Amber Archive Nov 2021: by author

ABDUL BASIT
- [AMBER] Entropy by quasi harmonic approximations on multiple CPU (Tue Nov 16 2021 - 20:49:59 PST)
ABEL Stephane
- Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? -- closed (Mon Nov 22 2021 - 08:31:43 PST)
- Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? --update (Thu Nov 18 2021 - 04:23:18 PST)
- Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? (Wed Nov 17 2021 - 02:26:15 PST)
- Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? (Tue Nov 16 2021 - 09:39:07 PST)
- Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? (Tue Nov 16 2021 - 09:29:50 PST)
- Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? (Mon Nov 15 2021 - 07:48:29 PST)
- [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? (Mon Nov 15 2021 - 05:11:52 PST)
- Re: [AMBER] Warnings for sp2 for two improper dihedrals (Wed Nov 10 2021 - 08:07:23 PST)
- [AMBER] Warnings for sp2 for two improper dihedrals (Wed Nov 10 2021 - 06:07:02 PST)
- Re: [AMBER] Hydrogen Mass Repartitioning without ParmEd (Tue Nov 09 2021 - 09:35:16 PST)
- Re: [AMBER] Hydrogen Mass Repartitioning without ParmEd (Tue Nov 09 2021 - 07:40:33 PST)
- Re: [AMBER] Hydrogen Mass Repartitioning without ParmEd (Tue Nov 09 2021 - 07:21:19 PST)
- [AMBER] Hydrogen Mass Repartitioning without ParmEd (Tue Nov 09 2021 - 05:49:40 PST)
Adrian Roitberg
- Re: [AMBER] Multiple Replicate Trajectories (Wed Nov 03 2021 - 08:53:57 PDT)
- Re: [AMBER] Multiple Replicate Trajectories (Wed Nov 03 2021 - 06:46:53 PDT)
Akash Deep Biswas
- Re: [AMBER] CUDA INSTALLATION FAILED (Error: Symbol ‘atompositions_fce’ at (1) has no IMPLICIT type) (Fri Nov 05 2021 - 06:17:37 PDT)
- Re: [AMBER] CUDA INSTALLATION FAILED (Error: Symbol ‘atompositions_fce’ at (1) has no IMPLICIT type) (Thu Nov 04 2021 - 07:19:39 PDT)
- [AMBER] CUDA INSTALLATION FAILED (Error: Symbol ‘atompositions_fce’ at (1) has no IMPLICIT type) (Thu Nov 04 2021 - 04:38:09 PDT)
Akinyemi Omoniyi
- [AMBER] Error: In _MMPBSA_complex.mdcrd.0, expect only 3 or 6 box coords, got 5 (Sat Nov 20 2021 - 16:47:45 PST)
Alan
- Re: [AMBER] 【tleap】 How to add water(TIP3P) to the right place in the protein？ (Tue Nov 30 2021 - 01:31:39 PST)
- Re: [AMBER] How to create a MOH box (only methanol molecules) (Thu Nov 25 2021 - 02:53:23 PST)
- Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? -- closed (Mon Nov 22 2021 - 11:22:58 PST)
- Re: [AMBER] How to create a MOH box (only methanol molecules) (Mon Nov 22 2021 - 08:03:54 PST)
- [AMBER] How to create a MOH box (only methanol molecules) (Thu Nov 18 2021 - 14:17:43 PST)
- Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? (Tue Nov 16 2021 - 00:28:13 PST)
- Re: [AMBER] when SLEAP got dropped? (Mon Nov 15 2021 - 08:08:59 PST)
- [AMBER] when SLEAP got dropped? (Sun Nov 14 2021 - 10:51:28 PST)
Ali Morshedi
- [AMBER] ParmEd: tiMerge error with ff19SB CMAP term (Thu Nov 18 2021 - 01:06:54 PST)
- [AMBER] Electrostatic energy in a simple non-periodic system (Wed Nov 17 2021 - 00:53:31 PST)
Alyemni, Saleh
- Re: [AMBER] Hydrogen Mass Repartitioning without ParmEd (Tue Nov 09 2021 - 07:06:30 PST)
Arash Elahi
- [AMBER] Cellulose-COOH modification (Tue Nov 09 2021 - 11:41:21 PST)
- [AMBER] Cellulose-COOH modification (Mon Nov 08 2021 - 19:57:11 PST)
Archana
- Re: [AMBER] Functional error (Mon Nov 15 2021 - 21:31:40 PST)
- [AMBER] Functional error (Sun Nov 14 2021 - 22:49:24 PST)
Ayesha Fatima
- Re: [AMBER] open mpi compiler error (Tue Nov 30 2021 - 09:35:53 PST)
- [AMBER] open mpi compiler error (Mon Nov 29 2021 - 23:50:38 PST)
- Re: [AMBER] installation error amber 18 in ubuntu 20.04 (Fri Nov 26 2021 - 01:51:42 PST)
- Re: [AMBER] installation error amber 18 in ubuntu 20.04 (Fri Nov 26 2021 - 00:27:19 PST)
- Re: [AMBER] installation error amber 18 in ubuntu 20.04 (Thu Nov 25 2021 - 06:19:25 PST)
- Re: [AMBER] installation error amber 18 in ubuntu 20.04 (Wed Nov 24 2021 - 23:34:52 PST)
- [AMBER] installation error amber 18 in ubuntu 20.04 (Wed Nov 24 2021 - 01:06:09 PST)
Baker, Joseph
- [AMBER] Lipid17 PGR vs PGS (Wed Nov 24 2021 - 09:01:19 PST)
Ben Roberts
- Re: [AMBER] ion concentration 150mM NaCl in (Wed Nov 10 2021 - 22:30:15 PST)
Bhat Zahoor
- [AMBER] How to generate the .mol2 and .frcmod files for a carbohydrate with GLYCAM06 atom types in Antechamber (Sun Nov 07 2021 - 01:48:23 PST)
Brandon Orzolek
- [AMBER] xLEaP Keyboard? (Fri Nov 19 2021 - 12:02:28 PST)
- [AMBER] Compilation Instructions for Mac M1? (Tue Nov 16 2021 - 17:05:03 PST)
Brian Radak
- Re: [AMBER] Restraint-like bonds using ParmEd setBond? (Tue Nov 02 2021 - 19:53:06 PDT)
- [AMBER] Restraint-like bonds using ParmEd setBond? (Mon Nov 01 2021 - 11:32:29 PDT)
Carlos Simmerling
- Re: [AMBER] Problems with RMSD of different proteins. (Mon Nov 29 2021 - 08:07:03 PST)
- Re: [AMBER] 【tleap】 How to add water(TIP3P) to the right place in the protein？ (Mon Nov 29 2021 - 02:38:35 PST)
- Re: [AMBER] How to create a MOH box (only methanol molecules) (Mon Nov 22 2021 - 13:39:48 PST)
- Re: [AMBER] How to add an amidated residue at the C-terminal in AMBER tleap ? (Thu Nov 18 2021 - 12:33:08 PST)
- Re: [AMBER] How to add an amidated residue at the C-terminal in AMBER tleap ? (Thu Nov 18 2021 - 11:55:32 PST)
- Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? (Tue Nov 16 2021 - 09:31:06 PST)
- Re: [AMBER] Running Simulations in a Vacuum (Mon Nov 15 2021 - 12:54:19 PST)
- Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? (Mon Nov 15 2021 - 05:28:50 PST)
- Re: [AMBER] Running Simulations in a Vacuum (Mon Nov 15 2021 - 03:18:33 PST)
- Re: [AMBER] Running Simulations in a Vacuum (Fri Nov 12 2021 - 06:32:48 PST)
- Re: [AMBER] Running Simulations in a Vacuum (Fri Nov 12 2021 - 04:37:55 PST)
- Re: [AMBER] ion concentration 150mM NaCl in (Thu Nov 11 2021 - 02:32:11 PST)
- Re: [AMBER] How to generate only CA (alpha) atoms trajectory in cpptraj Amber (Tue Nov 09 2021 - 08:09:54 PST)
- Re: [AMBER] Could tleap read in parameter and restart file instead of PDB or mol2? (Sun Nov 07 2021 - 07:43:01 PST)
- Re: [AMBER] Could tleap read in parameter and restart file instead of PDB or mol2? (Sun Nov 07 2021 - 03:32:21 PST)
- Re: [AMBER] Amber MD NAN (1-4 NB = ************** 1-4 EEL = ************** ) (Fri Nov 05 2021 - 06:54:53 PDT)
- Re: [AMBER] Amber calculate RMSF (Fri Nov 05 2021 - 04:20:52 PDT)
- Re: [AMBER] Preparing/generating input files for Amber MD (Mon Nov 01 2021 - 12:50:48 PDT)
Ch Bilal
- [AMBER] Ligand breaks during system preparation (Sat Nov 06 2021 - 00:02:48 PDT)
Chen, Guoquan
- [AMBER] Amber installation error for Intel Xeon machine (ubuntu 20.04) (Tue Nov 02 2021 - 14:51:25 PDT)
Chris Lee
- [AMBER] "unknown flag: filename.top" error with PMEMD and topology file from CHARMM-GUI (Mon Nov 22 2021 - 17:25:27 PST)
Damiano Spadoni
- Re: [AMBER] Protein in mixed of solvents (Wed Nov 24 2021 - 04:36:07 PST)
- [AMBER] Protein in mixed of solvents (Tue Nov 23 2021 - 12:26:45 PST)
Daniel Roe
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 (Thu Nov 11 2021 - 06:18:16 PST)
- Re: [AMBER] How to generate only CA (alpha) atoms trajectory in cpptraj Amber (Tue Nov 09 2021 - 08:21:53 PST)
- Re: [AMBER] cpptraj error with github version ubuntu 20.04 (Mon Nov 08 2021 - 05:35:24 PST)
- Re: [AMBER] Inquiry on CPPTRAJ (Wed Nov 03 2021 - 06:28:36 PDT)
- Re: [AMBER] Problem measuring angle in CPPTRAJ (Mon Nov 01 2021 - 07:05:01 PDT)
David A Case
- Re: [AMBER] open mpi compiler error (Tue Nov 30 2021 - 12:55:13 PST)
- Re: [AMBER] open mpi compiler error (Tue Nov 30 2021 - 05:46:14 PST)
- Re: [AMBER] amber20 - test suite picks up the wrong libgfortran (Fri Nov 26 2021 - 18:11:12 PST)
- Re: [AMBER] amber20 - test suite picks up the wrong libgfortran (Fri Nov 26 2021 - 06:15:16 PST)
- Re: [AMBER] installation error amber 18 in ubuntu 20.04 (Thu Nov 25 2021 - 17:41:05 PST)
- Re: [AMBER] installation error amber 18 in ubuntu 20.04 (Thu Nov 25 2021 - 06:08:35 PST)
- Re: [AMBER] duplicate simulations problem (Wed Nov 24 2021 - 12:34:23 PST)
- Re: [AMBER] installation error amber 18 in ubuntu 20.04 (Wed Nov 24 2021 - 05:47:33 PST)
- Re: [AMBER] duplicate simulations problem (Wed Nov 24 2021 - 05:34:36 PST)
- Re: [AMBER] Interesting findings regarding water density, ntf values, and total potential energy (Tue Nov 23 2021 - 13:35:30 PST)
- Re: [AMBER] Interesting findings regarding water density, ntf values, and total potential energy (Tue Nov 23 2021 - 12:07:15 PST)
- Re: [AMBER] amber20 - test suite picks up the wrong libgfortran (Tue Nov 23 2021 - 09:17:12 PST)
- Re: [AMBER] Interesting findings regarding water density, ntf values, and total potential energy (Tue Nov 23 2021 - 06:03:17 PST)
- Re: [AMBER] "unknown flag: filename.top" error with PMEMD and topology file from CHARMM-GUI (Mon Nov 22 2021 - 19:26:17 PST)
- Re: [AMBER] Summit compile and "Attempted to read inpcrd as a NetCDF restart file, but failed" (Sat Nov 20 2021 - 06:03:06 PST)
- Re: [AMBER] xLEaP Keyboard? (Sat Nov 20 2021 - 05:43:51 PST)
- Re: [AMBER] How to create a MOH box (only methanol molecules) (Fri Nov 19 2021 - 04:45:36 PST)
- Re: [AMBER] Electrostatic energy in a simple non-periodic system (Wed Nov 17 2021 - 06:20:03 PST)
- Re: [AMBER] Compilation Instructions for Mac M1? (Tue Nov 16 2021 - 18:11:40 PST)
- Re: [AMBER] Bug Encountered When sourcing GAFF in leap.in (Tue Nov 16 2021 - 08:56:14 PST)
- Re: [AMBER] Functional error (Tue Nov 16 2021 - 05:12:00 PST)
- Re: [AMBER] help, we are frequently face this error (Mon Nov 15 2021 - 12:37:02 PST)
- Re: [AMBER] help, we are frequently face this error (Mon Nov 15 2021 - 04:43:31 PST)
- Re: [AMBER] Functional error (Mon Nov 15 2021 - 04:38:44 PST)
- Re: [AMBER] when SLEAP got dropped? (Mon Nov 15 2021 - 04:33:26 PST)
- Re: [AMBER] MMGBSA error mitigation (Sat Nov 13 2021 - 18:52:02 PST)
- Re: [AMBER] MMGBSA error mitigation (Sat Nov 13 2021 - 05:42:25 PST)
- Re: [AMBER] What ion parameters can be used with non-water solvents? (Sat Nov 13 2021 - 05:37:05 PST)
- Re: [AMBER] amber20 - cmake cannot find cuda (Thu Nov 11 2021 - 17:58:40 PST)
- Re: [AMBER] CPPTRAJ (Wed Nov 10 2021 - 18:50:33 PST)
- Re: [AMBER] Fwd: Constant pH MD simulation (Wed Nov 10 2021 - 11:54:40 PST)
- Re: [AMBER] scientific issue (Wed Nov 10 2021 - 08:04:48 PST)
- Re: [AMBER] Warnings for sp2 for two improper dihedrals (Wed Nov 10 2021 - 07:56:38 PST)
- Re: [AMBER] How to generate the .mol2 and .frcmod files for a carbohydrate with GLYCAM06 atom types in Antechamber (Sun Nov 07 2021 - 04:56:40 PST)
- Re: [AMBER] Ligand breaks during system preparation (Sat Nov 06 2021 - 06:29:38 PDT)
- Re: [AMBER] antechamber use for two unit ligand (Sat Nov 06 2021 - 06:25:54 PDT)
- Re: [AMBER] Amber MD NAN (1-4 NB = ************** 1-4 EEL = ************** ) (Fri Nov 05 2021 - 06:38:01 PDT)
- Re: [AMBER] water box corrupted by minimization (Fri Nov 05 2021 - 06:30:00 PDT)
- Re: [AMBER] CUDA INSTALLATION FAILED (Error: Symbol ‘atompositions_fce’ at (1) has no IMPLICIT type) (Thu Nov 04 2021 - 12:53:37 PDT)
- Re: [AMBER] CUDA INSTALLATION FAILED (Error: Symbol ‘atompositions_fce’ at (1) has no IMPLICIT type) (Thu Nov 04 2021 - 05:44:28 PDT)
- Re: [AMBER] Amber MD NAN (1-4 NB = ************** 1-4 EEL = ************** ) (Wed Nov 03 2021 - 12:14:25 PDT)
- Re: [AMBER] Multiple Replicate Trajectories (Wed Nov 03 2021 - 08:52:16 PDT)
- Re: [AMBER] about pmemd.cuda (Wed Nov 03 2021 - 05:09:41 PDT)
- Re: [AMBER] Amber installation error for Intel Xeon machine (ubuntu 20.04) (Tue Nov 02 2021 - 16:58:59 PDT)
- Re: [AMBER] Question of Amber_ Sasaki (Tue Nov 02 2021 - 05:26:01 PDT)
Debarati DasGupta
- [AMBER] Dynamic cross correlation matrices in AMBER20 (Wed Nov 17 2021 - 08:50:00 PST)
- Re: [AMBER] MMGBSA error mitigation (Sun Nov 14 2021 - 05:13:37 PST)
- Re: [AMBER] MMGBSA error mitigation (Sat Nov 13 2021 - 15:21:05 PST)
- Re: [AMBER] MMGBSA error mitigation (Sat Nov 13 2021 - 14:53:36 PST)
- [AMBER] MMGBSA error mitigation (Sat Nov 13 2021 - 05:16:03 PST)
- [AMBER] Regarding setting up MMGBSA calculation (Fri Nov 12 2021 - 04:18:24 PST)
- Re: [AMBER] tleap problem (Thu Nov 11 2021 - 17:18:05 PST)
- [AMBER] tleap problem (Thu Nov 11 2021 - 13:11:51 PST)
Derek M Shore
- Re: [AMBER] Summit compile and "Attempted to read inpcrd as a NetCDF restart file, but failed" (Mon Nov 22 2021 - 16:53:53 PST)
- [AMBER] Summit compile and "Attempted to read inpcrd as a NetCDF restart file, but failed" (Fri Nov 19 2021 - 15:56:21 PST)
Divya Rai
- Re: [AMBER] Fwd: Constant pH MD simulation (Wed Nov 10 2021 - 04:35:19 PST)
Dr. Anselm Horn
- Re: [AMBER] Partial frame/traj dump during MD run. (Mon Nov 29 2021 - 03:18:01 PST)
- Re: [AMBER] Mutation of R to Histidine (Fri Nov 26 2021 - 10:01:47 PST)
- Re: [AMBER] Mutation of R to Histidine (Fri Nov 26 2021 - 09:02:14 PST)
- Re: [AMBER] Mutation of R to Histidine (Fri Nov 26 2021 - 08:34:05 PST)
- Re: [AMBER] S-adenosyl-L-methionine (SAM) ff parameters (Fri Nov 19 2021 - 03:16:12 PST)
- Re: [AMBER] S-adenosyl-L-methionine (SAM) ff parameters (Thu Nov 18 2021 - 00:08:14 PST)
- Re: [AMBER] parametrization with fixed charges on some atoms (Wed Nov 17 2021 - 00:47:25 PST)
- Re: [AMBER] Functional error (Tue Nov 16 2021 - 01:25:34 PST)
- Re: [AMBER] Building Forcefield for Glycolipid Molecule (Mon Nov 15 2021 - 03:13:39 PST)
- Re: [AMBER] Isopeptide bond parameterization (Thu Nov 11 2021 - 07:32:21 PST)
- Re: [AMBER] Using RESP charges in antechamber (Wed Nov 10 2021 - 03:23:01 PST)
- Re: [AMBER] How to change a Histidine protonation state (Tue Nov 09 2021 - 02:39:23 PST)
- Re: [AMBER] question of Amber calculate RMSF (Sun Nov 07 2021 - 13:57:58 PST)
Eugene huh
- [AMBER] How to generate mol2 file with topology and crd file? (Wed Nov 10 2021 - 01:25:17 PST)
Fabian Glaser
- [AMBER] amber20 - cmake cannot find cuda (Thu Nov 11 2021 - 08:21:51 PST)
Feng Pan
- Re: [AMBER] Error upon start of nfe-abmd (Thu Nov 04 2021 - 08:44:52 PDT)
Francesca Di Matteo - francesca.dimatteo5.studio.unibo.it
- [AMBER] INFO Steered Molecular Dynamics (Thu Nov 11 2021 - 07:12:04 PST)
He, Amy
- [AMBER] Parameterize small molecules with CGenFF in Amber (Wed Nov 17 2021 - 11:56:58 PST)
Hector A. Baldoni
- Re: [AMBER] antechamber use for two unit ligand (Fri Nov 05 2021 - 15:09:34 PDT)
Heng Cao
- [AMBER] How to gradually release the Cartesian restraint? (Tue Nov 02 2021 - 09:59:09 PDT)
Huimin Tian
- [AMBER] 【tleap】 How to add water(TIP3P) to the right place in the protein？ (Sun Nov 28 2021 - 18:29:57 PST)
- [AMBER] [MCPB] Why is the wrong file generated in tleap.in (Thu Nov 25 2021 - 22:54:48 PST)
- Re: [AMBER] 【MCPB】 Why is the wrong file generated in tleap.in (Mon Nov 08 2021 - 03:02:17 PST)
- [AMBER] 【MCPB】 Why is the wrong file generated in tleap.in (Mon Nov 08 2021 - 02:04:08 PST)
- [AMBER] 【MCPB】 Why is the wrong file generated in tleap.in (Mon Nov 08 2021 - 00:36:23 PST)
Jason Swails
- Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? --update (Mon Nov 22 2021 - 05:52:25 PST)
- Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? (Tue Nov 16 2021 - 19:16:58 PST)
- Re: [AMBER] Hydrogen Mass Repartitioning without ParmEd (Tue Nov 09 2021 - 08:46:31 PST)
- Re: [AMBER] Hydrogen Mass Repartitioning without ParmEd (Tue Nov 09 2021 - 06:35:36 PST)
- Re: [AMBER] Installation question (Mon Nov 08 2021 - 05:59:34 PST)
- Re: [AMBER] ParmEd error (Mon Nov 08 2021 - 05:58:24 PST)
- Re: [AMBER] ParmEd error (Fri Nov 05 2021 - 14:10:50 PDT)
- Re: [AMBER] ParmEd error (Fri Nov 05 2021 - 06:15:58 PDT)
- Re: [AMBER] Restraint-like bonds using ParmEd setBond? (Tue Nov 02 2021 - 13:52:09 PDT)
- Re: [AMBER] Fwd: Constant pH MD simulation (Mon Nov 01 2021 - 07:09:20 PDT)
Jhuma Das
- [AMBER] Preparing/generating input files for Amber MD (Mon Nov 01 2021 - 12:32:09 PDT)
Jon Uranga
- [AMBER] CartHess2FC (Tue Nov 02 2021 - 04:32:53 PDT)
Josh Berryman
- Re: [AMBER] scientific issue (Wed Nov 10 2021 - 08:17:21 PST)
Juliette Newell
- Re: [AMBER] Running Simulations in a Vacuum (Mon Nov 15 2021 - 03:42:43 PST)
- Re: [AMBER] Running Simulations in a Vacuum (Mon Nov 15 2021 - 03:16:19 PST)
- Re: [AMBER] Running Simulations in a Vacuum (Fri Nov 12 2021 - 04:39:54 PST)
- [AMBER] Running Simulations in a Vacuum (Fri Nov 12 2021 - 04:33:51 PST)
Karl Kirschner
- Re: [AMBER] Using RESP charges in antechamber (Tue Nov 09 2021 - 23:52:22 PST)
King Wu
- [AMBER] Equilibrate and Production Run Membrane-protein complex (Wed Nov 24 2021 - 17:15:40 PST)
- Re: [AMBER] ion concentration 150mM NaCl in (Thu Nov 11 2021 - 07:40:41 PST)
- [AMBER] ion concentration 150mM NaCl in (Wed Nov 10 2021 - 22:11:50 PST)
Li,Haoxi
- [AMBER] Multiple Replicate Trajectories (Wed Nov 03 2021 - 06:40:50 PDT)
Liao
- Re: [AMBER] Interesting findings regarding water density, ntf values, and total potential energy (Tue Nov 23 2021 - 13:38:13 PST)
- Re: [AMBER] Interesting findings regarding water density, ntf values, and total potential energy (Tue Nov 23 2021 - 12:39:36 PST)
- Re: [AMBER] Interesting findings regarding water density, ntf values, and total potential energy (Tue Nov 23 2021 - 09:04:57 PST)
- [AMBER] Interesting findings regarding water density, ntf values, and total potential energy (Tue Nov 23 2021 - 00:23:35 PST)
- Re: [AMBER] Using mmpbsa_py_nabnmode directly (Sun Nov 14 2021 - 21:25:01 PST)
- [AMBER] Using mmpbsa_py_nabnmode directly (Sun Nov 14 2021 - 12:29:43 PST)
- Re: [AMBER] Could tleap read in parameter and restart file instead of PDB or mol2? (Sun Nov 07 2021 - 06:59:41 PST)
- [AMBER] Could tleap read in parameter and restart file instead of PDB or mol2? (Sat Nov 06 2021 - 13:15:55 PDT)
Mark Dixon
- Re: [AMBER] amber20 - test suite picks up the wrong libgfortran (Fri Nov 26 2021 - 06:55:24 PST)
- Re: [AMBER] amber20 - test suite picks up the wrong libgfortran (Fri Nov 26 2021 - 00:46:24 PST)
- [AMBER] amber20 - test suite picks up the wrong libgfortran (Mon Nov 22 2021 - 09:12:07 PST)
Matias Machado
- Re: [AMBER] Interesting findings regarding water density, ntf values, and total potential energy (Tue Nov 23 2021 - 14:06:10 PST)
- Re: [AMBER] Dynamic cross correlation matrices in AMBER20 (Wed Nov 17 2021 - 12:53:51 PST)
- Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ? (Tue Nov 16 2021 - 07:06:05 PST)
- Re: [AMBER] tleap problem (Thu Nov 11 2021 - 15:17:04 PST)
Matthew Guberman-Pfeffer
- [AMBER] What ion parameters can be used with non-water solvents? (Fri Nov 12 2021 - 23:42:05 PST)
- Re: [AMBER] Problem measuring angle in CPPTRAJ (Tue Nov 02 2021 - 19:16:12 PDT)
- [AMBER] Is there a polarizable counterpart to FF99sb? (Mon Nov 01 2021 - 10:26:00 PDT)
Małgorzata Kogut
- [AMBER] problems with FEP calculations (Mon Nov 22 2021 - 06:45:25 PST)
Md Fulbabu Sk
- Re: [AMBER] How to generate only CA (alpha) atoms trajectory in cpptraj Amber (Tue Nov 09 2021 - 08:54:03 PST)
- [AMBER] How to generate only CA (alpha) atoms trajectory in cpptraj Amber (Tue Nov 09 2021 - 08:04:50 PST)
Michael Goldstein
- [AMBER] Installation question (Mon Nov 01 2021 - 11:28:18 PDT)
Michael Shokhen
- Re: [AMBER] water box corrupted by minimization (Sat Nov 06 2021 - 09:18:28 PDT)
- [AMBER] water box corrupted by minimization (Thu Nov 04 2021 - 10:07:41 PDT)
- [AMBER] NVT or NPT in aMD simulations? (Tue Nov 02 2021 - 02:15:51 PDT)
mish
- Re: [AMBER] Amber MD NAN (1-4 NB = ************** 1-4 EEL = ************** ) (Fri Nov 05 2021 - 07:19:22 PDT)
- Re: [AMBER] Amber MD NAN (1-4 NB = ************** 1-4 EEL = ************** ) (Wed Nov 03 2021 - 13:49:05 PDT)
- [AMBER] Amber MD NAN (1-4 NB = ************** 1-4 EEL = ************** ) (Wed Nov 03 2021 - 09:52:19 PDT)
Mohamed Aboelnga
- Re: [AMBER] How to gradually release the Cartesian restraint? (Tue Nov 02 2021 - 11:49:30 PDT)
mohamed marzouk
- Re: [AMBER] Mutation of R to Histidine (Fri Nov 26 2021 - 16:18:53 PST)
- Re: [AMBER] Mutation of R to Histidine (Fri Nov 26 2021 - 09:09:00 PST)
- Re: [AMBER] Mutation of R to Histidine (Fri Nov 26 2021 - 08:41:15 PST)
- Re: [AMBER] Mutation of R to Histidine (Fri Nov 26 2021 - 08:39:36 PST)
- [AMBER] Mutation of R to Histidine (Fri Nov 26 2021 - 08:13:07 PST)
Nagar, Hemant
- Re: [AMBER] water box corrupted by minimization (Fri Nov 05 2021 - 07:26:33 PDT)
Nousheen
- [AMBER] SelectionError: Invalid selection. Illegal residue range (Fri Nov 19 2021 - 02:06:00 PST)
Pedro Guillem
- [AMBER] Partial frame/traj dump during MD run. (Mon Nov 29 2021 - 02:52:14 PST)
Pedro Miguel Reis Figueiredo
- [AMBER] Interpolated Corrections (Tue Nov 30 2021 - 05:51:53 PST)
- [AMBER] interpolated corrections (Mon Nov 29 2021 - 05:59:58 PST)
Pengfei Li
- Re: [AMBER] Defining a new atom type (metal) (Thu Nov 18 2021 - 08:19:50 PST)
- Re: [AMBER] 【MCPB】 Why is the wrong file generated in tleap.in (Thu Nov 18 2021 - 08:11:38 PST)
- Re: [AMBER] Parameterize small molecules with CGenFF in Amber (Wed Nov 17 2021 - 17:06:43 PST)
- Re: [AMBER] Error running metalpdb2mol2 (Wed Nov 17 2021 - 17:03:30 PST)
- Re: [AMBER] What ion parameters can be used with non-water solvents? (Wed Nov 17 2021 - 16:59:01 PST)
Pratul Agarwal
- [AMBER] Post-doc opportunity (Fri Nov 12 2021 - 10:48:27 PST)
Qinghua Liao
- [AMBER] different performance with and without distance restraints in TI calculation (Mon Nov 29 2021 - 05:07:36 PST)
- [AMBER] end state in TI calculations with pmemd.cuda (Thu Nov 04 2021 - 08:21:09 PDT)
Rafał Madaj
- Re: [AMBER] Error upon start of nfe-abmd (Fri Nov 05 2021 - 01:15:14 PDT)
- [AMBER] Error upon start of nfe-abmd (Tue Nov 02 2021 - 04:03:53 PDT)
Rajarshi Roy
- [AMBER] Regarding two stage resp fittings (Using Gaussian 09 output) (Mon Nov 29 2021 - 06:59:51 PST)
Rana Rehan Khalid
- Re: [AMBER] CPPTRAJ (Wed Nov 10 2021 - 11:57:02 PST)
- [AMBER] CPPTRAJ (Wed Nov 10 2021 - 10:38:18 PST)
- Re: [AMBER] antechamber use for two unit ligand (Sat Nov 06 2021 - 06:32:17 PDT)
- [AMBER] antechamber use for two unit ligand (Fri Nov 05 2021 - 13:30:08 PDT)
Razil Tahir
- Re: [AMBER] Building Forcefield for Glycolipid Molecule (Fri Nov 12 2021 - 22:37:51 PST)
- [AMBER] Inquiry on CPPTRAJ (Tue Nov 02 2021 - 21:13:02 PDT)
Reza Esmaeeli
- [AMBER] parametrization with fixed charges on some atoms (Tue Nov 16 2021 - 16:03:24 PST)
Reza Khayat
- [AMBER] Available postdoctoral position (Tue Nov 23 2021 - 11:12:43 PST)
Ruibin Liu
- [AMBER] Compilation error (Tue Nov 16 2021 - 07:03:23 PST)
Sadaf Rani
- [AMBER] How to interpret clustering (Fri Nov 26 2021 - 08:16:21 PST)
- Re: [AMBER] duplicate simulations problem (Wed Nov 24 2021 - 22:04:16 PST)
- Re: [AMBER] duplicate simulations problem (Wed Nov 24 2021 - 11:08:38 PST)
- [AMBER] duplicate simulations problem (Wed Nov 24 2021 - 02:07:37 PST)
- [AMBER] How to change a Histidine protonation state (Tue Nov 09 2021 - 02:05:16 PST)
Sai Kumar Ramadugu
- Re: [AMBER] Unable to correctly identify element EPW (Thu Nov 11 2021 - 14:48:35 PST)
- [AMBER] Unable to correctly identify element EPW (Tue Nov 09 2021 - 11:14:22 PST)
Sam Walsworth (Researcher)
- [AMBER] Using predefined Ag+ parameters (Tue Nov 30 2021 - 05:48:02 PST)
- [AMBER] Error running metalpdb2mol2 (Wed Nov 10 2021 - 03:45:36 PST)
- [AMBER] Using RESP charges in antechamber (Tue Nov 09 2021 - 08:43:17 PST)
- [AMBER] Defining a new atom type (metal) (Thu Nov 04 2021 - 08:12:23 PDT)
Sangeetha B
- Re: [AMBER] ParmEd error (Tue Nov 09 2021 - 02:43:57 PST)
- Re: [AMBER] ParmEd error (Sat Nov 06 2021 - 03:33:32 PDT)
- Re: [AMBER] ParmEd error (Fri Nov 05 2021 - 06:49:05 PDT)
- Re: [AMBER] ParmEd error (Fri Nov 05 2021 - 06:43:09 PDT)
- [AMBER] ParmEd error (Wed Nov 03 2021 - 04:39:22 PDT)
Seibold, Steve Allan
- Re: [AMBER] Problems with RMSD of different proteins. (Mon Nov 29 2021 - 08:15:03 PST)
- [AMBER] Problems with RMSD of different proteins. (Sun Nov 28 2021 - 07:47:10 PST)
- [AMBER] RMSD of different protein PDBs (Sat Nov 27 2021 - 15:01:50 PST)
Shiho Ohno
- [AMBER] Question of Amber_ Sasaki (Mon Nov 01 2021 - 21:57:12 PDT)
SOMA ROY
- [AMBER] scientific issue (Wed Nov 10 2021 - 07:11:21 PST)
Thomas Cheatham
- Re: [AMBER] How to Compare RDFs for different systems (Mon Nov 01 2021 - 21:33:01 PDT)
Umesh Roy
- [AMBER] GIST: Entropy calculations (Mon Nov 15 2021 - 02:19:32 PST)
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces (Sun Oct 31 2021 - 23:40:59 PDT)
Vaibhav Dixit
- [AMBER] closest ions radiation distribution (Thu Nov 25 2021 - 01:28:15 PST)
- Re: [AMBER] cpptraj error with github version ubuntu 20.04 (Mon Nov 08 2021 - 06:58:22 PST)
- Re: [AMBER] cpptraj error with github version ubuntu 20.04 (Mon Nov 08 2021 - 01:49:36 PST)
- [AMBER] cpptraj error with github version ubuntu 20.04 (Mon Nov 08 2021 - 01:31:17 PST)
Venkatareddy Dadireddy
- Re: [AMBER] S-adenosyl-L-methionine (SAM) ff parameters (Fri Nov 19 2021 - 12:08:26 PST)
- Re: [AMBER] S-adenosyl-L-methionine (SAM) ff parameters (Thu Nov 18 2021 - 22:07:45 PST)
- [AMBER] S-adenosyl-L-methionine (SAM) ff parameters (Fri Nov 12 2021 - 20:53:39 PST)
- [AMBER] Isopeptide bond parameterization (Thu Nov 11 2021 - 05:51:34 PST)
Vinicius Wilian Cruzeiro
- Re: [AMBER] amber20 - cmake cannot find cuda (Thu Nov 11 2021 - 09:05:12 PST)
Vollmers, Luis
- [AMBER] Bug Encountered When sourcing GAFF in leap.in (Tue Nov 16 2021 - 07:28:27 PST)
Yen Nguyen
- Re: [AMBER] How to add an amidated residue at the C-terminal in AMBER tleap ? (Thu Nov 18 2021 - 12:49:27 PST)
- Re: [AMBER] How to add an amidated residue at the C-terminal in AMBER tleap ? (Thu Nov 18 2021 - 12:26:56 PST)
- [AMBER] How to add an amidated residue at the C-terminal in AMBER tleap ? (Thu Nov 18 2021 - 11:47:43 PST)
zeinab masoomi
- Re: [AMBER] help, we are frequently face this error (Mon Nov 15 2021 - 11:22:24 PST)
- [AMBER] help, we are frequently face this error (Mon Nov 15 2021 - 01:22:17 PST)
zmatovic.kg.ac.rs
- Re: [AMBER] MMGBSA error mitigation (Sat Nov 13 2021 - 15:37:55 PST)
吴晓东
- [AMBER] question of Amber calculate RMSF (Sun Nov 07 2021 - 00:45:55 PDT)
- [AMBER] Amber calculate RMSF (Thu Nov 04 2021 - 17:29:51 PDT)
田佳琪
- [AMBER] about pmemd.cuda (Tue Nov 02 2021 - 20:55:13 PDT)

Amber Archive Nov 2021 by author