archive Jul 2024 by date

97 messages: Starting Sun Jun 30 2024 - 10:30:01 PDT, Ending Tue Jul 30 2024 - 21:00:02 PDT
This period: Most recent messages
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Sunday, 30 June 2024
- Re: [AMBER] Using ntp=1 for membrane embedded Protein-Ligand System with ifsc=1 Option 변진영 / 학생 / 약학과 via AMBER
Tuesday, 2 July 2024
- [AMBER] Query on ASMD simulations Sruthi Sudhakar via AMBER
- Re: [AMBER] Analysis of the helix rotation Enrico Martinez via AMBER
- [AMBER] frcmod and lib files Prithviraj Nandigrami via AMBER
Wednesday, 3 July 2024
- [AMBER] Calculation time for GBSA/PBSA analysis Stéphane Téletchéa via AMBER
- Re: [AMBER] Analysis of the helix rotation Téletchéa Stéphane via AMBER
- [AMBER] Modified amino acids: Simulating the Green Fluorescent Protein and Building a Modified Amino Acid Residue Ingso Limbu via AMBER
- Re: [AMBER] MMPBSA and membrane effect incorporation for GBSA Ray Luo via AMBER
- Re: [AMBER] IndexError in pdb4amber He, Amy via AMBER
Thursday, 4 July 2024
- Re: [AMBER] Gaff Atom Type Duplicates, With Different Data Carlos Simmerling via AMBER
Friday, 5 July 2024
- [AMBER] Lipidated custom residues of protein within lipid membrane Ramdhan,Peter A via AMBER
Sunday, 7 July 2024
- Re: [AMBER] MCPB.py questions Li, Zhen via AMBER
- Re: [AMBER] MCPB.py questions Ingso Limbu via AMBER
Monday, 8 July 2024
- Re: [AMBER] Modified amino acids: Simulating the Green Fluorescent Protein and Building a Modified Amino Acid Residue Brent Krueger via AMBER
Tuesday, 9 July 2024
- [AMBER] installing Amber24 for non-commerical use and AmberTools24 Andriy Kovalenko via AMBER
- [AMBER] Questioning how mask works in MMPBSA 한지승 via AMBER
Thursday, 11 July 2024
- Re: [AMBER] AMBER24 error report when running pdb4amber command Nil Mu via AMBER
- Re: [AMBER] AMBER24 error report when running pdb4amber command James Kress via AMBER
- Re: [AMBER] AMBER24 error report when running pdb4amber command Michael Shokhen via AMBER
- [AMBER] [JUW79.pitt.edu: Re: [amber.ambermd.org: Re: Gaff Atom Type Duplicates, With Different Data]] David A Case via AMBER
Friday, 12 July 2024
- [AMBER] Constant pH simulation in explicit solvent: suggested update for the manual Dr. Anselm Horn via AMBER
- [AMBER] RDNA 3 Trevor Kramer via AMBER
- Re: [AMBER] AMBER24 error report when running pdb4amber command Daniel Roe via AMBER
- [AMBER] Cpptraj issue: stripped trajectory and topology Enrico Martinez via AMBER
- Re: [AMBER] Unable to compile Amber24 with gcc14.1.0 Edwin Helbert Aponte Angarita via AMBER
Saturday, 13 July 2024
- Re: [AMBER] RDNA 3 Trevor Kramer via AMBER
Sunday, 14 July 2024
- [AMBER] Unable to access AMBER home website Michael Shokhen via AMBER
- Re: [AMBER] Unable to access AMBER home website Maria Nagan via AMBER
Monday, 15 July 2024
- [AMBER] Rmsip calculation Jenny 148 via AMBER
- [AMBER] cpptraj analysis of RMSF Enrico Martinez via AMBER
- Re: [AMBER] MMPBSA and membrane effect incorporation for GBSA Téletchéa Stéphane via AMBER
- Re: [AMBER] RDNA 3 Trevor Kramer via AMBER
- [AMBER] Analysis of protein-ligand interactions Enrico Martinez via AMBER
- Re: [AMBER] Unable to compile Amber24 with gcc14.1.0 Tru Huynh via AMBER
- [AMBER] 回复: Unable to access AMBER home website Huang ZiJian via AMBER
- Re: [AMBER] 回复: Unable to access AMBER home website Suchetana Gupta via AMBER
- [AMBER] Constant pH simulations problem -no progress in the simulations Masoud Keramati via AMBER
- [AMBER] Alter method of distance calculated for "closest" command Alexander Hung Lee via AMBER
- [AMBER] Constant pH generalized Born MD tutorial: Use of tautp with ntt=3 Nitin Kulhar via AMBER
- [AMBER] C termini does not seem be read as CT in tleap Ingso Limbu via AMBER
Tuesday, 16 July 2024
- Re: [AMBER] Analysis of protein-ligand interactions Enrico Martinez via AMBER
- Re: [AMBER] C termini does not seem be read as CT in tleap Dr. Anselm Horn via AMBER
- Re: [AMBER] Constant pH generalized Born MD tutorial: Use of tautp with ntt=3 Carlos Simmerling via AMBER
- Re: [AMBER] Modified amino acids: Simulating the Green Fluorescent Protein and Building a Modified Amino Acid Residue Téletchéa Stéphane via AMBER
- [AMBER] Temperature of a system Zihan Zhou via AMBER
Wednesday, 17 July 2024
- Re: [AMBER] Analysis of protein-ligand interactions Enrico Martinez via AMBER
- Re: [AMBER] running tleap for complex having covalent bond between protein and ligand Ghose Shouryo via AMBER
- [AMBER] running tleap for complex having covalent bond between protein and ligand SUBHASMITA MAHAPATRA MAHAPATRA via AMBER
- Re: [AMBER] Temperature of a system Carlos Simmerling via AMBER
- Re: [AMBER] Temperature of a system Daniel Roe via AMBER
- Re: [AMBER] running tleap for complex having covalent bond between protein and ligand SUBHASMITA MAHAPATRA MAHAPATRA via AMBER
- Re: [AMBER] running tleap for complex having covalent bond between protein and ligand Ghose Shouryo via AMBER
- Re: [AMBER] running tleap for complex having covalent bond between protein and ligand Carlos Simmerling via AMBER
- Re: [AMBER] Temperature of a system Carlos Simmerling via AMBER
- Re: [AMBER] Temperature of a system David A Case via AMBER
- Re: [AMBER] C termini does not seem be read as CT in tleap He, Amy via AMBER
- Re: [AMBER] Unable to compile Amber24 with gcc14.1.0 Edwin Helbert Aponte Angarita via AMBER
- [AMBER] float and ion error with MCPB.py Vaibhav Dixit via AMBER
Thursday, 18 July 2024
- Re: [AMBER] running tleap for complex having covalent bond between protein and ligand Dr. Anselm Horn via AMBER
- [AMBER] Autocorrelation Function in Amber Abdelrahman, Noureen via AMBER
- [AMBER] amber24 compilation - how to Define THRUST_IGNORE_CUB_VERSION_CHECK Michael Brunsteiner via AMBER
- Re: [AMBER] [EXTERNAL] amber24 compilation - how to Define THRUST_IGNORE_CUB_VERSION_CHECK Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER
- Re: [AMBER] Unable to compile Amber24 with gcc14.1.0 Edwin Helbert Aponte Angarita via AMBER
- [AMBER] Umbrella sampling equilibriation Liyanage, Risi \(MU-Student\) via AMBER
- Re: [AMBER] Umbrella sampling equilibriation Sushil Mishra via AMBER
- Re: [AMBER] Umbrella sampling equilibriation Carlos Simmerling via AMBER
- Re: [AMBER] Unable to compile Amber24 with gcc14.1.0 Edwin Helbert Aponte Angarita via AMBER
- Re: [AMBER] [EXTERNAL] amber24 compilation - how to Define THRUST_IGNORE_CUB_VERSION_CHECK Masoud Keramati via AMBER
Friday, 19 July 2024
- [AMBER] ATOMS_PER_MOLECULE section corrupt! Vaibhav Dixit via AMBER
- [AMBER] Query regarding Amber QUICK program SUBHASMITA MAHAPATRA MAHAPATRA via AMBER
- Re: [AMBER] Unable to compile Amber24 with gcc14.1.0 Edwin Helbert Aponte Angarita via AMBER
- Re: [AMBER] Query regarding Amber QUICK program Goetz, Andreas via AMBER
Sunday, 21 July 2024
- [AMBER] Amber Tutorial Onur İŞCİL via AMBER
- Re: [AMBER] Amber Tutorial Masoud Keramati via AMBER
- [AMBER] MCPB.py keyerror Ingso Limbu via AMBER
Monday, 22 July 2024
- Re: [AMBER] Autocorrelation Function in Amber Daniel Roe via AMBER
- [AMBER] Question about conformation transition rate estimation in a protein Abhilash J via AMBER
- [AMBER] Does Amber 24 work on ubuntu 22.04? Ming Tang via AMBER
- Re: [AMBER] MCPB.py keyerror Li, Zhen via AMBER
- Re: [AMBER] MCPB.py keyerror Ingso Limbu via AMBER
Wednesday, 24 July 2024
- [AMBER] Calculating Unfolding Enthalpy Change Aravind R via AMBER
- [AMBER] Fwd: Analysis of lipids in membrane generated by PackMol memgen Enrico Martinez via AMBER
Thursday, 25 July 2024
- [AMBER] Atom types for oxetane/azetidine Daniella Hares via AMBER
- Re: [AMBER] Antechamber changes atom IDs from gaussian ESP calculations Timothy Giese via AMBER
- [AMBER] amber24 cuda installation error Dulal Mondal via AMBER
Monday, 29 July 2024
- Re: [AMBER] amber24 cuda installation error Masoud Keramati via AMBER
- [AMBER] missing parameters on GAFF2 Frederico De Santana Pontes via AMBER
Tuesday, 30 July 2024
- [AMBER] change the pdb coordinates 百毒不侵√ via AMBER
- Re: [AMBER] Running PMEMD for SOD1 with counterions in implicit solvent - 1 Carlos Simmerling via AMBER
- Re: [AMBER] amber24 cuda installation error Dulal Mondal via AMBER
- Re: [AMBER] amber24 cuda installation error Masoud Keramati via AMBER
- Re: [AMBER] amber24 cuda installation error Gert Kruger via AMBER
- Re: [AMBER] Running PMEMD for SOD1 with counterions in implicit solvent - 1 Andriy Kovalenko via AMBER
- Re: [AMBER] Optimal GPU configuration for REMD Masoud Keramati via AMBER
- Re: [AMBER] assign protonation states on a trajectory (from constant pH simulation) Quinn Yng via AMBER
- Re: [AMBER] output partial residues He, Amy via AMBER
- Re: [AMBER] change the pdb coordinates David A Case via AMBER

Last message date: Tue Jul 30 2024 - 21:00:02 PDT
Archived on: Mon Sep 16 2024 - 05:56:16 PDT