Amber Archive Jul 2021: by author

ABDUL BASIT
- [AMBER] Error in MC/MD+TI (Sat Jul 10 2021 - 22:30:29 PDT)
Abdul-Rashid III Sampaco
- [AMBER] CompEL in AMBER (Sun Jul 04 2021 - 22:10:21 PDT)
ABEL Stephane
- Re: [AMBER] Building Forcefield for Glycolipid Molecule (Tue Jul 27 2021 - 09:28:05 PDT)
- Re: [AMBER] Building Forcefield for Glycolipid Molecule (Wed Jul 21 2021 - 02:35:16 PDT)
- Re: [AMBER] Building Forcefield for Glycolipid Molecule (Mon Jul 19 2021 - 01:56:12 PDT)
Adrian Roitberg
- Re: [AMBER] SEBOMD topology issue (Mon Jul 26 2021 - 12:08:52 PDT)
- Re: [AMBER] The protonation state model of TYR in CpHMD (Mon Jul 19 2021 - 14:26:44 PDT)
- Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large (Thu Jul 15 2021 - 13:35:35 PDT)
- Re: [AMBER] Fortran runtime error: Bad value during integer read (Fri Jul 09 2021 - 06:51:33 PDT)
- Re: [AMBER] Segmentation Fault (Fri Jul 02 2021 - 13:33:48 PDT)
- Re: [AMBER] Segmentation Fault (Fri Jul 02 2021 - 11:37:42 PDT)
amin sagar
- [AMBER] Using ParmEd to convert gromacs truncated octahedron box to amber (Sat Jul 03 2021 - 08:13:25 PDT)
Amir Zeb
- [AMBER] How to assign/apply the negative lateral pressure to lipid bilayer in AMBER? (Sun Jul 04 2021 - 22:36:04 PDT)
Amit Sharma (Asstt. Prof., MCARS)
- [AMBER] Displacement of coordinated Zn during the simulation (Wed Jul 21 2021 - 08:27:08 PDT)
angad sharma
- [AMBER] Convergence issue in 1drism (Tue Jul 27 2021 - 11:51:32 PDT)
- [AMBER] sampling issue (Sun Jul 18 2021 - 11:28:11 PDT)
ankita mehta
- [AMBER] Running in a loop (Thu Jul 08 2021 - 07:37:40 PDT)
- [AMBER] Scripting (Thu Jul 08 2021 - 05:12:14 PDT)
Anthony Nash
- Re: [AMBER] Missing mtkpp directory after installation of AmberTools21 (Fri Jul 23 2021 - 08:38:17 PDT)
- Re: [AMBER] Missing mtkpp directory after installation of AmberTools21 (Fri Jul 23 2021 - 02:26:25 PDT)
- Re: [AMBER] Missing mtkpp directory after installation of AmberTools21 (Wed Jul 21 2021 - 06:10:41 PDT)
- Re: [AMBER] Missing mtkpp directory after installation of AmberTools21 (Tue Jul 20 2021 - 07:55:59 PDT)
- [AMBER] Missing mtkpp directory after installation of AmberTools21 (Mon Jul 19 2021 - 06:37:03 PDT)
BAS071501 Anupama KP PhD ANS
- [AMBER] How can I use desmond trajectory in Amber (Sat Jul 03 2021 - 09:08:12 PDT)
Blake Armstrong
- [AMBER] Simulating dehydrated bilayers with a vacuum above and below (Fri Jul 23 2021 - 00:50:52 PDT)
Carlos Simmerling
- Re: [AMBER] cudaMemcpy GpuBuffer ERROR (Mon Jul 19 2021 - 08:03:42 PDT)
- Re: [AMBER] sampling issue (Mon Jul 19 2021 - 07:14:07 PDT)
- Re: [AMBER] Structure alteration and shortening of loops using xleap (Mon Jul 19 2021 - 07:10:51 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer ERROR (Mon Jul 19 2021 - 07:08:04 PDT)
- Re: [AMBER] Where are the parameters for the SCREEN RADII section in prmtop (Mon Jul 19 2021 - 05:14:02 PDT)
- Re: [AMBER] Where are the parameters for the SCREEN RADII section in prmtop (Tue Jul 13 2021 - 13:27:25 PDT)
- Re: [AMBER] DNA Strand Broken after minimization (Tue Jul 13 2021 - 10:13:20 PDT)
- Re: [AMBER] vlimit exceeded for some step (Mon Jul 12 2021 - 07:44:24 PDT)
- Re: [AMBER] Stop PMEMD Terminated Aborally. Tutorial 1.7 An Amber Lipid Force Field Tutorial: Lipid14. (Thu Jul 08 2021 - 06:18:42 PDT)
- Re: [AMBER] Scripting (Thu Jul 08 2021 - 05:17:21 PDT)
Charo del Genio
- Re: [AMBER] Reweighting aMD conformations (Tue Jul 13 2021 - 06:30:48 PDT)
- Re: [AMBER] MCPB.py tutorial issues (Fri Jul 09 2021 - 09:44:54 PDT)
Cruzeiro, Vinicius
- Re: [AMBER] Cphstats unable to read cpin (Tue Jul 27 2021 - 20:23:56 PDT)
- Re: [AMBER] Cphstats unable to read cpin (Tue Jul 27 2021 - 17:43:15 PDT)
- Re: [AMBER] Cphstats unable to read cpin (Sun Jul 25 2021 - 23:30:18 PDT)
- Re: [AMBER] fitpkaeo.py not reading input from cestats (Sat Jul 17 2021 - 18:35:58 PDT)
- Re: [AMBER] fitpkaeo.py not reading input from cestats (Sat Jul 17 2021 - 18:17:11 PDT)
Daniel Konstantinovsky
- Re: [AMBER] SEBOMD topology issue (Mon Jul 26 2021 - 12:21:44 PDT)
- [AMBER] SEBOMD topology issue (Mon Jul 26 2021 - 12:03:29 PDT)
- [AMBER] velocity trajectory output (Mon Jul 19 2021 - 12:53:50 PDT)
Daniel Roe
- Re: [AMBER] pc1 vs pc2 principal component analysis (Tue Jul 20 2021 - 11:10:40 PDT)
- Re: [AMBER] [cluster] Not all arguments handled: [ sil Sil avgout Avg avgfmt restart ] (Tue Jul 20 2021 - 09:12:44 PDT)
- Re: [AMBER] Ligand clustering input .pdb file. (Tue Jul 20 2021 - 09:06:44 PDT)
- Re: [AMBER] adding counterions in cpptraj (Tue Jul 20 2021 - 08:43:40 PDT)
- Re: [AMBER] velocity trajectory output (Tue Jul 20 2021 - 08:41:06 PDT)
- Re: [AMBER] Error:[cluster] Not all arguments handled: [ sil Sil avgout Avg avgfmt restart ] (Thu Jul 15 2021 - 08:52:27 PDT)
- Re: [AMBER] [cluster] Not all arguments handled: [ sil Sil avgout Avg avgfmt restart ] (Thu Jul 15 2021 - 08:48:17 PDT)
- Re: [AMBER] Help with imagining curled protein (Tue Jul 13 2021 - 10:06:10 PDT)
- Re: [AMBER] PCA inconsistency on number of frames (Tue Jul 13 2021 - 06:31:24 PDT)
- Re: [AMBER] Questions about dPCA. (Tue Jul 13 2021 - 06:20:10 PDT)
- Re: [AMBER] Estimating protein-protein interactions (Tue Jul 06 2021 - 06:32:42 PDT)
- Re: [AMBER] Cluster RMSD (Tue Jul 06 2021 - 06:14:45 PDT)
- Re: [AMBER] A question for cpptraj cluster command (Tue Jul 06 2021 - 06:00:27 PDT)
- Re: [AMBER] How can I use desmond trajectory in Amber (Sat Jul 03 2021 - 09:39:13 PDT)
David A Case
- Re: [AMBER] questions about unbond parameters (Sat Jul 31 2021 - 05:11:31 PDT)
- Re: [AMBER] N_OF_BONDS colvar and PBC (Fri Jul 30 2021 - 18:25:01 PDT)
- Re: [AMBER] unexpected missing parameters for protein atoms? (Fri Jul 30 2021 - 06:03:47 PDT)
- Re: [AMBER] questions about unbond parameters (Fri Jul 30 2021 - 05:52:42 PDT)
- Re: [AMBER] Error message (Thu Jul 29 2021 - 10:55:29 PDT)
- Re: [AMBER] Physical chemistry question regarding entropy calculations in ligand-receptor system (Thu Jul 29 2021 - 04:59:46 PDT)
- Re: [AMBER] questions about unbond parameters (Thu Jul 29 2021 - 04:54:42 PDT)
- Re: [AMBER] Installing AmberTools with C++11 support (Wed Jul 28 2021 - 04:49:08 PDT)
- Re: [AMBER] questions about unbond parameters (Wed Jul 28 2021 - 04:40:20 PDT)
- Re: [AMBER] Convergence issue in 1drism (Tue Jul 27 2021 - 14:16:08 PDT)
- Re: [AMBER] Include specific solvent in constant pH MD simulation by CPHFIRST_SOL (Sun Jul 25 2021 - 05:24:03 PDT)
- Re: [AMBER] gpu error (Sat Jul 24 2021 - 18:31:40 PDT)
- Re: [AMBER] gpu error (Sat Jul 24 2021 - 04:37:33 PDT)
- Re: [AMBER] Regarding SHAKE Parameter (Fri Jul 23 2021 - 06:17:25 PDT)
- Re: [AMBER] Gas phase Simulations (Wed Jul 21 2021 - 06:57:07 PDT)
- Re: [AMBER] 3D-RISM in amber20 (Tue Jul 20 2021 - 18:21:09 PDT)
- Re: [AMBER] Gas phase Simulations (Tue Jul 20 2021 - 18:06:57 PDT)
- Re: [AMBER] tleap does not recognize inosine (Tue Jul 20 2021 - 18:03:19 PDT)
- Re: [AMBER] tleap does not recognize inosine (Tue Jul 20 2021 - 08:10:56 PDT)
- Re: [AMBER] Where are the parameters for the SCREEN RADII section in prmtop (Tue Jul 20 2021 - 08:03:51 PDT)
- Re: [AMBER] velocity trajectory output (Mon Jul 19 2021 - 18:25:16 PDT)
- Re: [AMBER] Missing mtkpp directory after installation of AmberTools21 (Mon Jul 19 2021 - 09:32:03 PDT)
- Re: [AMBER] To build a single covalent bond in a protein-ligand complex using AMBER18. (Mon Jul 19 2021 - 09:15:39 PDT)
- Re: [AMBER] pdb4amber (Fri Jul 16 2021 - 08:12:00 PDT)
- Re: [AMBER] Amber Tutorial for QM/MM/MD simulations (Fri Jul 16 2021 - 07:29:39 PDT)
- Re: [AMBER] Question of Amber_ Sasaki (Wed Jul 14 2021 - 19:25:53 PDT)
- Re: [AMBER] DNA Strand Broken after minimization (Tue Jul 13 2021 - 15:15:37 PDT)
- Re: [AMBER] Is Amber18 compatible with AmberTools21 (Tue Jul 13 2021 - 11:29:36 PDT)
- Re: [AMBER] installation error: /usr/bin/ld: final link failed: Nonrepresentable section on output (Mon Jul 12 2021 - 06:33:30 PDT)
- Re: [AMBER] installation error: /usr/bin/ld: final link failed: Nonrepresentable section on output (Mon Jul 12 2021 - 06:30:18 PDT)
- Re: [AMBER] installation error: /usr/bin/ld: final link failed: Nonrepresentable section on output (Sun Jul 11 2021 - 12:52:47 PDT)
- Re: [AMBER] old PREP-specified impropers (Sun Jul 11 2021 - 12:44:48 PDT)
- Re: [AMBER] Fortran runtime error: Bad value during integer read (Fri Jul 09 2021 - 10:11:17 PDT)
- Re: [AMBER] Stop PMEMD Terminated Aborally. Tutorial 1.7 An Amber Lipid Force Field Tutorial: Lipid14. (Fri Jul 09 2021 - 04:56:45 PDT)
- Re: [AMBER] - Free energy calculations of protein molecule with two binding sites (Thu Jul 08 2021 - 13:31:47 PDT)
- Re: [AMBER] Where are the parameters for the SCREEN RADII section in prmtop (Wed Jul 07 2021 - 13:26:07 PDT)
- Re: [AMBER] MD with emap restraints, restraints have no effect (Mon Jul 05 2021 - 05:11:50 PDT)
- Re: [AMBER] CompEL in AMBER (Mon Jul 05 2021 - 05:01:02 PDT)
- Re: [AMBER] MD with emap restraints, restraints have no effect (Sun Jul 04 2021 - 10:28:51 PDT)
- Re: [AMBER] MMGBSA bad atom type error not fixed by source code edits (Sat Jul 03 2021 - 05:04:07 PDT)
- Re: [AMBER] Segmentation Fault (Fri Jul 02 2021 - 19:21:43 PDT)
- Re: [AMBER] Warning of sp2 improper torsion from Amber tutorial 1.1.4 "Building Protein Systems in Explicit Water" (Thu Jul 01 2021 - 05:14:00 PDT)
David William Kastner
- [AMBER] MCPB.py 'OW' type error in AmberTools21 (Tue Jul 20 2021 - 07:51:12 PDT)
Debarati DasGupta
- Re: [AMBER] gpu error (Sat Jul 24 2021 - 17:41:35 PDT)
- [AMBER] gpu error (Fri Jul 23 2021 - 06:25:28 PDT)
Dr. Anselm Horn
- Re: [AMBER] Building Forcefield for Glycolipid Molecule (Wed Jul 21 2021 - 01:55:30 PDT)
- Re: [AMBER] Building Forcefield for Glycolipid Molecule (Mon Jul 19 2021 - 02:11:43 PDT)
- Re: [AMBER] Help with imagining curled protein (Thu Jul 15 2021 - 03:25:19 PDT)
- Re: [AMBER] Error charges ligand having Selenium (Thu Jul 01 2021 - 12:34:27 PDT)
Elvis A F Martis
- Re: [AMBER] To build a single covalent bond in a protein-ligand complex using AMBER18. (Mon Jul 19 2021 - 05:35:04 PDT)
- Re: [AMBER] To build a single covalent bond in a protein-ligand complex using AMBER18. (Sat Jul 03 2021 - 03:28:52 PDT)
Farkhad Maksudov
- [AMBER] What exactly calculates MMPBSA.py? (Wed Jul 14 2021 - 16:44:46 PDT)
Francis Acquah
- [AMBER] Is Amber18 compatible with AmberTools21 (Tue Jul 13 2021 - 07:31:41 PDT)
Gerald Monard
- Re: [AMBER] SEBOMD topology issue (Mon Jul 26 2021 - 16:57:11 PDT)
Gerardo Zerbetto De Palma
- Re: [AMBER] cudaMemcpy GpuBuffer ERROR (Tue Jul 20 2021 - 09:15:51 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer ERROR (Mon Jul 19 2021 - 08:13:11 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer ERROR (Mon Jul 19 2021 - 08:00:22 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer ERROR (Mon Jul 19 2021 - 06:46:05 PDT)
- [AMBER] cudaMemcpy GpuBuffer ERROR (Fri Jul 16 2021 - 09:01:56 PDT)
Gustaf Olsson
- Re: [AMBER] MCPB.py tutorial issues (Fri Jul 09 2021 - 07:54:59 PDT)
- Re: [AMBER] MCPB.py tutorial issues (Fri Jul 09 2021 - 02:12:32 PDT)
- [AMBER] MCPB.py tutorial issues (Fri Jul 09 2021 - 01:45:14 PDT)
- [AMBER] Ferrocene simulation (Thu Jul 08 2021 - 01:52:33 PDT)
He, Amy
- [AMBER] Solvate and manipulate order of atoms in Leap (Sun Jul 25 2021 - 15:26:06 PDT)
- Re: [AMBER] Include specific solvent in constant pH MD simulation by CPHFIRST_SOL (Sun Jul 25 2021 - 06:05:16 PDT)
- [AMBER] Include specific solvent in constant pH MD simulation by CPHFIRST_SOL (Sat Jul 24 2021 - 23:12:27 PDT)
- Re: [AMBER] The protonation state model of TYR in CpHMD (Mon Jul 19 2021 - 15:02:45 PDT)
- [AMBER] The protonation state model of TYR in CpHMD (Mon Jul 19 2021 - 11:14:21 PDT)
Hector A. Baldoni
- Re: [AMBER] tleap does not recognize inosine (Tue Jul 20 2021 - 15:29:00 PDT)
Hugo Macdermott-Opeskin
- [AMBER] N_OF_BONDS colvar and PBC (Fri Jul 30 2021 - 17:10:57 PDT)
James Kress
- Re: [AMBER] MCPB.py tutorial issues (Fri Jul 09 2021 - 11:43:57 PDT)
Jason Swails
- Re: [AMBER] Using ParmEd to convert gromacs truncated octahedron box to amber (Sun Jul 18 2021 - 07:42:52 PDT)
- Re: [AMBER] Constant pH for large number of titratable residues (Thu Jul 01 2021 - 08:41:55 PDT)
Jenny 148
- Re: [AMBER] pc1 vs pc2 principal component analysis (Wed Jul 21 2021 - 00:57:51 PDT)
- [AMBER] pc1 vs pc2 principal component analysis (Fri Jul 16 2021 - 12:42:29 PDT)
- [AMBER] Cluster RMSD (Wed Jun 30 2021 - 22:35:37 PDT)
jinfeng liu
- [AMBER] MD run on RTX-3070 gpu card is much slower than that on RTX-2080ti (Thu Jul 15 2021 - 21:40:18 PDT)
- Re: [AMBER] installation error: /usr/bin/ld: final link failed: Nonrepresentable section on output (Mon Jul 12 2021 - 18:10:36 PDT)
- Re: [AMBER] installation error: /usr/bin/ld: final link failed: Nonrepresentable section on output (Sun Jul 11 2021 - 18:47:22 PDT)
- [AMBER] installation error: /usr/bin/ld: final link failed: Nonrepresentable section on output (Sun Jul 11 2021 - 02:30:14 PDT)
Kashyap, Jatin
- [AMBER] Modeling 2D material with a bio-molecule/protein (Fri Jul 09 2021 - 22:56:47 PDT)
Kenneth Huang
- Re: [AMBER] unexpected missing parameters for protein atoms? (Fri Jul 30 2021 - 07:15:08 PDT)
Kolattukudy P. Santo
- Re: [AMBER] Gas phase Simulations (Wed Jul 21 2021 - 10:38:19 PDT)
- Re: [AMBER] Gas phase Simulations (Tue Jul 20 2021 - 18:55:57 PDT)
- [AMBER] Gas phase Simulations (Tue Jul 20 2021 - 11:17:32 PDT)
Laura SCALVINI
- [AMBER] running Free Energy Perturbation with amber20 (Mon Jul 26 2021 - 23:58:30 PDT)
Liao
- [AMBER] Physical chemistry question regarding entropy calculations in ligand-receptor system (Wed Jul 28 2021 - 12:33:34 PDT)
Mac Kevin Braza
- [AMBER] PCA inconsistency on number of frames (Sat Jul 10 2021 - 15:53:05 PDT)
Mandar Kulkarni
- [AMBER] RNA chiOL3 and LJbb with epsilon-zeta correction (Fri Jul 09 2021 - 03:02:53 PDT)
- Re: [AMBER] RNA chiOL3 tleap and ACPYPE conversion (Wed Jul 07 2021 - 06:59:37 PDT)
- [AMBER] RNA chiOL3 tleap and ACPYPE conversion (Wed Jul 07 2021 - 04:47:50 PDT)
Maria Nagan
- Re: [AMBER] tleap does not recognize inosine (Tue Jul 20 2021 - 08:51:30 PDT)
Mariangela Dametto
- Re: [AMBER] tleap does not recognize inosine (Wed Jul 21 2021 - 14:16:26 PDT)
Markowska
- [AMBER] Simulation of protein immobilization (Thu Jul 29 2021 - 05:13:36 PDT)
Maschietto, Federica
- [AMBER] MMGBSA CalcError: mmpbsa_py_energy failed with prmtop (Wed Jul 28 2021 - 10:46:46 PDT)
Matthew Guberman-Pfeffer
- Re: [AMBER] unexpected missing parameters for protein atoms? (Fri Jul 30 2021 - 07:35:41 PDT)
- Re: [AMBER] Cphstats unable to read cpin (Tue Jul 27 2021 - 19:54:24 PDT)
- Re: [AMBER] Cphstats unable to read cpin (Tue Jul 27 2021 - 16:41:01 PDT)
- Re: [AMBER] Cphstats unable to read cpin (Mon Jul 26 2021 - 04:05:55 PDT)
- [AMBER] Cphstats unable to read cpin (Sun Jul 25 2021 - 20:50:46 PDT)
- Re: [AMBER] fitpkaeo.py not reading input from cestats (Sat Jul 17 2021 - 18:55:52 PDT)
- Re: [AMBER] fitpkaeo.py not reading input from cestats (Sat Jul 17 2021 - 18:22:54 PDT)
- [AMBER] fitpkaeo.py not reading input from cestats (Sat Jul 17 2021 - 15:40:06 PDT)
- Re: [AMBER] Help with imagining curled protein (Thu Jul 15 2021 - 06:33:53 PDT)
- Re: [AMBER] Help with imagining curled protein (Wed Jul 14 2021 - 08:11:43 PDT)
- Re: [AMBER] Reweighting aMD conformations (Wed Jul 14 2021 - 06:42:51 PDT)
- Re: [AMBER] Split Coordinate files in Amber (Tue Jul 13 2021 - 10:54:04 PDT)
- [AMBER] Help with imagining curled protein (Tue Jul 13 2021 - 06:31:03 PDT)
- [AMBER] Reweighting aMD conformations (Tue Jul 13 2021 - 05:54:26 PDT)
- [AMBER] How to study the redox properties of a partially dried protein (Fri Jul 09 2021 - 13:41:45 PDT)
- Re: [AMBER] Running in a loop (Thu Jul 08 2021 - 08:29:43 PDT)
- Re: [AMBER] Constant pH for large number of titratable residues (Sat Jul 03 2021 - 08:10:51 PDT)
- Re: [AMBER] Constant pH for large number of titratable residues (Sat Jul 03 2021 - 08:05:42 PDT)
- Re: [AMBER] MMGBSA bad atom type error not fixed by source code edits (Sat Jul 03 2021 - 05:12:09 PDT)
- [AMBER] MMGBSA bad atom type error not fixed by source code edits (Fri Jul 02 2021 - 23:30:30 PDT)
Maximilian Ebert
- Re: [AMBER] Where are the parameters for the SCREEN RADII section in prmtop (Tue Jul 20 2021 - 05:21:33 PDT)
- Re: [AMBER] Where are the parameters for the SCREEN RADII section in prmtop (Mon Jul 19 2021 - 05:06:24 PDT)
- Re: [AMBER] Where are the parameters for the SCREEN RADII section in prmtop (Tue Jul 13 2021 - 11:26:28 PDT)
- [AMBER] Where are the parameters for the SCREEN RADII section in prmtop (Wed Jul 07 2021 - 07:15:58 PDT)
Mohamed M. Aboelnga
- [AMBER] MMPBSA.py error with "Error occured on rank 1" (Wed Jul 14 2021 - 07:34:02 PDT)
Muhammad Ayaz Anwar
- [AMBER] Installing AmberTools with C++11 support (Wed Jul 28 2021 - 02:20:22 PDT)
Neha Verma
- [AMBER] Amber Tutorial for QM/MM/MD simulations (Fri Jul 16 2021 - 04:46:15 PDT)
Patil Pranita Uttamrao
- [AMBER] - Free energy calculations of protein molecule with two binding sites (Thu Jul 08 2021 - 09:53:52 PDT)
Pengfei Li
- Re: [AMBER] Missing mtkpp directory after installation of AmberTools21 (Thu Jul 22 2021 - 19:24:56 PDT)
- Re: [AMBER] Missing mtkpp directory after installation of AmberTools21 (Tue Jul 20 2021 - 19:29:30 PDT)
- Re: [AMBER] MCPB.py tutorial issues (Tue Jul 13 2021 - 19:49:53 PDT)
- Re: [AMBER] MCPB.py tutorial issues (Tue Jul 13 2021 - 19:47:27 PDT)
Priya Dey
- [AMBER] 3D-RISM in amber20 (Mon Jul 19 2021 - 23:35:08 PDT)
PRIYANKA PUROHIT
- Re: [AMBER] To build a single covalent bond in a protein-ligand complex using AMBER18. (Mon Jul 19 2021 - 05:05:21 PDT)
- [AMBER] To build a single covalent bond between a protein and a ligand. (Wed Jul 07 2021 - 23:14:46 PDT)
- [AMBER] To build a single covalent bond in a protein-ligand complex using AMBER18. (Sat Jul 03 2021 - 00:44:59 PDT)
Rafał Madaj
- Re: [AMBER] cudaMemcpy GpuBuffer ERROR (Fri Jul 16 2021 - 14:28:43 PDT)
Rana Rehan Khalid
- [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large (Thu Jul 15 2021 - 13:32:49 PDT)
Razil Tahir
- Re: [AMBER] Building Forcefield for Glycolipid Molecule (Tue Jul 27 2021 - 07:42:57 PDT)
- Re: [AMBER] Building Forcefield for Glycolipid Molecule (Tue Jul 20 2021 - 18:38:42 PDT)
- Re: [AMBER] Building Forcefield for Glycolipid Molecule (Tue Jul 20 2021 - 18:36:13 PDT)
- Re: [AMBER] Building Forcefield for Glycolipid Molecule (Tue Jul 20 2021 - 18:23:34 PDT)
- [AMBER] Building Forcefield for Glycolipid Molecule (Sun Jul 18 2021 - 10:02:45 PDT)
- [AMBER] Forcefield for alkyl chain in glycolipid molecule (Sun Jul 18 2021 - 09:56:19 PDT)
Rohanizeidanlou, Sahar
- Re: [AMBER] adding counterions in cpptraj (Tue Jul 20 2021 - 11:57:07 PDT)
- [AMBER] adding counterions in cpptraj (Mon Jul 19 2021 - 13:48:31 PDT)
- Re: [AMBER] Split Coordinate files in Amber (Fri Jul 16 2021 - 09:03:43 PDT)
- [AMBER] Split Coordinate files in Amber (Tue Jul 13 2021 - 10:49:03 PDT)
Ross Walker
- Re: [AMBER] cudaMemcpy GpuBuffer ERROR (Tue Jul 20 2021 - 16:09:35 PDT)
- Re: [AMBER] MD run on RTX-3070 gpu card is much slower than that on RTX-2080ti (Fri Jul 16 2021 - 05:43:44 PDT)
Sadaf Rani
- [AMBER] pdb4amber (Thu Jul 15 2021 - 23:17:34 PDT)
- [AMBER] vlimit exceeded for some step (Mon Jul 12 2021 - 00:06:18 PDT)
- Re: [AMBER] old PREP-specified impropers (Sun Jul 11 2021 - 22:14:42 PDT)
- [AMBER] old PREP-specified impropers (Sat Jul 10 2021 - 08:57:05 PDT)
- Re: [AMBER] Fortran runtime error: Bad value during integer read (Fri Jul 09 2021 - 19:23:39 PDT)
- Re: [AMBER] Fortran runtime error: Bad value during integer read (Fri Jul 09 2021 - 06:59:18 PDT)
- [AMBER] Fortran runtime error: Bad value during integer read (Fri Jul 09 2021 - 06:48:06 PDT)
Samuele Di Cristofano
- [AMBER] Ligand clustering input .pdb file. (Mon Jul 19 2021 - 02:13:50 PDT)
SATYAJIT KHATUA
- [AMBER] Protein-protein interaction energy calculation (Sun Jul 25 2021 - 06:33:41 PDT)
Shawn Brown
- Re: [AMBER] Installing AmberTools with C++11 support (Wed Jul 28 2021 - 04:09:39 PDT)
Shiho Ohno
- [AMBER] Question of Amber_ Sasaki (Wed Jul 14 2021 - 16:14:59 PDT)
Song, Lin
- Re: [AMBER] To build a single covalent bond between a protein and a ligand. (Thu Jul 08 2021 - 10:19:26 PDT)
Sruthi Sudhakar
- Re: [AMBER] Structure alteration and shortening of loops using xleap (Mon Jul 19 2021 - 07:58:00 PDT)
- [AMBER] Structure alteration and shortening of loops using xleap (Mon Jul 19 2021 - 04:41:41 PDT)
Stephan Schott
- Re: [AMBER] CompEL in AMBER (Fri Jul 16 2021 - 05:14:13 PDT)
- Re: [AMBER] Amber Tutorial for QM/MM/MD simulations (Fri Jul 16 2021 - 05:10:22 PDT)
Sumon Naskar
- [AMBER] Regarding SHAKE Parameter (Fri Jul 23 2021 - 03:38:01 PDT)
- Re: [AMBER] DNA Strand Broken after minimization (Wed Jul 14 2021 - 14:05:31 PDT)
- Re: [AMBER] DNA Strand Broken after minimization (Tue Jul 13 2021 - 11:28:55 PDT)
- [AMBER] DNA Strand Broken after minimization (Tue Jul 13 2021 - 03:22:44 PDT)
Swisher, Justin S
- Re: [AMBER] Segmentation Fault (Fri Jul 02 2021 - 13:30:19 PDT)
- [AMBER] Segmentation Fault (Fri Jul 02 2021 - 11:32:58 PDT)
Thamires Rocco Machado
- Re: [AMBER] tleap does not recognize inosine (Wed Jul 21 2021 - 13:59:31 PDT)
- Re: [AMBER] tleap does not recognize inosine (Tue Jul 20 2021 - 14:42:46 PDT)
- [AMBER] tleap does not recognize inosine (Tue Jul 20 2021 - 07:12:54 PDT)
tluchko
- Re: [AMBER] Convergence issue in 1drism (Wed Jul 28 2021 - 10:11:04 PDT)
Vaibhav Dixit
- Re: [AMBER] unexpected missing parameters for protein atoms? (Fri Jul 30 2021 - 08:05:37 PDT)
- Re: [AMBER] unexpected missing parameters for protein atoms? (Fri Jul 30 2021 - 06:55:26 PDT)
- [AMBER] unexpected missing parameters for protein atoms? (Fri Jul 30 2021 - 04:09:08 PDT)
- Re: [AMBER] MCPB.py tutorial issues (Fri Jul 09 2021 - 01:58:55 PDT)
Vento, Gabby
- [AMBER] Error message (Wed Jul 28 2021 - 14:30:59 PDT)
Víctor Vargas
- Re: [AMBER] [cluster] Not all arguments handled: [ sil Sil avgout Avg avgfmt restart ] (Thu Jul 15 2021 - 11:38:30 PDT)
- [AMBER] "idecomp" in pairwise decomposition (Thu Jul 08 2021 - 10:11:40 PDT)
Will Gerrard
- Re: [AMBER] MD with emap restraints, restraints have no effect (Mon Jul 05 2021 - 01:53:15 PDT)
- [AMBER] MD with emap restraints, restraints have no effect (Sat Jul 03 2021 - 02:51:42 PDT)
Yeng-Tseng Wang
- [AMBER] A question for cpptraj cluster command (Mon Jul 05 2021 - 11:05:57 PDT)
余鸿艳
- Re: [AMBER] [cluster] Not all arguments handled: [ sil Sil avgout Avg avgfmt restart ] (Thu Jul 22 2021 - 18:34:21 PDT)
- Re: [AMBER] [cluster] Not all arguments handled: [ sil Sil avgout Avg avgfmt restart ] (Sat Jul 17 2021 - 01:06:29 PDT)
- Re: [AMBER] [cluster] Not all arguments handled: [ sil Sil avgout Avg avgfmt restart ] (Sat Jul 17 2021 - 01:00:39 PDT)
- [AMBER] Error:[cluster] Not all arguments handled: [ sil Sil avgout Avg avgfmt restart ] (Thu Jul 15 2021 - 00:06:02 PDT)
- [AMBER] [cluster] Not all arguments handled: [ sil Sil avgout Avg avgfmt restart ] (Thu Jul 15 2021 - 00:03:05 PDT)
刘保艳
- [AMBER] Questions about dPCA. (Thu Jul 08 2021 - 21:29:47 PDT)
李政新
- Re: [AMBER] questions about unbond parameters (Sat Jul 31 2021 - 05:50:15 PDT)
- Re: [AMBER] questions about unbond parameters (Fri Jul 30 2021 - 18:29:46 PDT)
- Re: [AMBER] questions about unbond parameters (Thu Jul 29 2021 - 18:29:01 PDT)
- Re: [AMBER] questions about unbond parameters (Wed Jul 28 2021 - 17:33:50 PDT)
- [AMBER] questions about unbond parameters (Tue Jul 27 2021 - 21:01:00 PDT)
王维
- Re: [AMBER] Stop PMEMD Terminated Aborally. Tutorial 1.7 An Amber Lipid Force Field Tutorial: Lipid14. (Fri Jul 09 2021 - 00:03:54 PDT)
- [AMBER] Stop PMEMD Terminated Aborally. Tutorial 1.7 An Amber Lipid Force Field Tutorial: Lipid14. (Thu Jul 08 2021 - 05:59:47 PDT)
- [AMBER] Question about bilayer lipid dimension estimation (online tutorial: 1.7 An Amber Lipid Force Field Tutorial: Lipid14) (Tue Jul 06 2021 - 03:01:32 PDT)
- [AMBER] Warning of sp2 improper torsion from Amber tutorial 1.1.4 "Building Protein Systems in Explicit Water" (Thu Jul 01 2021 - 02:39:24 PDT)

Amber Archive Jul 2021 by author