Amber Archive Jun 2020: by author

abhisek Mondal
- [AMBER] adding a new covalently-linked ligand (Sat Jun 13 2020 - 03:39:57 PDT)
Ahmed Elrashedy
- Re: [AMBER] Tutorials unavailable (Sat Jun 20 2020 - 23:58:38 PDT)
Alessandro Contini
- Re: [AMBER] Error: Could not determine format of topology (Wed Jun 17 2020 - 06:50:14 PDT)
- Re: [AMBER] About two amber REMD simulation problems (Wed Jun 17 2020 - 00:54:33 PDT)
Amanda Buyan
- [AMBER] using PLUMED with pmemd.cuda? (Thu Jun 04 2020 - 19:48:31 PDT)
- Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? (Thu Jun 04 2020 - 19:46:33 PDT)
- Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? (Wed Jun 03 2020 - 17:30:52 PDT)
- Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? (Wed Jun 03 2020 - 17:15:01 PDT)
- Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? (Wed Jun 03 2020 - 17:10:15 PDT)
- [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? (Tue Jun 02 2020 - 20:54:59 PDT)
angad sharma
- [AMBER] generating methane parameters (Fri Jun 26 2020 - 00:28:56 PDT)
- [AMBER] generating methane parameters (Mon Jun 22 2020 - 08:56:55 PDT)
- [AMBER] Fwd: generating parameters for methane (Mon Jun 22 2020 - 08:54:13 PDT)
- Re: [AMBER] generating parameters for methane (Fri Jun 19 2020 - 22:10:36 PDT)
- [AMBER] generating parameters for methane (Tue Jun 16 2020 - 02:37:55 PDT)
anirudh mantri
- [AMBER] Gold in PARMCHK.dat Antechamber. (Mon Jun 08 2020 - 01:59:25 PDT)
ankita mehta
- [AMBER] Amber installation error (Wed Jun 24 2020 - 06:41:57 PDT)
Athena N
- [AMBER] nastruct command query (Thu Jun 25 2020 - 12:25:31 PDT)
Baker, Joseph
- Re: [AMBER] amber20 output header (Thu Jun 11 2020 - 06:47:05 PDT)
- [AMBER] steered MD with restraints on a selection (Mon Jun 08 2020 - 19:44:03 PDT)
Barak Alnami
- [AMBER] MCPB.py problem to make step 1 works (Mon Jun 08 2020 - 04:19:56 PDT)
Batuhan Kav
- Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? (Wed Jun 03 2020 - 06:44:06 PDT)
Benedikt Flöser
- Re: [AMBER] tleap PDB file in ORCA (Thu Jun 18 2020 - 05:02:59 PDT)
- [AMBER] tleap PDB file in ORCA (Thu Jun 18 2020 - 00:22:46 PDT)
Billiot, Eugene
- Re: [AMBER] restraining surfactant tails in micelles intact (Sat Jun 27 2020 - 08:09:15 PDT)
- [AMBER] restraining surfactant tails in micelles intact (Fri Jun 26 2020 - 12:55:41 PDT)
- Re: [AMBER] Xleap - disappearance of selection when trying to relax selection (Wed Jun 10 2020 - 06:59:29 PDT)
- [AMBER] Xleap - disappearance of selection when trying to relax selection (Tue Jun 09 2020 - 11:18:43 PDT)
- Re: [AMBER] help with building an amino acid based surfactant molecule (Thu Jun 04 2020 - 15:55:54 PDT)
- Re: [AMBER] help with building an amino acid based surfactant molecule (Thu Jun 04 2020 - 10:12:12 PDT)
- Re: [AMBER] help with building an amino acid based surfactant molecule (Thu Jun 04 2020 - 08:28:57 PDT)
- [AMBER] help with building an amino acid based surfactant molecule (Thu Jun 04 2020 - 08:01:18 PDT)
Bowleg, Jerrano
- [AMBER] Adiabatic Mapping Info Request (Tue Jun 16 2020 - 10:02:23 PDT)
Busra Demir
- Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? (Thu Jun 04 2020 - 14:19:34 PDT)
Carlos Simmerling
- Re: [AMBER] ff14SBonlysc + OPC3 (Mon Jun 29 2020 - 08:52:20 PDT)
- Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? (Fri Jun 26 2020 - 11:20:39 PDT)
- Re: [AMBER] help with building an amino acid based surfactant molecule (Thu Jun 04 2020 - 10:13:21 PDT)
- Re: [AMBER] help with building an amino acid based surfactant molecule (Thu Jun 04 2020 - 09:52:10 PDT)
- Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? (Thu Jun 04 2020 - 08:57:57 PDT)
- Re: [AMBER] help with building an amino acid based surfactant molecule (Thu Jun 04 2020 - 08:56:50 PDT)
- Re: [AMBER] help with building an amino acid based surfactant molecule (Thu Jun 04 2020 - 08:21:36 PDT)
- Re: [AMBER] help with building an amino acid based surfactant molecule (Thu Jun 04 2020 - 08:20:24 PDT)
Casalini Tommaso
- Re: [AMBER] MMPBSA.py error (Tue Jun 16 2020 - 04:28:38 PDT)
- Re: [AMBER] MMPBSA.py error (Tue Jun 16 2020 - 04:09:30 PDT)
- Re: [AMBER] Python related problem running MMPBSA.py.MPI (Wed Jun 10 2020 - 08:57:54 PDT)
- Re: [AMBER] Python related problem running MMPBSA.py.MPI (Wed Jun 10 2020 - 08:37:07 PDT)
- [AMBER] Python related problem running MMPBSA.py.MPI (Wed Jun 10 2020 - 07:36:18 PDT)
- Re: [AMBER] protein on gold surface (Mon Jun 08 2020 - 03:14:47 PDT)
Christina Bergonzo
- Re: [AMBER] nastruct command query (Thu Jun 25 2020 - 12:29:01 PDT)
- Re: [AMBER] Cluster analysis: the result was strange (Thu Jun 25 2020 - 06:22:23 PDT)
Cruzeiro,Vinicius Wilian D
- Re: [AMBER] pH-REMD error (Sun Jun 21 2020 - 11:17:13 PDT)
Daniel Roe
- Re: [AMBER] Problems with RMSF calculations (Mon Jun 29 2020 - 17:58:44 PDT)
- Re: [AMBER] Ligand movement w.r.t protein backbone (Mon Jun 29 2020 - 17:35:07 PDT)
- Re: [AMBER] ff14SBonlysc + OPC3 (Mon Jun 29 2020 - 17:21:48 PDT)
- Re: [AMBER] ff14SBonlysc + OPC3 (Mon Jun 29 2020 - 10:54:57 PDT)
- Re: [AMBER] Ligand movement w.r.t protein backbone (Mon Jun 29 2020 - 09:07:27 PDT)
- Re: [AMBER] Problems with RMSF calculations (Mon Jun 29 2020 - 09:02:27 PDT)
- Re: [AMBER] Is there a method that can calculate the angle between two planes? (Mon Jun 29 2020 - 08:31:40 PDT)
- Re: [AMBER] ff14SBonlysc + OPC3 (Mon Jun 29 2020 - 08:25:38 PDT)
- Re: [AMBER] CPPTRAJ: Time Correlation Function (TCF) (Mon Jun 29 2020 - 08:16:11 PDT)
- Re: [AMBER] pmemd.MPI and minization trajectories (Mon Jun 29 2020 - 08:11:05 PDT)
- Re: [AMBER] Problems with Make install Amber 18 (Fri Jun 26 2020 - 03:11:32 PDT)
- Re: [AMBER] restraint 10 kcal/mol (Wed Jun 24 2020 - 13:42:12 PDT)
- Re: [AMBER] CPPtraj PCA error (Wed Jun 24 2020 - 09:13:47 PDT)
- Re: [AMBER] Problem in calculating pairwise interaction with CPPTRAJ (Wed Jun 24 2020 - 09:07:22 PDT)
- Re: [AMBER] Energy values from mdout files (excluding solvent molecules) (Wed Jun 24 2020 - 09:04:15 PDT)
- Re: [AMBER] How to get the eigenvalues from PCA (Wed Jun 24 2020 - 08:58:00 PDT)
- Re: [AMBER] nativecontacts (Wed Jun 24 2020 - 08:52:56 PDT)
- Re: [AMBER] clustering parameter files (Wed Jun 24 2020 - 05:42:40 PDT)
- Re: [AMBER] Fwd: Error: Could not determine format of topology (Wed Jun 24 2020 - 05:33:12 PDT)
- Re: [AMBER] Incompatibility of coordinate file with topology after minimization (Wed Jun 24 2020 - 05:26:02 PDT)
- Re: [AMBER] How to install Ambertools 20 using Cygwin and CMake on windows 7? (Wed Jun 24 2020 - 05:24:21 PDT)
- Re: [AMBER] Hoogsteen H-bond (Wed Jun 24 2020 - 05:20:41 PDT)
- Re: [AMBER] Cluster analysis: the result was strange (Wed Jun 24 2020 - 05:15:45 PDT)
- Re: [AMBER] Fwd: Error: Could not determine format of topology (Fri Jun 19 2020 - 19:05:11 PDT)
- Re: [AMBER] Fwd: Error: Could not determine format of topology (Fri Jun 19 2020 - 14:29:58 PDT)
- Re: [AMBER] tleap PDB file in ORCA (Thu Jun 18 2020 - 04:55:15 PDT)
- Re: [AMBER] tleap - extract ion molecules and save it as pdb (Wed Jun 10 2020 - 05:53:27 PDT)
- Re: [AMBER] Individual water lifetimes within a distance cutoff? (Tue Jun 09 2020 - 08:01:09 PDT)
- Re: [AMBER] COM position (Mon Jun 01 2020 - 12:26:00 PDT)
David A Case
- Re: [AMBER] centos 7 install Ambertools20 error, final link failed: Bad value (Tue Jun 30 2020 - 04:48:35 PDT)
- Re: [AMBER] Error in Installing Amber 20 on GPU (Tue Jun 30 2020 - 04:41:03 PDT)
- Re: [AMBER] ff14SBonlysc + OPC3 (Mon Jun 29 2020 - 18:30:50 PDT)
- Re: [AMBER] error message create parameters (Mon Jun 29 2020 - 11:27:40 PDT)
- Re: [AMBER] pmemd.MPI and minization trajectories (Mon Jun 29 2020 - 11:18:38 PDT)
- Re: [AMBER] centos 7 install Ambertools20 error, final link failed: Bad value (Mon Jun 29 2020 - 11:15:15 PDT)
- Re: [AMBER] Error in Installing Amber 20 on GPU (Mon Jun 29 2020 - 11:04:42 PDT)
- Re: [AMBER] ff14SBonlysc + OPC3 (Mon Jun 29 2020 - 10:54:28 PDT)
- Re: [AMBER] Is there a method that can calculate the angle between two planes? (Sun Jun 28 2020 - 12:33:40 PDT)
- Re: [AMBER] Error Message while using GPU (Sun Jun 28 2020 - 12:19:51 PDT)
- Re: [AMBER] Error in Antechamber (Sat Jun 27 2020 - 18:07:42 PDT)
- Re: [AMBER] restraining surfactant tails in micelles intact (Sat Jun 27 2020 - 04:53:01 PDT)
- Re: [AMBER] Problems with Make install Amber 18 (Fri Jun 26 2020 - 05:38:14 PDT)
- Re: [AMBER] generating methane parameters (Fri Jun 26 2020 - 05:04:06 PDT)
- Re: [AMBER] Problems with Make install Amber 18 (Fri Jun 26 2020 - 04:57:38 PDT)
- Re: [AMBER] ERROR:nfft1 must be in the range of 6 to 512! (Thu Jun 25 2020 - 05:09:24 PDT)
- Re: [AMBER] restraint 10 kcal/mol (Wed Jun 24 2020 - 18:36:37 PDT)
- Re: [AMBER] Amber20 update failure on RHEL7/CentOS7 (Wed Jun 24 2020 - 12:05:53 PDT)
- Re: [AMBER] Amber installation error (Wed Jun 24 2020 - 11:56:25 PDT)
- Re: [AMBER] Minimization erro (Tue Jun 23 2020 - 18:02:05 PDT)
- Re: [AMBER] Fwd: Error: Could not determine format of topology (Mon Jun 22 2020 - 18:27:32 PDT)
- Re: [AMBER] contents of AMBER Digest, Vol 3040, Issue 1, message 1 (Mon Jun 22 2020 - 06:51:46 PDT)
- Re: [AMBER] How to use Ambertools20 parmed.py? (Sun Jun 21 2020 - 07:57:26 PDT)
- Re: [AMBER] Incompatibility of coordinate file with topology after minimization (Sat Jun 20 2020 - 18:22:06 PDT)
- Re: [AMBER] generating parameters for methane (Sat Jun 20 2020 - 04:39:48 PDT)
- Re: [AMBER] Fwd: Error: Could not determine format of topology (Fri Jun 19 2020 - 13:41:21 PDT)
- Re: [AMBER] planarity issue during md (Thu Jun 18 2020 - 05:11:16 PDT)
- Re: [AMBER] tleap PDB file in ORCA (Thu Jun 18 2020 - 05:04:33 PDT)
- Re: [AMBER] Fwd: Error: Could not determine format of topology (Wed Jun 17 2020 - 12:12:16 PDT)
- Re: [AMBER] Error while using Parmchk2 (Wed Jun 17 2020 - 05:12:38 PDT)
- Re: [AMBER] mmgbsa question (Tue Jun 16 2020 - 05:02:35 PDT)
- Re: [AMBER] planarity issue during md (Mon Jun 15 2020 - 11:51:16 PDT)
- [AMBER] Apostrophe problems (Mon Jun 15 2020 - 11:47:13 PDT)
- Re: [AMBER] planarity issue during md (Mon Jun 15 2020 - 05:12:12 PDT)
- Re: [AMBER] question (Mon Jun 15 2020 - 05:09:18 PDT)
- Re: [AMBER] GLYCAM and scaling of electrostatic and nonbonded interactions (Thu Jun 11 2020 - 11:02:54 PDT)
- Re: [AMBER] Cellulose-lignin interaction (Thu Jun 11 2020 - 07:12:58 PDT)
- Re: [AMBER] Python related problem running MMPBSA.py.MPI (Wed Jun 10 2020 - 08:31:25 PDT)
- Re: [AMBER] Xleap - disappearance of selection when trying to relax selection (Wed Jun 10 2020 - 08:29:07 PDT)
- Re: [AMBER] tleap - extract ion molecules and save it as pdb (Wed Jun 10 2020 - 04:33:02 PDT)
- Re: [AMBER] Xleap - disappearance of selection when trying to relax selection (Tue Jun 09 2020 - 13:37:30 PDT)
- Re: [AMBER] Charge parameters in GAFF (Tue Jun 09 2020 - 05:00:34 PDT)
- Re: [AMBER] error installation mpi (Mon Jun 08 2020 - 08:56:02 PDT)
- Re: [AMBER] error installation mpi (Mon Jun 08 2020 - 07:41:09 PDT)
- Re: [AMBER] Gold in PARMCHK.dat Antechamber. (Mon Jun 08 2020 - 06:42:09 PDT)
- Re: [AMBER] tleap splitting the lipid (Mon Jun 08 2020 - 05:22:36 PDT)
- Re: [AMBER] MM/PBSA and GBSA fails (Sun Jun 07 2020 - 17:35:29 PDT)
- Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? (Sun Jun 07 2020 - 17:31:25 PDT)
- Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? (Sat Jun 06 2020 - 18:07:27 PDT)
- Re: [AMBER] ambertools19 (Sat Jun 06 2020 - 06:07:35 PDT)
- Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? (Wed Jun 03 2020 - 06:17:56 PDT)
- Re: [AMBER] igb for non-aqueous solvent? (Mon Jun 01 2020 - 07:00:00 PDT)
David Cerutti
- Re: [AMBER] generating methane parameters (Mon Jun 22 2020 - 09:17:04 PDT)
- Re: [AMBER] tleap PDB file in ORCA (Thu Jun 18 2020 - 01:18:50 PDT)
- Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? (Thu Jun 04 2020 - 09:07:19 PDT)
- Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? (Wed Jun 03 2020 - 01:29:31 PDT)
- Re: [AMBER] AMBER Digest, Vol 3019, Issue 1 (Mon Jun 01 2020 - 03:28:03 PDT)
Debarati DasGupta
- Re: [AMBER] Ligand movement w.r.t protein backbone (Tue Jun 30 2020 - 05:07:11 PDT)
- Re: [AMBER] Ligand movement w.r.t protein backbone (Mon Jun 29 2020 - 09:24:30 PDT)
- [AMBER] FW: restraint 10 kcal/mol (Fri Jun 26 2020 - 05:49:49 PDT)
- Re: [AMBER] restraint 10 kcal/mol (Thu Jun 25 2020 - 06:12:18 PDT)
- Re: [AMBER] restraint 10 kcal/mol (Wed Jun 24 2020 - 14:54:20 PDT)
- [AMBER] restraint 10 kcal/mol (Wed Jun 24 2020 - 11:35:38 PDT)
- Re: [AMBER] Minimization erro (Wed Jun 24 2020 - 05:44:11 PDT)
- Re: [AMBER] Minimization erro (Tue Jun 23 2020 - 15:50:09 PDT)
- [AMBER] MC barostat (Thu Jun 04 2020 - 07:25:10 PDT)
Delwakkada Liyanage, Senal Dinuka
- [AMBER] Steered MD with highly charged species (Tue Jun 09 2020 - 08:55:06 PDT)
Dr. Anselm Horn
- Re: [AMBER] Zwitter ionic form of a residue (Tue Jun 30 2020 - 06:22:20 PDT)
Elvis Martis
- Re: [AMBER] "Does not have a type" error in tleap (Tue Jun 30 2020 - 00:10:12 PDT)
- Re: [AMBER] error message create parameters (Mon Jun 29 2020 - 06:05:26 PDT)
- Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies (Sun Jun 28 2020 - 05:11:54 PDT)
- Re: [AMBER] how to combine several stripped trajectory netcdf files (Tue Jun 16 2020 - 21:01:47 PDT)
- Re: [AMBER] Average structure of production run (Tue Jun 16 2020 - 21:00:45 PDT)
- Re: [AMBER] how to combine several stripped trajectory netcdf files (Tue Jun 16 2020 - 20:38:50 PDT)
- Re: [AMBER] Average structure of production run (Tue Jun 16 2020 - 20:36:40 PDT)
- Re: [AMBER] generating parameters for methane (Tue Jun 16 2020 - 03:04:16 PDT)
- Re: [AMBER] question (Sun Jun 14 2020 - 07:17:47 PDT)
emanuele falbo
- [AMBER] CPPTRAJ: Time Correlation Function (TCF) (Mon Jun 29 2020 - 06:26:06 PDT)
Erdem Yeler
- Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? (Fri Jun 26 2020 - 10:50:47 PDT)
- Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? (Fri Jun 12 2020 - 09:49:45 PDT)
- Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? (Sun Jun 07 2020 - 14:01:41 PDT)
- Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? (Sat Jun 06 2020 - 15:52:23 PDT)
- [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? (Thu Jun 04 2020 - 08:34:26 PDT)
Eric Chen
- [AMBER] Epot value in Amber TI output (Fri Jun 12 2020 - 10:24:20 PDT)
Fabian Glaser
- Re: [AMBER] ff14SBonlysc + OPC3 (Tue Jun 30 2020 - 01:09:29 PDT)
- [AMBER] ff14SBonlysc + OPC3 (Mon Jun 29 2020 - 05:40:11 PDT)
Gao J
- Re: [AMBER] AMBER Digest, Vol 3020, Issue 1 (Mon Jun 01 2020 - 18:17:05 PDT)
- Re: [AMBER] AMBER Digest, Vol 3019, Issue 1 (Sun May 31 2020 - 19:05:05 PDT)
gaohanlu
- Re: [AMBER] contents of AMBER Digest, Vol 3040, Issue 1, message 1 (Sun Jun 21 2020 - 18:59:39 PDT)
- [AMBER] error: installing amber18 on MacOS (Thu Jun 18 2020 - 07:29:58 PDT)
Garcia, Mauro
- Re: [AMBER] help with building an amino acid based surfactant molecule (Fri Jun 12 2020 - 11:22:46 PDT)
- Re: [AMBER] help with building an amino acid based surfactant molecule (Fri Jun 12 2020 - 11:08:54 PDT)
Gard Nelson
- Re: [AMBER] nmropt vs infe (Wed Jun 24 2020 - 15:58:53 PDT)
- [AMBER] nmropt vs infe (Mon Jun 22 2020 - 14:56:17 PDT)
Gerald Monard
- Re: [AMBER] pmemd.MPI and minization trajectories (Mon Jun 29 2020 - 09:53:53 PDT)
Gerardo Zerbetto De Palma
- Re: [AMBER] GPU error in the heating step of PMEMD.CUDA (Mon Jun 22 2020 - 04:44:38 PDT)
- Re: [AMBER] GPU error in the heating step of PMEMD.CUDA (Mon Jun 22 2020 - 04:39:30 PDT)
Gould, Ian R
- Re: [AMBER] Amber parameters for sphingomyelin (Thu Jun 11 2020 - 01:10:09 PDT)
Gustaf Olsson
- Re: [AMBER] centos 7 install Ambertools20 error, final link failed: Bad value (Mon Jun 29 2020 - 23:18:29 PDT)
- Re: [AMBER] Problems with Make install Amber 18 (Fri Jun 26 2020 - 00:58:03 PDT)
- Re: [AMBER] Problems with Make install Amber 18 (Thu Jun 25 2020 - 23:03:48 PDT)
- [AMBER] Compiling Amber18 AmberTools19 on CentOS 7 (Thu Jun 25 2020 - 02:02:03 PDT)
- Re: [AMBER] Problems with Make install Amber 18 (Wed Jun 24 2020 - 23:15:12 PDT)
- Re: [AMBER] error: installing amber18 on MacOS (Sat Jun 20 2020 - 14:19:07 PDT)
- Re: [AMBER] protein on gold surface (Wed Jun 10 2020 - 22:59:27 PDT)
Gustavo Seabra
- Re: [AMBER] question (Sun Jun 14 2020 - 16:32:59 PDT)
He DC
- [AMBER] centos 7 install Ambertools20 error, final link failed: Bad value (Mon Jun 29 2020 - 07:50:32 PDT)
Hector A. Baldoni
- [AMBER] interaction entropy calculation (Tue Jun 30 2020 - 12:41:22 PDT)
HOCHEOL LIM
- [AMBER] tiMerge error with ff19SB (Wed Jun 10 2020 - 01:30:47 PDT)
- [AMBER] tleap - extract ion molecules and save it as pdb (Tue Jun 09 2020 - 16:14:02 PDT)
Houcemeddine Othman
- Re: [AMBER] Incompatibility of coordinate file with topology after minimization (Sun Jun 21 2020 - 06:04:04 PDT)
- [AMBER] Incompatibility of coordinate file with topology after minimization (Sat Jun 20 2020 - 06:16:13 PDT)
Ibrahim Mohamed
- [AMBER] An Error with MMPBSA.py in AmberTools 17 (Mon Jun 29 2020 - 15:23:34 PDT)
- [AMBER] How to use Ambertools20 parmed.py? (Sun Jun 21 2020 - 00:53:49 PDT)
- [AMBER] How to install Ambertools 20 using Cygwin and CMake on windows 7? (Sat Jun 20 2020 - 14:32:32 PDT)
Jade Shi
- [AMBER] Setting custom parameters for CpHMD simulations (Wed Jun 10 2020 - 15:38:59 PDT)
Jag Silwal
- Re: [AMBER] Fwd: Error: Could not determine format of topology (Mon Jun 22 2020 - 11:37:13 PDT)
- Re: [AMBER] Fwd: Error: Could not determine format of topology (Fri Jun 19 2020 - 14:55:42 PDT)
- Re: [AMBER] Fwd: Error: Could not determine format of topology (Fri Jun 19 2020 - 07:07:10 PDT)
- [AMBER] Fwd: Error: Could not determine format of topology (Wed Jun 17 2020 - 06:37:19 PDT)
- [AMBER] Error: Could not determine format of topology (Wed Jun 17 2020 - 06:36:26 PDT)
James Kress
- Re: [AMBER] question (Sun Jun 14 2020 - 11:53:25 PDT)
Jatin Kashyap
- Re: [AMBER] "Does not have a type" error in tleap (Tue Jun 30 2020 - 12:48:43 PDT)
- [AMBER] "Does not have a type" error in tleap (Tue Jun 30 2020 - 00:00:30 PDT)
Jianguo Li
- Re: [AMBER] Amber parameters for sphingomyelin (Thu Jun 11 2020 - 01:27:52 PDT)
- [AMBER] Amber parameters for sphingomyelin (Thu Jun 11 2020 - 01:00:14 PDT)
- [AMBER] Parameters for sphingomyelin (Tue Jun 09 2020 - 02:11:55 PDT)
Jisha B
- [AMBER] Hoogsteen H-bond (Fri Jun 19 2020 - 22:20:58 PDT)
Joanna Michelle E. Chua
- Re: [AMBER] Problems with Make install Amber 18 (Fri Jun 26 2020 - 05:03:03 PDT)
- Re: [AMBER] Problems with Make install Amber 18 (Fri Jun 26 2020 - 04:20:31 PDT)
- Re: [AMBER] Problems with Make install Amber 18 (Fri Jun 26 2020 - 00:25:15 PDT)
- Re: [AMBER] Problems with Make install Amber 18 (Thu Jun 25 2020 - 16:38:06 PDT)
- Re: [AMBER] Problems with Make install Amber 18 (Thu Jun 25 2020 - 09:08:20 PDT)
- [AMBER] Problems with Make install Amber 18 (Wed Jun 24 2020 - 20:26:44 PDT)
Jordi Bujons
- [AMBER] GLYCAM and scaling of electrostatic and nonbonded interactions (Thu Jun 11 2020 - 09:17:29 PDT)
Karl Kirschner
- Re: [AMBER] ambertools19 (Fri Jun 05 2020 - 23:45:07 PDT)
kartik.lakshmi.gmail.com
- Re: [AMBER] Problems with RMSF calculations (Mon Jun 29 2020 - 18:22:56 PDT)
- Re: [AMBER] Problems with RMSF calculations (Mon Jun 29 2020 - 13:46:47 PDT)
- Re: [AMBER] Problems with RMSF calculations (Sat Jun 27 2020 - 12:56:05 PDT)
- [AMBER] Problems with RMSF calculations (Fri Jun 26 2020 - 11:48:47 PDT)
Kenneth Huang
- Re: [AMBER] Problems with RMSF calculations (Sat Jun 27 2020 - 15:58:53 PDT)
- Re: [AMBER] Problems with RMSF calculations (Fri Jun 26 2020 - 14:50:04 PDT)
- Re: [AMBER] pmemd.cuda for heating and equilibration? (Wed Jun 24 2020 - 21:44:11 PDT)
- Re: [AMBER] Individual water lifetimes within a distance cutoff? (Tue Jun 09 2020 - 20:55:20 PDT)
- [AMBER] Individual water lifetimes within a distance cutoff? (Mon Jun 08 2020 - 16:18:17 PDT)
- Re: [AMBER] residue renumbering in trajectory files (Mon Jun 08 2020 - 15:51:27 PDT)
Kolattukudy P. Santo
- Re: [AMBER] pH-REMD error (Sun Jun 21 2020 - 11:50:54 PDT)
- [AMBER] pH-REMD error (Sun Jun 21 2020 - 09:35:12 PDT)
Lachele Foley
- Re: [AMBER] Cellulose-lignin interaction (Fri Jun 19 2020 - 21:06:50 PDT)
Li,Haoxi
- Re: [AMBER] Parameters for Implicit Membrane in MMPBSA.py (Wed Jun 17 2020 - 14:41:35 PDT)
- [AMBER] Parameters for Implicit Membrane in MMPBSA.py (Wed Jun 10 2020 - 12:08:14 PDT)
Liao
- Re: [AMBER] how to combine several stripped trajectory netcdf files (Tue Jun 16 2020 - 21:08:52 PDT)
- Re: [AMBER] Average structure of production run (Tue Jun 16 2020 - 13:02:32 PDT)
Lorenzo Gontrani
- Re: [AMBER] Charge parameters in GAFF (Tue Jun 09 2020 - 05:18:36 PDT)
- Re: [AMBER] Charge parameters in GAFF (Mon Jun 08 2020 - 23:35:12 PDT)
Manish Manish
- Re: [AMBER] AMBER Digest, Vol 3020, Issue 1 (Mon Jun 01 2020 - 18:27:55 PDT)
Markowska
- Re: [AMBER] Individual water lifetimes within a distance cutoff? (Tue Jun 09 2020 - 05:49:16 PDT)
Matias Machado
- Re: [AMBER] ff14SBonlysc + OPC3 (Mon Jun 29 2020 - 11:33:29 PDT)
- Re: [AMBER] ff14SBonlysc + OPC3 (Mon Jun 29 2020 - 11:23:40 PDT)
- Re: [AMBER] ff14SBonlysc + OPC3 (Mon Jun 29 2020 - 10:14:07 PDT)
- Re: [AMBER] ff14SBonlysc + OPC3 (Mon Jun 29 2020 - 10:03:05 PDT)
- Re: [AMBER] tleap splitting the lipid (Mon Jun 08 2020 - 08:46:00 PDT)
- Re: [AMBER] tleap splitting the lipid (Mon Jun 08 2020 - 06:12:34 PDT)
- Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? (Wed Jun 03 2020 - 07:51:32 PDT)
mohamed marzouk
- Re: [AMBER] COM position (Tue Jun 02 2020 - 16:48:06 PDT)
MYRIAN TORRES RICO
- [AMBER] mmgbsa question (Tue Jun 16 2020 - 02:16:37 PDT)
Nada Afiva
- Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies (Sun Jun 28 2020 - 15:24:36 PDT)
- Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies (Sun Jun 28 2020 - 05:04:44 PDT)
- Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies (Fri Jun 26 2020 - 22:59:48 PDT)
- Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies (Thu Jun 25 2020 - 18:10:52 PDT)
- [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies (Thu Jun 25 2020 - 15:08:24 PDT)
- Re: [AMBER] Cluster analysis: the result was strange (Thu Jun 25 2020 - 14:52:23 PDT)
- Re: [AMBER] Cluster analysis: the result was strange (Thu Jun 25 2020 - 01:27:41 PDT)
- Re: [AMBER] pmemd.cuda for heating and equilibration? (Thu Jun 25 2020 - 00:06:27 PDT)
- [AMBER] pmemd.cuda for heating and equilibration? (Wed Jun 24 2020 - 18:27:34 PDT)
- [AMBER] Cluster analysis: the result was strange (Sat Jun 20 2020 - 01:57:48 PDT)
- Re: [AMBER] how to combine several stripped trajectory netcdf files (Wed Jun 17 2020 - 00:02:02 PDT)
- Re: [AMBER] Average structure of production run (Tue Jun 16 2020 - 21:04:11 PDT)
- Re: [AMBER] how to combine several stripped trajectory netcdf files (Tue Jun 16 2020 - 21:03:04 PDT)
- Re: [AMBER] how to combine several stripped trajectory netcdf files (Tue Jun 16 2020 - 20:44:22 PDT)
- Re: [AMBER] Average structure of production run (Tue Jun 16 2020 - 20:42:44 PDT)
- Re: [AMBER] Average structure of production run (Tue Jun 16 2020 - 20:12:00 PDT)
- [AMBER] how to combine several stripped trajectory netcdf files (Tue Jun 16 2020 - 20:09:05 PDT)
- [AMBER] Converting Amber trajectory NetCDF file to Desmond readable (Sun Jun 07 2020 - 03:38:11 PDT)
Oanh Thuy Ngoc Tran
- Re: [AMBER] MMPBSA.py error (Wed Jun 17 2020 - 14:10:45 PDT)
- [AMBER] MMPBSA.py error (Mon Jun 15 2020 - 14:57:20 PDT)
Peng Wang
- [AMBER] Amber20 update failure on RHEL7/CentOS7 (Wed Jun 24 2020 - 11:14:29 PDT)
Pengfei Li
- Re: [AMBER] MCPB.py problem to make step 1 works (Thu Jun 11 2020 - 08:30:37 PDT)
Pinky Mazumder
- Re: [AMBER] Cellulose-lignin interaction (Wed Jun 17 2020 - 17:06:39 PDT)
- [AMBER] Cellulose-lignin interaction (Wed Jun 10 2020 - 21:25:36 PDT)
Prasanth G, Research Scholar
- Re: [AMBER] Ligand movement w.r.t protein backbone (Mon Jun 29 2020 - 10:36:38 PDT)
- [AMBER] Ligand movement w.r.t protein backbone (Sat Jun 27 2020 - 02:29:21 PDT)
- Re: [AMBER] Error with MMPBSA - per residue decomposition (Fri Jun 19 2020 - 12:50:27 PDT)
- Re: [AMBER] Error with MMPBSA - per residue decomposition (Thu Jun 18 2020 - 10:18:51 PDT)
- [AMBER] Error with MMPBSA - per residue decomposition (Sat Jun 13 2020 - 00:51:15 PDT)
Preeti Pandey
- Re: [AMBER] Tutorials unavailable (Sat Jun 20 2020 - 11:46:16 PDT)
Raik Grünberg
- Re: [AMBER] protein on gold surface (Wed Jun 10 2020 - 12:43:47 PDT)
- [AMBER] protein on gold surface (Thu Jun 04 2020 - 11:26:15 PDT)
Rana Rehan Khalid
- Re: [AMBER] CPPtraj PCA error (Wed Jun 24 2020 - 09:16:09 PDT)
Ranim Maaieh
- [AMBER] residue renumbering in trajectory files (Mon Jun 08 2020 - 13:40:51 PDT)
- Re: [AMBER] clustering parameter files (Sun Jun 07 2020 - 16:43:21 PDT)
Ray Luo
- Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies (Sun Jun 28 2020 - 09:30:41 PDT)
- Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies (Sat Jun 27 2020 - 08:20:22 PDT)
- Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies (Fri Jun 26 2020 - 08:19:35 PDT)
- Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies (Thu Jun 25 2020 - 16:59:14 PDT)
- Re: [AMBER] Parameters for Implicit Membrane in MMPBSA.py (Thu Jun 18 2020 - 12:30:54 PDT)
- Re: [AMBER] Parameters for Implicit Membrane in MMPBSA.py (Thu Jun 11 2020 - 07:27:48 PDT)
Renato Araujo
- Re: [AMBER] error message create parameters (Mon Jun 29 2020 - 06:10:16 PDT)
- [AMBER] error message create parameters (Mon Jun 29 2020 - 05:49:42 PDT)
- Re: [AMBER] Problems with Make install Amber 18 (Thu Jun 25 2020 - 19:02:03 PDT)
- [AMBER] Help GPU support information (Thu Jun 25 2020 - 13:45:10 PDT)
- Re: [AMBER] Problems with Make install Amber 18 (Thu Jun 25 2020 - 10:32:54 PDT)
- Re: [AMBER] Minimization erro (Wed Jun 24 2020 - 06:06:32 PDT)
- Re: [AMBER] Minimization erro (Tue Jun 23 2020 - 18:51:42 PDT)
- [AMBER] Minimization erro (Tue Jun 23 2020 - 12:05:59 PDT)
- Re: [AMBER] error installation mpi (Mon Jun 08 2020 - 08:29:28 PDT)
- [AMBER] error installation mpi (Mon Jun 08 2020 - 07:18:21 PDT)
- [AMBER] ambertools19 (Fri Jun 05 2020 - 18:39:28 PDT)
Richter, Stefan
- [AMBER] RAMD implementation in the new Amber 20 package (Mon Jun 22 2020 - 08:12:36 PDT)
Rinsha Chk
- [AMBER] ERROR:nfft1 must be in the range of 6 to 512! (Thu Jun 25 2020 - 02:28:26 PDT)
Rodrigo Galindo-Murillo
- Re: [AMBER] Tutorials unavailable (Sun Jun 21 2020 - 08:58:34 PDT)
- Re: [AMBER] Tutorials unavailable (Sat Jun 20 2020 - 08:55:26 PDT)
rosaester.forgione.unina.it
- [AMBER] bulding a monosaccharide with N-acetylation (Thu Jun 25 2020 - 06:34:36 PDT)
- Re: [AMBER] GPU error in the heating step of PMEMD.CUDA (Mon Jun 22 2020 - 04:22:22 PDT)
- [AMBER] GPU error in the heating step of PMEMD.CUDA (Mon Jun 22 2020 - 04:05:51 PDT)
Rosellen, Martin
- [AMBER] OPLS-AA/M force field (Tue Jun 16 2020 - 03:35:36 PDT)
Ross Walker
- Re: [AMBER] Amber20 update failure on RHEL7/CentOS7 (Wed Jun 24 2020 - 12:33:56 PDT)
Sally Pias
- Re: [AMBER] Amber parameters for sphingomyelin (Thu Jun 11 2020 - 11:37:03 PDT)
- Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? (Fri Jun 05 2020 - 10:52:33 PDT)
- Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? (Thu Jun 04 2020 - 20:16:59 PDT)
- Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? (Thu Jun 04 2020 - 14:08:08 PDT)
Scott Brozell
- Re: [AMBER] Error in Antechamber (Fri Jun 26 2020 - 13:04:24 PDT)
- Re: [AMBER] Xleap - disappearance of selection when trying to relax selection (Wed Jun 10 2020 - 23:32:57 PDT)
Seibold, Steve Allan
- Re: [AMBER] pmemd.MPI and minization trajectories (Mon Jun 29 2020 - 11:38:51 PDT)
- Re: [AMBER] pmemd.MPI and minization trajectories (Mon Jun 29 2020 - 09:22:48 PDT)
- [AMBER] pmemd.MPI and minization trajectories (Mon Jun 29 2020 - 08:09:07 PDT)
Shreeramesh
- Re: [AMBER] Error in Antechamber (Sat Jun 27 2020 - 05:10:53 PDT)
- [AMBER] Error in Antechamber (Fri Jun 26 2020 - 07:38:55 PDT)
Sivanandam Magudeeswaran
- [AMBER] Error Message while using GPU (Sat Jun 27 2020 - 22:53:34 PDT)
Sodiq Waheed
- [AMBER] Error while using Parmchk2 (Tue Jun 16 2020 - 09:51:22 PDT)
Sofia Vasilakaki
- Re: [AMBER] planarity issue during md (Thu Jun 18 2020 - 02:58:09 PDT)
- Re: [AMBER] planarity issue during md (Mon Jun 15 2020 - 07:33:55 PDT)
- [AMBER] planarity issue during md (Mon Jun 15 2020 - 00:23:42 PDT)
- [AMBER] atom type in a substituted pyrimidine (Wed Jun 10 2020 - 00:10:50 PDT)
Souvik Dey
- [AMBER] Steered MD in AMBER using GPU (Tue Jun 23 2020 - 19:30:02 PDT)
Sruthi Sudhakar
- Re: [AMBER] Tutorials unavailable (Sat Jun 20 2020 - 23:08:32 PDT)
- [AMBER] Tutorials unavailable (Sat Jun 20 2020 - 08:33:32 PDT)
- [AMBER] Average structure of production run (Tue Jun 16 2020 - 10:26:44 PDT)
Stefan Menzel
- Re: [AMBER] Charge parameters in GAFF (Tue Jun 09 2020 - 01:14:04 PDT)
- [AMBER] Charge parameters in GAFF (Mon Jun 08 2020 - 22:52:45 PDT)
Suchetana Gupta
- Re: [AMBER] Error in Installing Amber 20 on GPU (Mon Jun 29 2020 - 20:30:46 PDT)
- [AMBER] Error in Installing Amber 20 on GPU (Mon Jun 29 2020 - 05:55:25 PDT)
- [AMBER] Regarding Amber 20 License (Tue Jun 23 2020 - 03:09:47 PDT)
Sunita Patel
- [AMBER] Zwitter ionic form of a residue (Tue Jun 30 2020 - 04:20:44 PDT)
Thakur, Abhishek
- [AMBER] MM/PBSA and GBSA fails (Sun Jun 07 2020 - 16:02:48 PDT)
Timothy Schutt
- Re: [AMBER] igb for non-aqueous solvent? (Mon Jun 01 2020 - 07:34:27 PDT)
Tony Yang
- Re: [AMBER] MMPBSA.py error (Tue Jun 16 2020 - 04:52:10 PDT)
- Re: [AMBER] MMPBSA.py error (Tue Jun 16 2020 - 04:23:10 PDT)
- Re: [AMBER] MMPBSA.py error (Tue Jun 16 2020 - 03:48:25 PDT)
Vikram Dalal
- [AMBER] suggestion for generation of prmtop and inpcrd file at different pH (Wed Jun 03 2020 - 14:04:52 PDT)
viktor drobot
- Re: [AMBER] using PLUMED with pmemd.cuda? (Fri Jun 05 2020 - 02:34:35 PDT)
Vishal Singh
- [AMBER] Steered Molecular Dynamics Simulation (Sun Jun 28 2020 - 11:55:13 PDT)
Wan, Shunzhou
- [AMBER] Truncated NMODE calculation with MMPBSA.py.MPI (Tue Jun 23 2020 - 09:34:57 PDT)
Wesley Michael Botello-Smith
- Re: [AMBER] Is there a method that can calculate the angle between two planes? (Mon Jun 29 2020 - 13:11:36 PDT)
- Re: [AMBER] nmropt vs infe (Tue Jun 23 2020 - 14:11:51 PDT)
xmgign.126.com
- [AMBER] Is there a method that can calculate the angle between two planes? (Sun Jun 28 2020 - 02:59:25 PDT)
zhiyi wu
- [AMBER] tleap splitting the lipid (Mon Jun 08 2020 - 02:58:22 PDT)
毛君
- [AMBER] About two amber REMD simulation problems (Wed Jun 17 2020 - 00:26:42 PDT)
- [AMBER] junmaozb.foxmail.com (Tue Jun 16 2020 - 21:11:16 PDT)
费俊文
- [AMBER] add NO3- ions (Mon Jun 29 2020 - 23:29:48 PDT)
闫芳芳
- Re: [AMBER] question (Mon Jun 15 2020 - 05:52:52 PDT)
- [AMBER] question (Sun Jun 14 2020 - 07:08:52 PDT)

Amber Archive Jun 2020 by author