Amber Archive Oct 2021: by author

Adrian Roitberg
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 (Mon Oct 25 2021 - 12:26:50 PDT)
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 (Mon Oct 25 2021 - 07:52:10 PDT)
Alessandro Contini
- [AMBER] buffer overflow in tleap, AmberTools21, gcc 9.3 (Fri Oct 01 2021 - 03:02:44 PDT)
Archana
- [AMBER] Regarding xleap error (Wed Oct 06 2021 - 08:17:25 PDT)
Athena N
- Re: [AMBER] Regarding area calculation of protein cavity (Thu Oct 28 2021 - 07:57:56 PDT)
- [AMBER] Regarding area calculation of protein cavity (Thu Oct 28 2021 - 04:12:15 PDT)
Ben Roberts
- Re: [AMBER] VDWAALS = ************* in minimization (Sat Oct 09 2021 - 11:13:41 PDT)
Bhat Zahoor
- [AMBER] How to handle Ca2+ ion with 8 coordination Geometry in lectin domain for MD simulation. (Thu Oct 28 2021 - 01:20:17 PDT)
Brian Radak
- Re: [AMBER] Automated capping of missing loops? (Mon Oct 18 2021 - 09:11:41 PDT)
- Re: [AMBER] Automated capping of missing loops? (Fri Oct 15 2021 - 10:52:48 PDT)
- [AMBER] Automated capping of missing loops? (Thu Oct 14 2021 - 13:54:34 PDT)
Carlos Simmerling
- Re: [AMBER] unable to get response from mailing list (Sat Oct 30 2021 - 06:29:41 PDT)
- Re: [AMBER] Regarding area calculation of protein cavity (Thu Oct 28 2021 - 09:41:38 PDT)
- Re: [AMBER] How to minimize a pdb format file in Amber 16 (Thu Oct 28 2021 - 05:40:04 PDT)
- Re: [AMBER] Parameters for non-standard residues (Mon Oct 18 2021 - 13:51:40 PDT)
- Re: [AMBER] Accelerated dissociation events in MD simulation by temperature increase? (Mon Oct 11 2021 - 12:40:09 PDT)
- Re: [AMBER] How to generate different velocities for same structure during equilibration (Mon Oct 11 2021 - 07:20:24 PDT)
- Re: [AMBER] How to turn H-bonding point charges (Mon Oct 11 2021 - 07:18:40 PDT)
- Re: [AMBER] VDWAALS = ************* in minimization (Sat Oct 09 2021 - 15:22:03 PDT)
- Re: [AMBER] How to set multiple positional restraints during minimization (Fri Oct 08 2021 - 08:34:47 PDT)
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? (Tue Oct 05 2021 - 04:27:03 PDT)
Cato, Lee
- [AMBER] Zn sim (Tue Oct 05 2021 - 07:05:10 PDT)
Cenk Andac
- [AMBER] How many complex trajectories for mmpbsa computations ? (Sun Oct 10 2021 - 13:20:30 PDT)
Chloe Jaiswal
- [AMBER] Calculating viscosity, thermal conductivity and self-diffusion coefficient (Fri Oct 08 2021 - 02:31:48 PDT)
Christian Seitz
- [AMBER] reasonable GIST griddim values (Sun Oct 24 2021 - 13:27:07 PDT)
Daniel Fowles
- [AMBER] Ambertools18 tleap scripts not working when run on Ambertools21 (Thu Oct 21 2021 - 04:21:32 PDT)
Daniel Hall
- [AMBER] ZAFF Simulation Error (Thu Oct 21 2021 - 13:48:27 PDT)
Daniel Roe
- Re: [AMBER] reasonable GIST griddim values (Mon Oct 25 2021 - 07:38:11 PDT)
- Re: [AMBER] Can I used AMBER 16 CPPTRAJ to perform dynamic cross correlation map? (Mon Oct 25 2021 - 07:31:47 PDT)
- Re: [AMBER] VDWAALS = ************* in minimization (Thu Oct 14 2021 - 07:32:33 PDT)
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? (Thu Oct 14 2021 - 07:21:14 PDT)
- Re: [AMBER] How to depict Atomic Fluctuations of a specific residue Versus Frames by CPPTRAJ (Thu Oct 14 2021 - 07:17:04 PDT)
- Re: [AMBER] [SPAM] Help with carbohydrate nomenclature (Fri Oct 08 2021 - 12:53:40 PDT)
- Re: [AMBER] Help with carbohydrate nomenclature (Fri Oct 08 2021 - 03:07:55 PDT)
- [AMBER] Help with carbohydrate nomenclature (Thu Oct 07 2021 - 16:09:28 PDT)
- Re: [AMBER] CPPTRAJ (Wed Oct 06 2021 - 09:18:47 PDT)
- Re: [AMBER] Distanced-based atom selection from the center of mass (Tue Oct 05 2021 - 07:03:45 PDT)
- Re: [AMBER] Restart/Reference file for targeted MD (Tue Oct 05 2021 - 05:47:08 PDT)
- Re: [AMBER] Cpptraj hbond criteria (Tue Oct 05 2021 - 05:43:48 PDT)
- Re: [AMBER] How to reshuffle traj frames (Sat Oct 02 2021 - 06:13:20 PDT)
- Re: [AMBER] Distanced-based atom selection from the center of mass (Sat Oct 02 2021 - 06:10:00 PDT)
David A Case
- Re: [AMBER] weired Ligand conformation during simulation (Sun Oct 31 2021 - 13:22:55 PDT)
- Re: [AMBER] unable to get response from mailing list (Sat Oct 30 2021 - 06:11:01 PDT)
- Re: [AMBER] weired Ligand conformation during simulation (Sat Oct 30 2021 - 06:06:45 PDT)
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces (Fri Oct 29 2021 - 14:25:26 PDT)
- Re: [AMBER] Regarding Amber20 installation (Fri Oct 29 2021 - 14:22:16 PDT)
- Re: [AMBER] Regarding Amber20 installation (Wed Oct 27 2021 - 14:19:31 PDT)
- Re: [AMBER] bug in pmemd/src/cuda/gpu.cpp line 2852? (Mon Oct 25 2021 - 13:56:50 PDT)
- Re: [AMBER] Fwd: Ambertools21 installation problems (Mon Oct 25 2021 - 06:42:28 PDT)
- Re: [AMBER] Fwd: Ambertools21 installation problems (Sun Oct 24 2021 - 16:41:37 PDT)
- Re: [AMBER] LINMIN ERROR (Sun Oct 24 2021 - 13:12:54 PDT)
- Re: [AMBER] Fwd: Ambertools21 installation problems (Sun Oct 24 2021 - 13:10:39 PDT)
- Re: [AMBER] How can I download amber 18？ (Sun Oct 24 2021 - 12:44:38 PDT)
- Re: [AMBER] Query regarding not integral charge in RNA (Thu Oct 21 2021 - 15:46:13 PDT)
- Re: [AMBER] Query regarding not integral charge in RNA (Thu Oct 21 2021 - 11:17:23 PDT)
- Re: [AMBER] Parameters for non-standard residues (Wed Oct 20 2021 - 09:22:50 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Wed Oct 20 2021 - 09:17:34 PDT)
- Re: [AMBER] How I can Remove dna form .rst files (Tue Oct 19 2021 - 05:46:24 PDT)
- Re: [AMBER] Parameters for non-standard residues (Mon Oct 18 2021 - 13:54:06 PDT)
- Re: [AMBER] Automated capping of missing loops? (Mon Oct 18 2021 - 13:44:38 PDT)
- Re: [AMBER] Regarding entropy calculations in MMPBSA.py when enthalpy is either from GBSA or PBSA? (Sun Oct 17 2021 - 03:34:32 PDT)
- Re: [AMBER] Unwanted water protein interaction (Sun Oct 17 2021 - 03:30:08 PDT)
- Re: [AMBER] Rotation Matrix (Sat Oct 16 2021 - 04:40:51 PDT)
- Re: [AMBER] FixCondaShebang persists (Sat Oct 16 2021 - 04:38:26 PDT)
- Re: [AMBER] calculate potential energies with imin=5 (Fri Oct 15 2021 - 05:09:02 PDT)
- Re: [AMBER] Problems with mm_pbsa tests (Fri Oct 15 2021 - 05:01:30 PDT)
- Re: [AMBER] Protein-protein binding free energy MMPBSA (Thu Oct 14 2021 - 18:26:58 PDT)
- Re: [AMBER] Automated capping of missing loops? (Thu Oct 14 2021 - 18:19:23 PDT)
- Re: [AMBER] FixCondaShebang persists (Thu Oct 14 2021 - 18:06:59 PDT)
- Re: [AMBER] FixCondaShebang persists (Thu Oct 14 2021 - 08:41:12 PDT)
- Re: [AMBER] FixCondaShebang persists (Thu Oct 14 2021 - 06:15:16 PDT)
- Re: [AMBER] Problems with mm_pbsa tests (Thu Oct 14 2021 - 06:13:50 PDT)
- Re: [AMBER] Explicit water molecules in MMPBSA.py: OPC vs TIP3P (Thu Oct 14 2021 - 05:58:38 PDT)
- Re: [AMBER] buffer overflow in tleap, AmberTools21, gcc 9.3 (Wed Oct 13 2021 - 08:55:28 PDT)
- Re: [AMBER] Amber20/AmberTools21 Installation Test Errors (Wed Oct 13 2021 - 06:16:07 PDT)
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? (Tue Oct 12 2021 - 13:31:38 PDT)
- Re: [AMBER] FixCondaShebang persists (Tue Oct 12 2021 - 13:16:25 PDT)
- Re: [AMBER] Rotation Matrix (Sun Oct 10 2021 - 05:29:21 PDT)
- Re: [AMBER] parameters for ions in Amber (Thu Oct 07 2021 - 04:39:04 PDT)
- Re: [AMBER] Error installing amber macOS M1 (Tue Oct 05 2021 - 14:23:08 PDT)
- Re: [AMBER] FixCondaShebang Error (Tue Oct 05 2021 - 05:44:29 PDT)
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? (Tue Oct 05 2021 - 05:40:42 PDT)
- Re: [AMBER] Ligand is unstable in simulations (Mon Oct 04 2021 - 07:06:09 PDT)
- Re: [AMBER] Question of Amber_ Sasaki (Mon Oct 04 2021 - 05:26:40 PDT)
- Re: [AMBER] How to combine the coordinate and parm7 files of the glycolipid into a protein complex system (Sat Oct 02 2021 - 05:23:44 PDT)
- Re: [AMBER] Error installing amber macOS M1 (Fri Oct 01 2021 - 05:13:42 PDT)
Debarati DasGupta
- [AMBER] MMGBSA error help (Fri Oct 15 2021 - 06:50:37 PDT)
Delwakkada Liyanage, Senal Dinuka
- [AMBER] Restraining ligand for TI (Tue Oct 19 2021 - 15:34:13 PDT)
Divya Rai
- [AMBER] Fwd: Constant pH MD simulation (Sat Oct 30 2021 - 12:21:19 PDT)
- [AMBER] Constant pH MD simulation (Fri Oct 29 2021 - 07:19:15 PDT)
Dow Hurst
- Re: [AMBER] Regarding Amber20 installation (Thu Oct 28 2021 - 21:46:27 PDT)
Dr. Anselm Horn
- Re: [AMBER] mm_pbsa and MMPBSA.py (Thu Oct 28 2021 - 08:21:16 PDT)
- Re: [AMBER] How to handle Ca2+ ion with 8 coordination Geometry in lectin domain for MD simulation. (Thu Oct 28 2021 - 04:35:18 PDT)
- Re: [AMBER] Regarding area calculation of protein cavity (Thu Oct 28 2021 - 04:19:47 PDT)
- Re: [AMBER] Atom type does not shown up in PARMCHK.DAT (Wed Oct 27 2021 - 00:36:35 PDT)
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 (Mon Oct 25 2021 - 02:32:36 PDT)
- Re: [AMBER] Fwd: topology file and co-ordinate file making by amber tool (gaff.dat) (Fri Oct 22 2021 - 05:20:52 PDT)
- Re: [AMBER] Parameters for non-standard residues (Thu Oct 21 2021 - 07:21:57 PDT)
- Re: [AMBER] Fwd: topology file and co-ordinate file making by amber tool (gaff.dat) (Wed Oct 20 2021 - 07:13:19 PDT)
- Re: [AMBER] Fwd: topology file and co-ordinate file making by amber tool (gaff.dat) (Wed Oct 20 2021 - 03:26:23 PDT)
- Re: [AMBER] Error with PDB4AMBER (Tue Oct 19 2021 - 12:43:08 PDT)
- Re: [AMBER] Regarding xleap error (Wed Oct 06 2021 - 08:53:12 PDT)
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? (Tue Oct 05 2021 - 01:51:03 PDT)
- [AMBER] Atomistic Simulation Center - Invitation to virtual inauguration symposium (Mon Oct 04 2021 - 05:00:37 PDT)
Erdem Yeler
- [AMBER] Amber21 installation using Docker will be Parallel or Serial? (Tue Oct 26 2021 - 06:32:10 PDT)
Gao Zhenting
- [AMBER] Meaning of 3D-RISM output files? (Sun Oct 17 2021 - 03:42:43 PDT)
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? (Tue Oct 05 2021 - 08:49:50 PDT)
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? (Tue Oct 05 2021 - 04:04:07 PDT)
- [AMBER] How to superpose the solvated box to the original pdb structure? (Mon Oct 04 2021 - 20:32:48 PDT)
German P. Barletta
- Re: [AMBER] FixCondaShebang persists (Fri Oct 15 2021 - 12:54:15 PDT)
- Re: [AMBER] FixCondaShebang persists (Thu Oct 14 2021 - 12:40:30 PDT)
- Re: [AMBER] FixCondaShebang persists (Thu Oct 14 2021 - 00:42:48 PDT)
- [AMBER] FixCondaShebang persists (Mon Oct 11 2021 - 04:10:37 PDT)
Gustavo Seabra
- [AMBER] Restraining the distance between two groups of residues? (Fri Oct 08 2021 - 11:34:46 PDT)
Hecate Me
- [AMBER] How can I download amber 18？ (Sat Oct 23 2021 - 01:09:25 PDT)
Hector A. Baldoni
- Re: [AMBER] How to minimize a pdb format file in Amber 16 (Thu Oct 28 2021 - 05:36:13 PDT)
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 (Mon Oct 25 2021 - 05:57:02 PDT)
- Re: [AMBER] Help with carbohydrate nomenclature (Thu Oct 07 2021 - 19:34:10 PDT)
James Kress
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 (Mon Oct 25 2021 - 12:48:46 PDT)
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 (Mon Oct 25 2021 - 11:53:57 PDT)
- Re: [AMBER] Maximizing GROMACS Throughput with Multiple Simulations per GPU Using MPS and MIG (Fri Oct 22 2021 - 11:40:40 PDT)
- [AMBER] Maximizing GROMACS Throughput with Multiple Simulations per GPU Using MPS and MIG (Thu Oct 21 2021 - 13:29:16 PDT)
Jan Brezovsky
- [AMBER] Several postdoctoral positions available in EU (Mon Oct 25 2021 - 09:19:37 PDT)
Jason Hogrefe
- Re: [AMBER] Maximizing GROMACS Throughput with Multiple Simulations per GPU Using MPS and MIG (Fri Oct 22 2021 - 10:07:01 PDT)
Jason Swails
- Re: [AMBER] Constant pH MD simulation (Fri Oct 29 2021 - 08:22:21 PDT)
- Re: [AMBER] {SPAM?} trajectory of mutation generation (Geng Dong) (Fri Oct 29 2021 - 06:27:25 PDT)
- Re: [AMBER] Amber21 installation using Docker will be Parallel or Serial? (Fri Oct 29 2021 - 06:05:34 PDT)
- Re: [AMBER] Ambertools18 tleap scripts not working when run on Ambertools21 (Thu Oct 21 2021 - 05:47:35 PDT)
- Re: [AMBER] Automated capping of missing loops? (Mon Oct 18 2021 - 07:32:16 PDT)
- Re: [AMBER] parmed for two atom type with the same LJ parameters (Thu Oct 14 2021 - 13:29:14 PDT)
Kellon Belfon
- Re: [AMBER] bug in pmemd/src/cuda/gpu.cpp line 2852? (Tue Oct 26 2021 - 12:54:03 PDT)
Lara rajam
- [AMBER] Reg: Cpptraj-Hierarchical Agglomerative Reference paper for methodology and result analysis (Mon Oct 25 2021 - 18:01:23 PDT)
Lennart Gundelach
- Re: [AMBER] Explicit water molecules in MMPBSA.py: OPC vs TIP3P (Thu Oct 14 2021 - 00:58:38 PDT)
Li,Haoxi
- [AMBER] Multiple Replicate Trajectories (Thu Oct 28 2021 - 08:21:17 PDT)
Liao
- [AMBER] Regarding entropy calculations in MMPBSA.py when enthalpy is either from GBSA or PBSA? (Sat Oct 16 2021 - 09:43:52 PDT)
- Re: [AMBER] How to minimize average structure (pdb) using Amber 16 (Wed Oct 13 2021 - 11:05:27 PDT)
- [AMBER] Accelerated dissociation events in MD simulation by temperature increase? (Mon Oct 11 2021 - 12:33:53 PDT)
- Re: [AMBER] How many complex trajectories for mmpbsa computations ? (Sun Oct 10 2021 - 16:39:36 PDT)
- Re: [AMBER] How many complex trajectories for mmpbsa computations ? (Sun Oct 10 2021 - 16:07:44 PDT)
Mac Kevin Braza
- Re: [AMBER] cpptraj RMSD reference (Sat Oct 16 2021 - 16:28:02 PDT)
- [AMBER] cpptraj RMSD reference (Sat Oct 16 2021 - 16:16:54 PDT)
Maghsoud, Yazdan
- [AMBER] How to depict Atomic Fluctuations of a specific residue Versus Frames by CPPTRAJ (Tue Oct 12 2021 - 14:23:11 PDT)
Marawan Hussien
- [AMBER] Postdoctoral fellowship Computational Drug Discovery (Fri Oct 01 2021 - 10:50:10 PDT)
Maria Nagan
- Re: [AMBER] ZAFF Simulation Error (Tue Oct 26 2021 - 17:11:26 PDT)
- Re: [AMBER] Query regarding ZAFF Modeling Tutorial (Tue Oct 26 2021 - 17:06:41 PDT)
Matias Machado
- Re: [AMBER] Maximizing GROMACS Throughput with Multiple Simulations per GPU Using MPS and MIG (Fri Oct 22 2021 - 08:35:56 PDT)
- Re: [AMBER] Automated capping of missing loops? (Sun Oct 17 2021 - 13:26:37 PDT)
Matthew Guberman-Pfeffer
- [AMBER] How to Compare RDFs for different systems (Sat Oct 30 2021 - 14:15:01 PDT)
- [AMBER] Problem measuring angle in CPPTRAJ (Sat Oct 30 2021 - 13:14:13 PDT)
- [AMBER] Wrong Angel Given by Cpptraj? (Fri Oct 29 2021 - 03:38:16 PDT)
- Re: [AMBER] How is correlation computed in cpptraj (Mon Oct 25 2021 - 08:07:22 PDT)
- [AMBER] How is correlation computed in cpptraj (Mon Oct 25 2021 - 01:45:55 PDT)
- Re: [AMBER] {SPAM?} trajectory of mutation generation (Geng Dong) (Sun Oct 17 2021 - 05:51:58 PDT)
- [AMBER] How to characterize Binding Sites with cpptraj (Wed Oct 13 2021 - 11:07:47 PDT)
- Re: [AMBER] Accelerated dissociation events in MD simulation by temperature increase? (Mon Oct 11 2021 - 12:49:06 PDT)
- Re: [AMBER] How to turn H-bonding point charges (Mon Oct 11 2021 - 09:23:41 PDT)
- [AMBER] How to turn H-bonding point charges (Mon Oct 11 2021 - 05:59:05 PDT)
- [AMBER] How to reshuffle traj frames (Fri Oct 01 2021 - 20:51:41 PDT)
Małgorzata Kogut
- [AMBER] parameters for ions (Thu Oct 07 2021 - 00:14:01 PDT)
- [AMBER] parameters for ions in Amber (Wed Oct 06 2021 - 23:57:58 PDT)
Midhun K Madhu
- [AMBER] Ligand is unstable in simulations (Mon Oct 04 2021 - 05:10:24 PDT)
Mohamed Aboelnga
- [AMBER] Restraint COM between two proteins (Tue Oct 05 2021 - 06:19:23 PDT)
mohamed marzouk
- Re: [AMBER] Rotation Matrix (Thu Oct 21 2021 - 16:55:25 PDT)
- Re: [AMBER] Unwanted water protein interaction (Sun Oct 17 2021 - 03:34:20 PDT)
- [AMBER] Unwanted water protein interaction (Sat Oct 16 2021 - 08:15:04 PDT)
- Re: [AMBER] Rotation Matrix (Sat Oct 16 2021 - 05:00:02 PDT)
- Re: [AMBER] Rotation Matrix (Sat Oct 16 2021 - 03:09:05 PDT)
- [AMBER] Mutation by pdb4amber (Fri Oct 15 2021 - 05:41:50 PDT)
- Re: [AMBER] Rotation Matrix (Sun Oct 10 2021 - 05:36:08 PDT)
- [AMBER] Rotation Matrix (Sat Oct 09 2021 - 18:58:13 PDT)
Nagar, Hemant
- Re: [AMBER] Parameters for non-standard residues (Tue Oct 19 2021 - 13:44:59 PDT)
- [AMBER] Parameters for non-standard residues (Mon Oct 18 2021 - 13:07:04 PDT)
- [AMBER] Symmetrical voids during heating stage (Wed Oct 06 2021 - 16:38:09 PDT)
nali
- [AMBER] The silver ion parameter (Tue Oct 05 2021 - 10:01:14 PDT)
neildancer
- Re: [AMBER] How to combine the coordinate and parm7 files of the glycolipid into a protein complex system (Sun Oct 03 2021 - 07:33:49 PDT)
- Re: [AMBER] How to combine the coordinate and parm7 files of the glycolipid into a protein complex system (Fri Oct 01 2021 - 21:09:32 PDT)
Pengfei Li
- Re: [AMBER] parmed for 12-6-4 LJ (Geng Dong) (Sat Oct 02 2021 - 17:47:19 PDT)
priya murugan
- Re: [AMBER] How to minimize a pdb format file in Amber 16 (Thu Oct 28 2021 - 17:00:00 PDT)
- [AMBER] How to minimize a pdb format file in Amber 16 (Wed Oct 27 2021 - 21:52:36 PDT)
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 (Tue Oct 26 2021 - 03:15:58 PDT)
- Re: [AMBER] Can I used AMBER 16 CPPTRAJ to perform dynamic cross correlation map? (Mon Oct 25 2021 - 20:00:09 PDT)
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 (Mon Oct 25 2021 - 06:28:52 PDT)
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 (Mon Oct 25 2021 - 03:17:17 PDT)
- [AMBER] Can I used AMBER 16 CPPTRAJ to perform dynamic cross correlation map? (Sun Oct 24 2021 - 20:35:21 PDT)
- [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 (Sun Oct 24 2021 - 20:27:09 PDT)
- [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 (Sun Oct 24 2021 - 19:23:06 PDT)
- [AMBER] How to minimize average structure (pdb) using Amber 16 (Wed Oct 13 2021 - 09:23:48 PDT)
Qinghua Liao
- [AMBER] parmed for two atom type with the same LJ parameters (Thu Oct 14 2021 - 05:27:33 PDT)
Rafael Nunes
- Re: [AMBER] [SPAM] Help with carbohydrate nomenclature (Fri Oct 08 2021 - 09:22:15 PDT)
Rafał Madaj
- Re: [AMBER] Restart/Reference file for targeted MD (Tue Oct 05 2021 - 06:01:25 PDT)
Rajarshi Roy
- Re: [AMBER] Regarding Amber20 installation (Wed Oct 27 2021 - 21:36:01 PDT)
- [AMBER] Regarding Amber20 installation (Tue Oct 26 2021 - 06:59:33 PDT)
Rana Rehan Khalid
- [AMBER] MMPBSA (Unable to read script file because of error: invalid option argument "-O") (Sat Oct 30 2021 - 15:40:00 PDT)
- [AMBER] Freeze DNA during simulation. (Wed Oct 20 2021 - 12:34:43 PDT)
- [AMBER] How I can Remove dna form .rst files (Mon Oct 18 2021 - 14:00:16 PDT)
- [AMBER] Protein-protein binding free energy MMPBSA (Thu Oct 14 2021 - 15:43:43 PDT)
- Re: [AMBER] CPPTRAJ (Wed Oct 06 2021 - 10:55:54 PDT)
- Re: [AMBER] CPPTRAJ (Wed Oct 06 2021 - 09:47:59 PDT)
- Re: [AMBER] CPPTRAJ (Wed Oct 06 2021 - 09:41:52 PDT)
- [AMBER] CPPTRAJ (Wed Oct 06 2021 - 09:11:45 PDT)
Rangarajan, Amith
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Wed Oct 20 2021 - 09:44:56 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Tue Oct 19 2021 - 12:08:42 PDT)
- Re: [AMBER] Error with PDB4AMBER (Tue Oct 19 2021 - 11:51:30 PDT)
- [AMBER] Error with PDB4AMBER (Tue Oct 19 2021 - 11:28:29 PDT)
Ravi Abrol
- Re: [AMBER] Problems with mm_pbsa tests (Thu Oct 14 2021 - 23:12:35 PDT)
- Re: [AMBER] Amber20/AmberTools21 Installation Test Errors (Thu Oct 14 2021 - 01:03:24 PDT)
- [AMBER] Amber20/AmberTools21 Installation Test Errors (Wed Oct 13 2021 - 00:23:21 PDT)
Reyes Nuñez Franco
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? (Tue Oct 05 2021 - 04:21:06 PDT)
Richard Kullmann
- [AMBER] calculate potential energies with imin=5 (Fri Oct 15 2021 - 02:11:06 PDT)
Robert Molt
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 (Mon Oct 25 2021 - 12:54:17 PDT)
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 (Mon Oct 25 2021 - 12:31:04 PDT)
- [AMBER] On Ion Distribution and "Replicates" (Mon Oct 11 2021 - 07:26:39 PDT)
Rodrigo da Silva Bitzer
- Re: [AMBER] Error installing amber macOS M1 (Tue Oct 05 2021 - 14:58:31 PDT)
- Re: [AMBER] Error installing amber macOS M1 (Tue Oct 05 2021 - 11:56:19 PDT)
Rohanizeidanlou, Sahar
- [AMBER] Atom type does not shown up in PARMCHK.DAT (Tue Oct 26 2021 - 16:38:13 PDT)
Sadaf Rani
- Re: [AMBER] weired Ligand conformation during simulation (Sun Oct 31 2021 - 11:38:09 PDT)
- [AMBER] unable to get response from mailing list (Fri Oct 29 2021 - 19:20:21 PDT)
- [AMBER] weired Ligand conformation during simulation (Fri Oct 29 2021 - 19:10:22 PDT)
- [AMBER] RMSD of residues within 3A of ligand (Fri Oct 22 2021 - 06:56:41 PDT)
- [AMBER] How to generate different velocities for same structure during equilibration (Mon Oct 11 2021 - 04:20:32 PDT)
- [AMBER] VDWAALS = ************* in minimization (Sat Oct 09 2021 - 10:59:56 PDT)
- [AMBER] How to set multiple positional restraints during minimization (Fri Oct 08 2021 - 08:25:06 PDT)
Saikat Pal
- [AMBER] Query regarding ZAFF Modeling Tutorial (Fri Oct 22 2021 - 14:58:03 PDT)
- Re: [AMBER] Query regarding not integral charge in RNA (Thu Oct 21 2021 - 12:24:34 PDT)
- [AMBER] Query regarding not integral charge in RNA (Thu Oct 21 2021 - 08:44:38 PDT)
- [AMBER] Query regarding missing oxygen atom in RNA sequence (Wed Oct 20 2021 - 15:10:26 PDT)
Sam Walsworth (Researcher)
- [AMBER] Organometallic RESP charge derivation for use with AmberTools (Tue Oct 26 2021 - 11:58:00 PDT)
Satya Pal Singh
- [AMBER] FixCondaShebang Error (Mon Oct 04 2021 - 23:15:37 PDT)
Shiho Ohno
- [AMBER] Tohoku Medical and Pharmaceutical University Sasaki　It's resolved (Wed Oct 06 2021 - 17:45:36 PDT)
- [AMBER] Question of Amber_ Sasaki (Wed Oct 06 2021 - 17:08:07 PDT)
- [AMBER] Question of Amber_ Sasaki (Mon Oct 04 2021 - 01:34:16 PDT)
Song, Lin
- Re: [AMBER] parmed for two atom type with the same LJ parameters (Thu Oct 14 2021 - 08:44:21 PDT)
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? (Mon Oct 04 2021 - 21:33:34 PDT)
Stephan Schott
- Re: [AMBER] FixCondaShebang persists (Thu Oct 14 2021 - 09:02:37 PDT)
- Re: [AMBER] FixCondaShebang persists (Thu Oct 14 2021 - 07:05:17 PDT)
Suitian Lai
- [AMBER] What is the default value of tishake (Mon Oct 18 2021 - 07:48:19 PDT)
Sumon Naskar
- [AMBER] LINMIN ERROR (Sat Oct 23 2021 - 13:07:25 PDT)
Thomas Cheatham
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 (Mon Oct 25 2021 - 13:21:11 PDT)
- Re: [AMBER] How many complex trajectories for mmpbsa computations ? (Sun Oct 10 2021 - 15:33:15 PDT)
- Re: [AMBER] Symmetrical voids during heating stage (Wed Oct 06 2021 - 21:22:00 PDT)
- Re: [AMBER] Symmetrical voids during heating stage (Wed Oct 06 2021 - 20:48:50 PDT)
Thomas Zeiser
- [AMBER] bug in pmemd/src/cuda/gpu.cpp line 2852? (Mon Oct 25 2021 - 12:47:41 PDT)
thomas.zeiser.rrze.uni-erlangen.de
- Re: [AMBER] bug in pmemd/src/cuda/gpu.cpp line 2852? (Mon Oct 25 2021 - 23:19:51 PDT)
tluchko
- Re: [AMBER] Meaning of 3D-RISM output files? (Mon Oct 18 2021 - 10:52:10 PDT)
Umesh Roy
- [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces (Wed Oct 27 2021 - 00:08:33 PDT)
- Re: [AMBER] Distanced-based atom selection from the center of mass (Mon Oct 11 2021 - 02:29:59 PDT)
- [AMBER] Distanced-based atom selection from the center of mass (Sat Oct 02 2021 - 05:01:20 PDT)
Vaibhav Dixit
- Re: [AMBER] Organometallic RESP charge derivation for use with AmberTools (Tue Oct 26 2021 - 18:34:16 PDT)
- [AMBER] Amber20 benchmarks for RTX A4000 (Fri Oct 22 2021 - 09:14:00 PDT)
- [AMBER] TI for DG when only cofactor charge changes (Sat Oct 02 2021 - 23:21:35 PDT)
Victor Nazarychev
- Re: [AMBER] Fwd: Ambertools21 installation problems (Wed Oct 27 2021 - 02:37:29 PDT)
- Re: [AMBER] Fwd: Ambertools21 installation problems (Mon Oct 25 2021 - 07:36:28 PDT)
- Re: [AMBER] Fwd: Ambertools21 installation problems (Mon Oct 25 2021 - 01:53:39 PDT)
- [AMBER] Fwd: Ambertools21 installation problems (Sat Oct 23 2021 - 05:46:43 PDT)
Vinicius Wilian Cruzeiro
- Re: [AMBER] Constant pH MD simulation (Fri Oct 29 2021 - 08:24:22 PDT)
- Re: [AMBER] Error with PDB4AMBER (Tue Oct 19 2021 - 11:33:30 PDT)
vivek rabha
- Re: [AMBER] Fwd: topology file and co-ordinate file making by amber tool (gaff.dat) (Wed Oct 20 2021 - 22:06:44 PDT)
- Re: [AMBER] Fwd: topology file and co-ordinate file making by amber tool (gaff.dat) (Wed Oct 20 2021 - 03:41:09 PDT)
- [AMBER] Fwd: topology file and co-ordinate file making by amber tool (gaff.dat) (Wed Oct 20 2021 - 02:58:09 PDT)
zmatovic.kg.ac.rs
- Re: [AMBER] mm_pbsa and MMPBSA.py (Thu Oct 28 2021 - 10:06:16 PDT)
- [AMBER] mm_pbsa and MMPBSA.py (Thu Oct 28 2021 - 06:57:15 PDT)
东庚
- [AMBER] trajectory of mutation generation (Geng Dong) (Sun Oct 17 2021 - 02:32:48 PDT)

Amber Archive Oct 2021 by author