Amber Archive Jul 2024: by thread

Re: [AMBER] Using ntp=1 for membrane embedded Protein-Ligand System with ifsc=1 Option 변진영 / 학생 / 약학과 via AMBER (Sun Jun 30 2024 - 10:15:18 PDT)
[AMBER] Query on ASMD simulations Sruthi Sudhakar via AMBER (Tue Jul 02 2024 - 02:24:19 PDT)
Re: [AMBER] Analysis of the helix rotation Enrico Martinez via AMBER (Tue Jul 02 2024 - 08:49:53 PDT)
- Re: [AMBER] Analysis of the helix rotation Téletchéa Stéphane via AMBER (Wed Jul 03 2024 - 06:25:38 PDT)
[AMBER] frcmod and lib files Prithviraj Nandigrami via AMBER (Tue Jul 02 2024 - 10:32:09 PDT)
[AMBER] Calculation time for GBSA/PBSA analysis Stéphane Téletchéa via AMBER (Wed Jul 03 2024 - 01:37:38 PDT)
[AMBER] Modified amino acids: Simulating the Green Fluorescent Protein and Building a Modified Amino Acid Residue Ingso Limbu via AMBER (Wed Jul 03 2024 - 09:56:37 PDT)
- Re: [AMBER] Modified amino acids: Simulating the Green Fluorescent Protein and Building a Modified Amino Acid Residue Brent Krueger via AMBER (Mon Jul 08 2024 - 08:38:14 PDT)
  - [AMBER] Constant pH simulation in explicit solvent: suggested update for the manual Dr. Anselm Horn via AMBER (Fri Jul 12 2024 - 01:44:55 PDT)
  - Re: [AMBER] Modified amino acids: Simulating the Green Fluorescent Protein and Building a Modified Amino Acid Residue Téletchéa Stéphane via AMBER (Tue Jul 16 2024 - 09:51:05 PDT)
Re: [AMBER] MMPBSA and membrane effect incorporation for GBSA Ray Luo via AMBER (Wed Jul 03 2024 - 14:33:50 PDT)
- Re: [AMBER] MMPBSA and membrane effect incorporation for GBSA Téletchéa Stéphane via AMBER (Mon Jul 15 2024 - 05:18:00 PDT)
Re: [AMBER] IndexError in pdb4amber He, Amy via AMBER (Wed Jul 03 2024 - 17:16:45 PDT)
Re: [AMBER] Gaff Atom Type Duplicates, With Different Data Carlos Simmerling via AMBER (Thu Jul 04 2024 - 11:39:43 PDT)
[AMBER] Lipidated custom residues of protein within lipid membrane Ramdhan,Peter A via AMBER (Fri Jul 05 2024 - 08:29:08 PDT)
Re: [AMBER] MCPB.py questions Li, Zhen via AMBER (Sun Jul 07 2024 - 20:13:38 PDT)
- Re: [AMBER] MCPB.py questions Ingso Limbu via AMBER (Sun Jul 07 2024 - 20:52:55 PDT)
[AMBER] installing Amber24 for non-commerical use and AmberTools24 Andriy Kovalenko via AMBER (Tue Jul 09 2024 - 11:25:14 PDT)
[AMBER] Questioning how mask works in MMPBSA 한지승 via AMBER (Tue Jul 09 2024 - 17:23:40 PDT)
Re: [AMBER] AMBER24 error report when running pdb4amber command Nil Mu via AMBER (Thu Jul 11 2024 - 10:55:07 PDT)
- Re: [AMBER] AMBER24 error report when running pdb4amber command James Kress via AMBER (Thu Jul 11 2024 - 12:00:51 PDT)
  - Re: [AMBER] AMBER24 error report when running pdb4amber command Michael Shokhen via AMBER (Thu Jul 11 2024 - 12:25:10 PDT)
- Re: [AMBER] AMBER24 error report when running pdb4amber command Daniel Roe via AMBER (Fri Jul 12 2024 - 05:47:49 PDT)
[AMBER] [JUW79.pitt.edu: Re: [amber.ambermd.org: Re: Gaff Atom Type Duplicates, With Different Data]] David A Case via AMBER (Thu Jul 11 2024 - 13:42:47 PDT)
[AMBER] RDNA 3 Trevor Kramer via AMBER (Fri Jul 12 2024 - 05:03:01 PDT)
- Re: [AMBER] RDNA 3 Trevor Kramer via AMBER (Sat Jul 13 2024 - 06:34:47 PDT)
  - Re: [AMBER] RDNA 3 Trevor Kramer via AMBER (Mon Jul 15 2024 - 06:34:07 PDT)
[AMBER] Cpptraj issue: stripped trajectory and topology Enrico Martinez via AMBER (Fri Jul 12 2024 - 08:58:45 PDT)
Re: [AMBER] Unable to compile Amber24 with gcc14.1.0 Edwin Helbert Aponte Angarita via AMBER (Fri Jul 12 2024 - 12:38:48 PDT)
- Re: [AMBER] Unable to compile Amber24 with gcc14.1.0 Tru Huynh via AMBER (Mon Jul 15 2024 - 07:34:45 PDT)
- Re: [AMBER] Unable to compile Amber24 with gcc14.1.0 Edwin Helbert Aponte Angarita via AMBER (Wed Jul 17 2024 - 18:31:55 PDT)
- Re: [AMBER] Unable to compile Amber24 with gcc14.1.0 Edwin Helbert Aponte Angarita via AMBER (Thu Jul 18 2024 - 11:09:57 PDT)
  - Re: [AMBER] Unable to compile Amber24 with gcc14.1.0 Edwin Helbert Aponte Angarita via AMBER (Thu Jul 18 2024 - 13:31:08 PDT)
    - Re: [AMBER] Unable to compile Amber24 with gcc14.1.0 Edwin Helbert Aponte Angarita via AMBER (Fri Jul 19 2024 - 11:18:25 PDT)
[AMBER] Unable to access AMBER home website Michael Shokhen via AMBER (Sun Jul 14 2024 - 05:08:57 PDT)
- Re: [AMBER] Unable to access AMBER home website Maria Nagan via AMBER (Sun Jul 14 2024 - 08:16:30 PDT)
  - [AMBER] 回复: Unable to access AMBER home website Huang ZiJian via AMBER (Mon Jul 15 2024 - 08:08:26 PDT)
    - Re: [AMBER] 回复: Unable to access AMBER home website Suchetana Gupta via AMBER (Mon Jul 15 2024 - 08:11:08 PDT)
[AMBER] Rmsip calculation Jenny 148 via AMBER (Mon Jul 15 2024 - 00:50:42 PDT)
[AMBER] cpptraj analysis of RMSF Enrico Martinez via AMBER (Mon Jul 15 2024 - 01:39:27 PDT)
[AMBER] Analysis of protein-ligand interactions Enrico Martinez via AMBER (Mon Jul 15 2024 - 07:31:33 PDT)
- Re: [AMBER] Analysis of protein-ligand interactions Enrico Martinez via AMBER (Tue Jul 16 2024 - 01:04:38 PDT)
- Re: [AMBER] Analysis of protein-ligand interactions Enrico Martinez via AMBER (Wed Jul 17 2024 - 02:32:13 PDT)
[AMBER] Constant pH simulations problem -no progress in the simulations Masoud Keramati via AMBER (Mon Jul 15 2024 - 10:20:19 PDT)
[AMBER] Alter method of distance calculated for "closest" command Alexander Hung Lee via AMBER (Mon Jul 15 2024 - 11:04:57 PDT)
[AMBER] Constant pH generalized Born MD tutorial: Use of tautp with ntt=3 Nitin Kulhar via AMBER (Mon Jul 15 2024 - 23:06:36 PDT)
- Re: [AMBER] Constant pH generalized Born MD tutorial: Use of tautp with ntt=3 Carlos Simmerling via AMBER (Tue Jul 16 2024 - 03:45:29 PDT)
[AMBER] C termini does not seem be read as CT in tleap Ingso Limbu via AMBER (Mon Jul 15 2024 - 23:26:09 PDT)
- Re: [AMBER] C termini does not seem be read as CT in tleap Dr. Anselm Horn via AMBER (Tue Jul 16 2024 - 01:16:57 PDT)
- Re: [AMBER] C termini does not seem be read as CT in tleap He, Amy via AMBER (Wed Jul 17 2024 - 13:15:30 PDT)
[AMBER] Temperature of a system Zihan Zhou via AMBER (Tue Jul 16 2024 - 23:21:17 PDT)
- Re: [AMBER] Temperature of a system Carlos Simmerling via AMBER (Wed Jul 17 2024 - 03:50:28 PDT)
  - Re: [AMBER] Temperature of a system Daniel Roe via AMBER (Wed Jul 17 2024 - 06:32:46 PDT)
- Re: [AMBER] Temperature of a system Carlos Simmerling via AMBER (Wed Jul 17 2024 - 11:29:00 PDT)
- Re: [AMBER] Temperature of a system David A Case via AMBER (Wed Jul 17 2024 - 11:58:56 PDT)
[AMBER] running tleap for complex having covalent bond between protein and ligand SUBHASMITA MAHAPATRA MAHAPATRA via AMBER (Wed Jul 17 2024 - 03:30:17 PDT)
- Re: [AMBER] running tleap for complex having covalent bond between protein and ligand Ghose Shouryo via AMBER (Wed Jul 17 2024 - 03:34:06 PDT)
  - Re: [AMBER] running tleap for complex having covalent bond between protein and ligand SUBHASMITA MAHAPATRA MAHAPATRA via AMBER (Wed Jul 17 2024 - 11:09:42 PDT)
    - Re: [AMBER] running tleap for complex having covalent bond between protein and ligand Ghose Shouryo via AMBER (Wed Jul 17 2024 - 11:24:24 PDT)
    - Re: [AMBER] running tleap for complex having covalent bond between protein and ligand Carlos Simmerling via AMBER (Wed Jul 17 2024 - 11:26:54 PDT)
- Re: [AMBER] running tleap for complex having covalent bond between protein and ligand Dr. Anselm Horn via AMBER (Thu Jul 18 2024 - 02:28:54 PDT)
[AMBER] float and ion error with MCPB.py Vaibhav Dixit via AMBER (Wed Jul 17 2024 - 22:54:10 PDT)
[AMBER] Autocorrelation Function in Amber Abdelrahman, Noureen via AMBER (Thu Jul 18 2024 - 03:53:08 PDT)
- Re: [AMBER] Autocorrelation Function in Amber Daniel Roe via AMBER (Mon Jul 22 2024 - 05:42:23 PDT)
[AMBER] amber24 compilation - how to Define THRUST_IGNORE_CUB_VERSION_CHECK Michael Brunsteiner via AMBER (Thu Jul 18 2024 - 08:59:13 PDT)
- Re: [AMBER] [EXTERNAL] amber24 compilation - how to Define THRUST_IGNORE_CUB_VERSION_CHECK Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER (Thu Jul 18 2024 - 09:51:28 PDT)
  - Re: [AMBER] [EXTERNAL] amber24 compilation - how to Define THRUST_IGNORE_CUB_VERSION_CHECK Masoud Keramati via AMBER (Thu Jul 18 2024 - 19:08:52 PDT)
[AMBER] Umbrella sampling equilibriation Liyanage, Risi \(MU-Student\) via AMBER (Thu Jul 18 2024 - 11:43:47 PDT)
- Re: [AMBER] Umbrella sampling equilibriation Sushil Mishra via AMBER (Thu Jul 18 2024 - 11:49:52 PDT)
- Re: [AMBER] Umbrella sampling equilibriation Carlos Simmerling via AMBER (Thu Jul 18 2024 - 11:54:42 PDT)
[AMBER] ATOMS_PER_MOLECULE section corrupt! Vaibhav Dixit via AMBER (Fri Jul 19 2024 - 06:21:40 PDT)
[AMBER] Query regarding Amber QUICK program SUBHASMITA MAHAPATRA MAHAPATRA via AMBER (Fri Jul 19 2024 - 10:35:07 PDT)
- Re: [AMBER] Query regarding Amber QUICK program Goetz, Andreas via AMBER (Fri Jul 19 2024 - 20:06:08 PDT)
[AMBER] Amber Tutorial Onur İŞCİL via AMBER (Sun Jul 21 2024 - 05:13:42 PDT)
- Re: [AMBER] Amber Tutorial Masoud Keramati via AMBER (Sun Jul 21 2024 - 05:31:43 PDT)
[AMBER] MCPB.py keyerror Ingso Limbu via AMBER (Sun Jul 21 2024 - 16:21:36 PDT)
- Re: [AMBER] MCPB.py keyerror Li, Zhen via AMBER (Mon Jul 22 2024 - 14:47:15 PDT)
  - Re: [AMBER] MCPB.py keyerror Ingso Limbu via AMBER (Mon Jul 22 2024 - 15:00:22 PDT)
[AMBER] Question about conformation transition rate estimation in a protein Abhilash J via AMBER (Mon Jul 22 2024 - 09:26:52 PDT)
[AMBER] Does Amber 24 work on ubuntu 22.04? Ming Tang via AMBER (Mon Jul 22 2024 - 14:19:12 PDT)
[AMBER] Calculating Unfolding Enthalpy Change Aravind R via AMBER (Wed Jul 24 2024 - 00:15:33 PDT)
[AMBER] Fwd: Analysis of lipids in membrane generated by PackMol memgen Enrico Martinez via AMBER (Wed Jul 24 2024 - 07:21:02 PDT)
[AMBER] Atom types for oxetane/azetidine Daniella Hares via AMBER (Thu Jul 25 2024 - 02:26:33 PDT)
Re: [AMBER] Antechamber changes atom IDs from gaussian ESP calculations Timothy Giese via AMBER (Thu Jul 25 2024 - 08:46:55 PDT)
[AMBER] amber24 cuda installation error Dulal Mondal via AMBER (Thu Jul 25 2024 - 22:40:42 PDT)
- Re: [AMBER] amber24 cuda installation error Masoud Keramati via AMBER (Mon Jul 29 2024 - 10:20:20 PDT)
- Re: [AMBER] amber24 cuda installation error Dulal Mondal via AMBER (Tue Jul 30 2024 - 10:33:20 PDT)
  - Re: [AMBER] amber24 cuda installation error Masoud Keramati via AMBER (Tue Jul 30 2024 - 10:50:59 PDT)
  - Re: [AMBER] amber24 cuda installation error Gert Kruger via AMBER (Tue Jul 30 2024 - 10:51:30 PDT)
[AMBER] missing parameters on GAFF2 Frederico De Santana Pontes via AMBER (Mon Jul 29 2024 - 14:58:09 PDT)
[AMBER] change the pdb coordinates 百毒不侵√ via AMBER (Tue Jul 30 2024 - 02:15:33 PDT)
- Re: [AMBER] change the pdb coordinates David A Case via AMBER (Tue Jul 30 2024 - 20:53:07 PDT)
Re: [AMBER] Running PMEMD for SOD1 with counterions in implicit solvent - 1 Carlos Simmerling via AMBER (Tue Jul 30 2024 - 09:38:28 PDT)
- Re: [AMBER] Running PMEMD for SOD1 with counterions in implicit solvent - 1 Andriy Kovalenko via AMBER (Tue Jul 30 2024 - 11:11:29 PDT)
Re: [AMBER] Optimal GPU configuration for REMD Masoud Keramati via AMBER (Tue Jul 30 2024 - 12:10:03 PDT)
Re: [AMBER] assign protonation states on a trajectory (from constant pH simulation) Quinn Yng via AMBER (Tue Jul 30 2024 - 12:11:36 PDT)
Re: [AMBER] output partial residues He, Amy via AMBER (Tue Jul 30 2024 - 14:45:40 PDT)

Amber Archive Jul 2024 by thread