Amber Archive Mar 2019: by author

A K
- [AMBER] Question about Amber TUTORIAL B5: Simulating the Green Fluorescent Protein (Tue Mar 26 2019 - 10:12:13 PDT)
Abhilash J
- Re: [AMBER] MMPBSA (Sat Mar 30 2019 - 01:42:49 PDT)
- Re: [AMBER] AMBER 18 error in QM region of QMMM (Tue Mar 26 2019 - 23:02:49 PDT)
- Re: [AMBER] AMBER 18 error in QM region of QMMM (Tue Mar 26 2019 - 19:21:31 PDT)
- Re: [AMBER] AMBER 18 error in QM region of QMMM (Tue Mar 26 2019 - 06:33:03 PDT)
- [AMBER] AMBER 18 error in QM region of QMMM (Tue Mar 26 2019 - 02:27:05 PDT)
accuratefreeenergy.gmail.com
- Re: [AMBER] TI atom limit (Wed Mar 27 2019 - 06:27:26 PDT)
- Re: [AMBER] TI atom limit (Wed Mar 27 2019 - 04:53:19 PDT)
Akshay Prabhakant
- [AMBER] using amber parameters in namd (Thu Mar 21 2019 - 06:27:22 PDT)
- [AMBER] Use of amber force field in gromacs (Tue Mar 05 2019 - 01:39:49 PST)
Andrea Cavalli
- Re: [AMBER] TI atom limit (Wed Mar 27 2019 - 05:37:46 PDT)
- [AMBER] TI atom limit (Wed Mar 27 2019 - 01:14:32 PDT)
angad sharma
- [AMBER] regarding simulation (Thu Mar 28 2019 - 23:59:05 PDT)
Anthony Bogetti
- [AMBER] Single point energy calculation SCC-DFTB (Mon Mar 25 2019 - 05:40:28 PDT)
Antoine MARION
- [AMBER] huge reference.frc in MMPBSA (Sun Mar 31 2019 - 10:44:56 PDT)
anu chandra
- [AMBER] Occupancy values in pseudo PDB from CPPRAJ grid analysis (Fri Mar 22 2019 - 14:42:04 PDT)
Arun Srikanth
- [AMBER] metal-oxide-metal interactions (Tue Mar 26 2019 - 15:34:21 PDT)
Ashutosh Mishra
- Re: [AMBER] Incorrect electric field (Thu Mar 21 2019 - 23:48:05 PDT)
- Re: [AMBER] Incorrect electric field (Thu Mar 21 2019 - 23:43:27 PDT)
- [AMBER] Incorrect electric field (Thu Mar 21 2019 - 23:26:14 PDT)
Ashutosh Shandilya
- Re: [AMBER] PNEB simulation transition (Thu Mar 14 2019 - 12:11:39 PDT)
- [AMBER] PNEB simulation transition (Thu Mar 14 2019 - 09:04:18 PDT)
Bharat Manna
- [AMBER] Assigning protonation states manually to the amino vs CpH MD simulation (Mon Mar 18 2019 - 11:50:23 PDT)
Bill Ross
- Re: [AMBER] How the instantaneous temperature is calculated in Amber ? (Sun Mar 31 2019 - 21:51:19 PDT)
- Re: [AMBER] How the instantaneous temperature is calculated in Amber ? (Sun Mar 31 2019 - 17:57:02 PDT)
- Re: [AMBER] AMBER 18 error in QM region of QMMM (Tue Mar 26 2019 - 03:39:46 PDT)
- Re: [AMBER] Incorrect electric field (Mon Mar 25 2019 - 12:18:47 PDT)
- Re: [AMBER] Incorrect electric field (Fri Mar 22 2019 - 00:40:31 PDT)
- Re: [AMBER] Incorrect electric field (Thu Mar 21 2019 - 23:45:34 PDT)
- Re: [AMBER] Incorrect electric field (Thu Mar 21 2019 - 23:40:21 PDT)
- Re: [AMBER] Installation Problem (Mon Mar 18 2019 - 05:18:51 PDT)
- Re: [AMBER] Installation Problem (Mon Mar 18 2019 - 05:00:04 PDT)
- Re: [AMBER] Error in Minimization (Fri Mar 08 2019 - 02:21:21 PST)
- Re: [AMBER] [error] The system has extended beyond the extent of the virtual box (Sun Mar 03 2019 - 03:18:30 PST)
- Re: [AMBER] [error] The system has extended beyond the extent of the virtual box (Sun Mar 03 2019 - 01:20:06 PST)
bjyx20090941
- [AMBER] pdb file with 4 atoms coordinates of water molecules with TIP4PFB model (Mon Mar 18 2019 - 05:41:16 PDT)
- [AMBER] A confused question about calculate the binding free energy from MMPBSA.py (Sun Mar 17 2019 - 18:13:28 PDT)
- [AMBER] the question of calculate the binding free energy by MMPBSA.py (Fri Mar 15 2019 - 00:28:05 PDT)
bjyx20090941
- [AMBER] A confused question about calculate the binding free energy from MMPBSA.py (Thu Mar 28 2019 - 05:29:53 PDT)
Brian Radak
- Re: [AMBER] Gpu illegal memory code accessed (Wed Mar 20 2019 - 07:53:17 PDT)
- Re: [AMBER] Reference energies in CpHMD (constant pH MD) for HIP (Sat Mar 02 2019 - 08:39:54 PST)
Carlos Simmerling
- Re: [AMBER] regarding simulation (Fri Mar 29 2019 - 04:43:17 PDT)
- Re: [AMBER] Assigning protonation states manually to the amino vs CpH MD simulation (Mon Mar 18 2019 - 07:05:15 PDT)
Casalini Tommaso
- Re: [AMBER] Hyaluronic acid using Glycam06 (Wed Mar 20 2019 - 04:00:26 PDT)
Charles Lin
- Re: [AMBER] Incorrect electric field (Mon Mar 25 2019 - 08:28:12 PDT)
- Re: [AMBER] Problem with distance restraints in membrane system with pmemd.cuda (Mon Mar 11 2019 - 08:44:58 PDT)
- Re: [AMBER] CUDA COM distance restraint (v18 with patch.7 applied) (Mon Mar 11 2019 - 08:05:29 PDT)
- Re: [AMBER] Potential bug in sander/LMOD (Fri Mar 08 2019 - 11:05:50 PST)
Christina Bergonzo
- Re: [AMBER] Doubt regarding input files in NMR refinement (Fri Mar 01 2019 - 06:51:30 PST)
Cruzeiro,Vinicius Wilian D
- Re: [AMBER] CEMD protcnt meaning (Thu Mar 21 2019 - 09:41:42 PDT)
- Re: [AMBER] Error in REMD with pmemd.cuda.MPI (Wed Mar 06 2019 - 06:58:25 PST)
- Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? (Fri Mar 01 2019 - 14:38:17 PST)
- Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? (Fri Mar 01 2019 - 12:00:31 PST)
Daniel Roe
- Re: [AMBER] nativecontacs in ccptraj (Sat Mar 30 2019 - 06:03:30 PDT)
- Re: [AMBER] Installation of AmberTools18 in macOS Mojave (Fri Mar 29 2019 - 07:41:49 PDT)
- Re: [AMBER] Query about plotting/visualizing the lifetime curve from H-Bond analysis using CPPTRAJ (Fri Mar 29 2019 - 07:34:55 PDT)
- Re: [AMBER] locating the single probe out of 80000 snapshots (Wed Mar 27 2019 - 06:42:56 PDT)
- Re: [AMBER] locating the single probe out of 80000 snapshots (Wed Mar 27 2019 - 06:23:30 PDT)
- Re: [AMBER] locating the single probe out of 80000 snapshots (Tue Mar 26 2019 - 17:36:02 PDT)
- Re: [AMBER] Retrieving topology file (Tue Mar 26 2019 - 12:16:08 PDT)
- Re: [AMBER] locating the single probe out of 80000 snapshots (Tue Mar 26 2019 - 12:12:30 PDT)
- Re: [AMBER] PCA analysis of NM (Tue Mar 26 2019 - 12:09:37 PDT)
- Re: [AMBER] Problems calculating density over distance (Tue Mar 26 2019 - 12:08:03 PDT)
- Re: [AMBER] Closest command in cpptraj for non aqeous solvents (Tue Mar 26 2019 - 08:32:06 PDT)
- Re: [AMBER] Occupancy values in pseudo PDB from CPPRAJ grid analysis (Tue Mar 26 2019 - 05:34:54 PDT)
- Re: [AMBER] Closest command in cpptraj for non aqeous solvents (Fri Mar 22 2019 - 12:32:04 PDT)
- Re: [AMBER] Installation error AmberTools18 - [test.rism1d] Error (Thu Mar 21 2019 - 07:50:03 PDT)
- Re: [AMBER] Nastruct vs 3DNA: Files used for analysis and the output (Wed Mar 20 2019 - 12:23:59 PDT)
- Re: [AMBER] Query regarding secondary structure (Wed Mar 20 2019 - 05:09:21 PDT)
- Re: [AMBER] Nastruct vs 3DNA (Mon Mar 18 2019 - 12:33:47 PDT)
- Re: [AMBER] Nastruct vs 3DNA (Mon Mar 18 2019 - 10:37:04 PDT)
- Re: [AMBER] pdb file with 4 atoms coordinates of water molecules with TIP4PFB model (Mon Mar 18 2019 - 05:49:47 PDT)
- Re: [AMBER] velocities from and velocityautocorr (Fri Mar 15 2019 - 12:30:59 PDT)
- Re: [AMBER] ValueError: invalid literal for int() with base 10: '-3.0' (Thu Mar 14 2019 - 05:26:50 PDT)
- Re: [AMBER] DSSP residue vs time graph (Thu Mar 14 2019 - 05:20:47 PDT)
- Re: [AMBER] velocities from and velocityautocorr (Wed Mar 13 2019 - 10:17:47 PDT)
- Re: [AMBER] CPPTRAJ Grid with COM (Wed Mar 13 2019 - 10:03:09 PDT)
- Re: [AMBER] CPPTRAJ Grid with COM (Wed Mar 13 2019 - 09:08:55 PDT)
- Re: [AMBER] simulating a box of pure TIP3P water (Mon Mar 11 2019 - 12:31:50 PDT)
- Re: [AMBER] simulating a box of pure TIP3P water (Mon Mar 11 2019 - 12:30:28 PDT)
- Re: [AMBER] CPPTRAJ grid unknown command (Mon Mar 11 2019 - 12:17:28 PDT)
- Re: [AMBER] One query about SPAM type calculations (Mon Mar 11 2019 - 12:15:14 PDT)
- Re: [AMBER] SPAM analysis (Mon Mar 11 2019 - 12:14:34 PDT)
- Re: [AMBER] chi1 angle of amino acids not having a CG atom (Mon Mar 11 2019 - 12:07:20 PDT)
- Re: [AMBER] calculate RDF using COM (Mon Mar 11 2019 - 11:12:25 PDT)
- Re: [AMBER] CPPTRAJ SPAM error while executing the input file (Tue Mar 05 2019 - 09:09:44 PST)
- Re: [AMBER] Converting Charmm forcefileld to Amber (Tue Mar 05 2019 - 06:21:29 PST)
- Re: [AMBER] CPPTRAJ SPAM error while executing the input file (Tue Mar 05 2019 - 05:41:17 PST)
- Re: [AMBER] Message-ID: <20190301134103.u232i6wjibdt4cav@godel.rutgers.edu> (Mon Mar 04 2019 - 12:00:06 PST)
- Re: [AMBER] Two dimensional replica exchange MD: Success rate (Mon Mar 04 2019 - 11:58:09 PST)
- Re: [AMBER] Converting Charmm forcefileld to Amber (Mon Mar 04 2019 - 11:36:03 PST)
- Re: [AMBER] CPPTRAJ SPAM error while executing the input file (Mon Mar 04 2019 - 11:31:25 PST)
- Re: [AMBER] Retrieving topology file (Mon Mar 04 2019 - 05:53:38 PST)
- Re: [AMBER] Atom type of Calcium (Fri Mar 01 2019 - 07:10:01 PST)
- Re: [AMBER] CPPTRAJ grid unknown command (Fri Mar 01 2019 - 07:08:17 PST)
David A Case
- Re: [AMBER] Question about Amber TUTORIAL B5: Simulating the Green Fluorescent Protein (Wed Mar 27 2019 - 04:28:35 PDT)
- Re: [AMBER] Single point energy calculation SCC-DFTB (Mon Mar 25 2019 - 07:33:45 PDT)
- Re: [AMBER] Gpu illegal memory code accessed (Thu Mar 21 2019 - 11:38:16 PDT)
- Re: [AMBER] using amber parameters in namd (Thu Mar 21 2019 - 11:34:07 PDT)
- Re: [AMBER] Installation error AmberTools18 - [test.rism1d] Error (Wed Mar 20 2019 - 13:25:08 PDT)
- Re: [AMBER] Installation problem AMBER16 (Tue Mar 19 2019 - 06:51:50 PDT)
- Re: [AMBER] Amber Installation (Tue Mar 19 2019 - 06:50:10 PDT)
- Re: [AMBER] antechamber bcc error (Mon Mar 11 2019 - 07:36:40 PDT)
- Re: [AMBER] Query about protein DNA MD (Fri Mar 08 2019 - 11:00:35 PST)
- Re: [AMBER] Error in Minimization (Fri Mar 08 2019 - 06:13:54 PST)
- Re: [AMBER] MMPBSA.py Calculation error (Fri Mar 08 2019 - 06:06:45 PST)
- Re: [AMBER] system explosion (Fri Mar 08 2019 - 06:04:02 PST)
- Re: [AMBER] 1/2 term in dihdral (Thu Mar 07 2019 - 08:54:17 PST)
- Re: [AMBER] Help regarding protein DNA MD in AMBER (Thu Mar 07 2019 - 06:09:15 PST)
- Re: [AMBER] Use of amber force field in gromacs (Tue Mar 05 2019 - 06:46:23 PST)
- Re: [AMBER] MM/PBSA topfile question (Tue Mar 05 2019 - 06:38:01 PST)
- Re: [AMBER] [error] The system has extended beyond the extent of the virtual box (Tue Mar 05 2019 - 06:35:42 PST)
- Re: [AMBER] Ligand autoimaging issue Amber18 (Fri Mar 01 2019 - 05:41:03 PST)
David Bickel
- Re: [AMBER] Problem with distance restraints in membrane system with pmemd.cuda (Mon Mar 11 2019 - 05:10:32 PDT)
- Re: [AMBER] Problem with distance restraints in membrane system with pmemd.cuda (Fri Mar 08 2019 - 07:29:28 PST)
- [AMBER] Problem with distance restraints in membrane system with pmemd.cuda (Wed Mar 06 2019 - 01:18:40 PST)
David Case
- Re: [AMBER] varying pressure conditions? (Sat Mar 30 2019 - 13:53:00 PDT)
- Re: [AMBER] Job position (Sat Mar 30 2019 - 13:30:02 PDT)
- Re: [AMBER] Building pmemd.cuda.MPI error in amber18 (Fri Mar 29 2019 - 04:15:39 PDT)
- Re: [AMBER] Installation of AmberTools18 in macOS Mojave (Wed Mar 27 2019 - 19:02:52 PDT)
- Re: [AMBER] cuda test failing after installation (Sun Mar 24 2019 - 05:35:00 PDT)
- Re: [AMBER] Restraint and ambmask syntax issue (Fri Mar 15 2019 - 12:29:20 PDT)
- Re: [AMBER] gaff2 parameters of c3-c3-os-c3 (Fri Mar 15 2019 - 12:20:19 PDT)
- Re: [AMBER] parameters for cc and cd (Wed Mar 13 2019 - 16:46:18 PDT)
- Re: [AMBER] Directly Set Restraint for Chilarity to Prmtop File (Wed Mar 13 2019 - 08:39:54 PDT)
- Re: [AMBER] Problem with distance restraints in membrane system with pmemd.cuda (Sat Mar 09 2019 - 06:01:53 PST)
- Re: [AMBER] improper dihedral (Thu Mar 07 2019 - 06:17:07 PST)
- Re: [AMBER] What does "0 Kb value" mean in dihedrals (Wed Mar 06 2019 - 14:27:08 PST)
Debarati DasGupta
- [AMBER] nativecontacs in ccptraj (Fri Mar 29 2019 - 10:49:51 PDT)
- Re: [AMBER] locating the single probe out of 80000 snapshots (Wed Mar 27 2019 - 07:02:18 PDT)
- Re: [AMBER] locating the single probe out of 80000 snapshots (Wed Mar 27 2019 - 06:24:59 PDT)
- Re: [AMBER] locating the single probe out of 80000 snapshots (Wed Mar 27 2019 - 06:12:45 PDT)
- Re: [AMBER] locating the single probe out of 80000 snapshots (Tue Mar 26 2019 - 14:05:36 PDT)
- Re: [AMBER] Question about Amber TUTORIAL B5: Simulating the Green Fluorescent Protein (Tue Mar 26 2019 - 10:17:13 PDT)
- Re: [AMBER] Solvate with methanol and acetone using free energy methods? (Tue Mar 26 2019 - 09:53:33 PDT)
- [AMBER] locating the single probe out of 80000 snapshots (Mon Mar 25 2019 - 07:58:20 PDT)
- Re: [AMBER] Closest command in cpptraj for non aqeous solvents (Fri Mar 22 2019 - 13:40:58 PDT)
- Re: [AMBER] Closest command in cpptraj for non aqeous solvents (Fri Mar 22 2019 - 13:09:10 PDT)
- [AMBER] Closest command in cpptraj for non aqeous solvents (Fri Mar 22 2019 - 12:23:32 PDT)
- Re: [AMBER] Gpu illegal memory code accessed (Thu Mar 21 2019 - 07:03:35 PDT)
- [AMBER] Gpu illegal memory code accessed (Wed Mar 20 2019 - 07:39:25 PDT)
- [AMBER] Homodimerization of IRF3 protein (Sat Mar 16 2019 - 14:38:05 PDT)
- [AMBER] SPAM analysis (Tue Mar 05 2019 - 14:05:41 PST)
- [AMBER] One query about SPAM type calculations (Tue Mar 05 2019 - 09:45:26 PST)
- [AMBER] simulating a box of pure TIP3P water (Tue Mar 05 2019 - 07:32:16 PST)
- [AMBER] CPPTRAJ SPAM error while executing the input file (Mon Mar 04 2019 - 09:14:52 PST)
- Re: [AMBER] CPPTRAJ grid unknown command (Fri Mar 01 2019 - 09:41:16 PST)
- Re: [AMBER] CPPTRAJ grid unknown command (Fri Mar 01 2019 - 09:23:50 PST)
- Re: [AMBER] CPPTRAJ grid unknown command (Fri Mar 01 2019 - 09:17:44 PST)
Defrese, Matthew
- [AMBER] Solvate with methanol and acetone using free energy methods? (Tue Mar 26 2019 - 08:27:31 PDT)
Dickson, Callum
- Re: [AMBER] write equilibrium bond lengths, angles and dihedrals from a ligand structure file to a frcmod file (Sat Mar 09 2019 - 19:03:29 PST)
Dr. Anselm Horn
- [AMBER] [MGMS-DS]: Molecular Modelling Workshop + Tim Clark Birthday Symposium: April 08-11, 2019 in Erlangen, Germany (Thu Mar 14 2019 - 02:24:46 PDT)
- Re: [AMBER] Query about metal RMSD regarding residue number or atom number (Thu Mar 07 2019 - 04:09:55 PST)
Dreab, Ana
- Re: [AMBER] DFTB3/MM simulations of CCCC zinc finger (Thu Mar 28 2019 - 08:27:33 PDT)
- [AMBER] DFTB3/MM simulations of CCCC zinc finger (Thu Mar 21 2019 - 09:18:35 PDT)
Elvis Martis
- Re: [AMBER] MMPBSA (Fri Mar 29 2019 - 21:38:19 PDT)
emanuele falbo
- Re: [AMBER] Retrieving topology file (Mon Mar 04 2019 - 06:57:27 PST)
- [AMBER] Retrieving topology file (Mon Mar 04 2019 - 02:08:01 PST)
Erdem Yeler
- Re: [AMBER] What does "0 Kb value" mean in dihedrals (Sat Mar 09 2019 - 05:47:12 PST)
- [AMBER] What does "0 Kb value" mean in dihedrals (Tue Mar 05 2019 - 11:35:33 PST)
Fabian Glaser
- [AMBER] Metal parameters method (Tue Mar 12 2019 - 09:09:27 PDT)
- [AMBER] metal parameters (Tue Mar 12 2019 - 07:00:06 PDT)
Feng Pan
- Re: [AMBER] NFE error: Cannot read &abmd namelist (Sat Mar 30 2019 - 20:52:49 PDT)
- Re: [AMBER] Amber18: Adaptively Biased MD (Metadynalmics) (Sun Mar 24 2019 - 20:37:50 PDT)
- Re: [AMBER] Amber18 STSM (Sun Mar 17 2019 - 21:48:00 PDT)
Feng, Zimin
- Re: [AMBER] CEMD protcnt meaning (Thu Mar 21 2019 - 10:18:48 PDT)
- [AMBER] CEMD protcnt meaning (Thu Mar 21 2019 - 09:31:40 PDT)
- Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? (Fri Mar 01 2019 - 12:35:23 PST)
- Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? (Fri Mar 01 2019 - 12:32:39 PST)
- Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? (Fri Mar 01 2019 - 12:28:39 PST)
- Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? (Fri Mar 01 2019 - 07:47:20 PST)
Fulbabu Sk
- [AMBER] Regarding solvated interaction energy (SIE) method in Amber 16 (Thu Mar 28 2019 - 03:27:00 PDT)
Ganesh Kamath
- [AMBER] Job position (Thu Mar 28 2019 - 18:31:02 PDT)
George M. Giambasu
- Re: [AMBER] NMR order parameters from MD trajectories (Wed Mar 27 2019 - 19:36:50 PDT)
Gerardo Zerbetto De Palma
- Re: [AMBER] Installation Problem (Mon Mar 18 2019 - 05:08:11 PDT)
- Re: [AMBER] Jar pulling (Fri Mar 15 2019 - 05:00:28 PDT)
- [AMBER] Jar pulling (Wed Mar 13 2019 - 10:21:47 PDT)
Ghoreishi, Delaram
- Re: [AMBER] PNEB simulation transition (Thu Mar 14 2019 - 11:23:14 PDT)
- Re: [AMBER] how to make sure .prmtop is the same for NEB calculation when using explicit solvent? (Sun Mar 03 2019 - 23:11:02 PST)
giulia palermo
- [AMBER] NMR order parameters from MD trajectories (Wed Mar 27 2019 - 18:41:09 PDT)
Goetz, Andreas
- Re: [AMBER] AMBER 18 error in QM region of QMMM (Tue Mar 26 2019 - 14:49:26 PDT)
Gustaf Olsson
- Re: [AMBER] Installation of AmberTools18 in macOS Mojave (Fri Mar 29 2019 - 08:15:17 PDT)
- Re: [AMBER] Installation of AmberTools18 in macOS Mojave (Fri Mar 29 2019 - 07:22:10 PDT)
- Re: [AMBER] Installation of AmberTools18 in macOS Mojave (Thu Mar 28 2019 - 08:18:33 PDT)
- Re: [AMBER] Installation of AmberTools18 in macOS Mojave (Thu Mar 28 2019 - 07:58:26 PDT)
- Re: [AMBER] Installation of AmberTools18 in macOS Mojave (Thu Mar 28 2019 - 07:08:46 PDT)
- Re: [AMBER] Installation of AmberTools18 in macOS Mojave (Thu Mar 28 2019 - 04:32:42 PDT)
- Re: [AMBER] Installation of AmberTools18 in macOS Mojave (Wed Mar 27 2019 - 23:41:42 PDT)
Hadi Rahmaninejad
- [AMBER] system explosion (Thu Mar 07 2019 - 15:18:30 PST)
- Re: [AMBER] Converting Charmm forcefileld to Amber (Mon Mar 04 2019 - 12:43:49 PST)
- [AMBER] Converting Charmm forcefileld to Amber (Mon Mar 04 2019 - 09:23:26 PST)
Hosein Geraili Daronkola
- [AMBER] charged residue mutation free energy (Fri Mar 15 2019 - 06:32:43 PDT)
- [AMBER] Amber18 pmemd TI (Tue Mar 05 2019 - 06:12:43 PST)
Ikuo KURISAKI
- [AMBER] Directly Set Restraint for Chilarity to Prmtop File (Tue Mar 12 2019 - 18:16:01 PDT)
- [AMBER] Chirality Restraint on a Part of Replica (Wed Mar 06 2019 - 22:19:51 PST)
- Re: [AMBER] Error in REMD with pmemd.cuda.MPI (Wed Mar 06 2019 - 22:05:10 PST)
- [AMBER] Error in REMD with pmemd.cuda.MPI (Wed Mar 06 2019 - 00:24:07 PST)
Jason Imamoto
- [AMBER] NFE error: Cannot read &abmd namelist (Sat Mar 30 2019 - 04:26:33 PDT)
- Re: [AMBER] Nastruct vs 3DNA: Files used for analysis and the output (Wed Mar 20 2019 - 11:00:51 PDT)
- Re: [AMBER] Nastruct vs 3DNA (Mon Mar 18 2019 - 12:14:24 PDT)
- [AMBER] Nastruct vs 3DNA (Mon Mar 18 2019 - 10:12:37 PDT)
Jason Swails
- Re: [AMBER] Converting Charmm forcefileld to Amber (Tue Mar 05 2019 - 15:02:19 PST)
- Re: [AMBER] Reference energies in CpHMD (constant pH MD) for HIP (Sat Mar 02 2019 - 06:54:39 PST)
João Ribeiro
- [AMBER] Research Programmer for VMD/NAMD at UIUC (Tue Mar 12 2019 - 11:33:01 PDT)
Keiran Corbett
- [AMBER] Running a MMPBSA calculation on only the structure (Thu Mar 07 2019 - 06:32:17 PST)
Kellon Belfon
- Re: [AMBER] CUDA COM distance restraint (v18 with patch.7 applied) (Sun Mar 10 2019 - 13:44:31 PDT)
koushik kasavajhala
- Re: [AMBER] Input Reservoir REMD (Tue Mar 19 2019 - 02:47:31 PDT)
Kung, Ryan
- Re: [AMBER] CPPTRAJ Grid with COM (Wed Mar 13 2019 - 09:57:16 PDT)
- [AMBER] CPPTRAJ Grid with COM (Wed Mar 13 2019 - 09:03:55 PDT)
Lin Song
- [AMBER] Setbox and ChBox (Thu Mar 07 2019 - 09:48:14 PST)
Lucas Bandeira
- [AMBER] Problems calculating density over distance (Mon Mar 25 2019 - 10:41:48 PDT)
Manyi Yang
- [AMBER] MM/PBSA topfile question (Sun Mar 03 2019 - 17:35:51 PST)
Marcelo Andrade Chagas
- Re: [AMBER] metal parameters (Sat Mar 16 2019 - 08:49:45 PDT)
Margarita I. Bernal-Uruchurtu
- [AMBER] Error in `sander': malloc(): smallbin double linked list corrupted: (Tue Mar 26 2019 - 14:53:00 PDT)
Mariana Simões Ferreira
- [AMBER] Installation error AmberTools18 - [test.rism1d] Error (Wed Mar 20 2019 - 10:02:37 PDT)
maya nair
- [AMBER] PCA analysis of NM (Mon Mar 25 2019 - 05:05:01 PDT)
Mayank Dixit
- [AMBER] how to get unbiased trajectories from biased trajectories (Wed Mar 27 2019 - 07:33:36 PDT)
- [AMBER] improper dihedral (Tue Mar 05 2019 - 08:59:58 PST)
- Re: [AMBER] Use of amber force field in gromacs (Tue Mar 05 2019 - 06:16:49 PST)
- [AMBER] 1/2 term in dihdral (Fri Mar 01 2019 - 14:27:36 PST)
Meng Wu
- [AMBER] Building pmemd.cuda.MPI error in amber18 (Fri Mar 29 2019 - 01:13:48 PDT)
- [AMBER] Building pmemd.cuda.MPI error in amber18 (Thu Mar 28 2019 - 04:11:23 PDT)
Michael Shokhen
- Re: [AMBER] antechamber bcc error (Tue Mar 12 2019 - 06:16:19 PDT)
- [AMBER] antechamber bcc error (Mon Mar 11 2019 - 04:09:32 PDT)
Mohd moid khan
- [AMBER] TIP4P Ice1h phase initial structure (Tue Mar 26 2019 - 13:11:14 PDT)
monia kam
- [AMBER] Hyaluronic acid using Glycam06 (Tue Mar 19 2019 - 08:15:18 PDT)
Myriam Hanna
- Re: [AMBER] DSSP residue vs time graph (Thu Mar 14 2019 - 06:44:14 PDT)
- Re: [AMBER] DSSP residue vs time graph (Wed Mar 13 2019 - 09:54:12 PDT)
- [AMBER] DSSP residue vs time graph (Wed Mar 13 2019 - 08:30:27 PDT)
pavel.banas.upol.cz
- Re: [AMBER] Design of graphene quantum dots (Wed Mar 27 2019 - 01:35:55 PDT)
Pengfei Li
- Re: [AMBER] DFTB3/MM simulations of CCCC zinc finger (Thu Mar 28 2019 - 09:09:44 PDT)
- Re: [AMBER] DFTB3/MM simulations of CCCC zinc finger (Sat Mar 23 2019 - 12:35:59 PDT)
- Re: [AMBER] metal parameters (Sat Mar 16 2019 - 08:19:13 PDT)
- Re: [AMBER] Atom type of Calcium (Sat Mar 02 2019 - 19:14:17 PST)
Prabir Khatua
- Re: [AMBER] MMPBSA (Sat Mar 30 2019 - 16:12:36 PDT)
- Re: [AMBER] MMPBSA (Sat Mar 30 2019 - 09:39:40 PDT)
- Re: [AMBER] MMPBSA (Fri Mar 29 2019 - 22:46:23 PDT)
- [AMBER] MMPBSA (Fri Mar 29 2019 - 14:14:33 PDT)
- [AMBER] MMPBSA.py.MPI error (Thu Mar 14 2019 - 15:24:21 PDT)
Prasanth G, Research Scholar
- [AMBER] Protein - Ligand simulation on amber and PBSA (Wed Mar 06 2019 - 05:35:34 PST)
Pratul Agarwal
- Re: [AMBER] Jar pulling (Wed Mar 13 2019 - 13:46:49 PDT)
- Re: [AMBER] CUDA COM distance restraint (v18 with patch.7 applied) (Sun Mar 10 2019 - 16:19:06 PDT)
- Re: [AMBER] CUDA COM distance restraint (v18 with patch.7 applied) (Sun Mar 10 2019 - 13:38:51 PDT)
- [AMBER] CUDA COM distance restraint (v18 with patch.7 applied) (Sun Mar 10 2019 - 11:48:33 PDT)
Premila Samuel Mohan Dass
- Re: [AMBER] DSSP residue vs time graph (Wed Mar 13 2019 - 09:18:21 PDT)
Raimon Fabregat
- [AMBER] Input Reservoir REMD (Tue Mar 19 2019 - 01:17:13 PDT)
Rakesh Srivastava
- [AMBER] Simulation of spherical macroion system (Mon Mar 25 2019 - 06:17:24 PDT)
- [AMBER] Quantitative measurement of hydrophobic and polar contacts (Wed Mar 13 2019 - 00:13:07 PDT)
Ravi Abrol
- Re: [AMBER] cuda test failing after installation (Sun Mar 24 2019 - 22:35:49 PDT)
- [AMBER] cuda test failing after installation (Wed Mar 20 2019 - 10:09:32 PDT)
Ray Luo
- Re: [AMBER] huge reference.frc in MMPBSA (Sun Mar 31 2019 - 13:51:03 PDT)
- Re: [AMBER] A confused question about calculate the binding free energy from MMPBSA.py (Fri Mar 29 2019 - 07:38:02 PDT)
Reza Esmaeeli
- Re: [AMBER] Installation of AmberTools18 in macOS Mojave (Thu Mar 28 2019 - 08:21:37 PDT)
- Re: [AMBER] Installation of AmberTools18 in macOS Mojave (Thu Mar 28 2019 - 07:15:01 PDT)
- Re: [AMBER] Installation of AmberTools18 in macOS Mojave (Wed Mar 27 2019 - 23:59:26 PDT)
- [AMBER] Installation of AmberTools18 in macOS Mojave (Wed Mar 27 2019 - 11:48:21 PDT)
Rinsha Chk
- Re: [AMBER] MMPBSA.py Calculation error (Fri Mar 08 2019 - 06:21:05 PST)
- [AMBER] MMPBSA.py Calculation error (Thu Mar 07 2019 - 21:52:40 PST)
RITUPARNA ROY
- [AMBER] Design of graphene quantum dots (Tue Mar 26 2019 - 20:50:50 PDT)
- [AMBER] Doubt regarding input files in NMR refinement (Fri Mar 01 2019 - 06:34:13 PST)
Rosellen, Martin
- [AMBER] chi1 angle of amino acids not having a CG atom (Wed Mar 06 2019 - 09:21:34 PST)
Ruth Helena Tichauer
- Re: [AMBER] velocities from and velocityautocorr (Mon Mar 18 2019 - 00:36:08 PDT)
- Re: [AMBER] velocities from and velocityautocorr (Fri Mar 15 2019 - 07:08:02 PDT)
- Re: [AMBER] velocities from and velocityautocorr (Wed Mar 13 2019 - 13:56:51 PDT)
- Re: [AMBER] velocities from and velocityautocorr (Wed Mar 13 2019 - 09:25:43 PDT)
- [AMBER] velocities from and velocityautocorr (Wed Mar 13 2019 - 09:07:37 PDT)
Saikat Pal
- [AMBER] Query regarding secondary structure (Tue Mar 19 2019 - 22:08:42 PDT)
- [AMBER] calculate RDF using COM (Thu Mar 07 2019 - 22:57:51 PST)
SATYAJIT KHATUA
- [AMBER] Query about plotting/visualizing the lifetime curve from H-Bond analysis using CPPTRAJ (Fri Mar 29 2019 - 07:12:27 PDT)
- Re: [AMBER] ValueError: invalid literal for int() with base 10: '-3.0' (Wed Mar 13 2019 - 21:19:19 PDT)
- [AMBER] ValueError: invalid literal for int() with base 10: '-3.0' (Thu Mar 07 2019 - 20:29:11 PST)
Scott Brozell
- Re: [AMBER] Potential bug in sander/LMOD (Fri Mar 08 2019 - 18:02:40 PST)
Setyanto Md
- Re: [AMBER] Single point energy calculation SCC-DFTB (Mon Mar 25 2019 - 05:47:53 PDT)
shahid khan
- [AMBER] Query about metal RMSD regarding residue number or atom number (Thu Mar 07 2019 - 03:21:39 PST)
Shayna Hilburg
- [AMBER] varying pressure conditions? (Mon Mar 25 2019 - 11:06:06 PDT)
Souvik Dey
- [AMBER] Solvating a Lipid bilayer in Amber (Sun Mar 03 2019 - 18:13:59 PST)
Sowmya Indrakumar
- Re: [AMBER] FEW amber- LIE analysis (Wed Mar 27 2019 - 03:36:06 PDT)
- [AMBER] FEW amber- LIE analysis (Thu Mar 21 2019 - 06:38:37 PDT)
Stephan Schott
- Re: [AMBER] Solvate with methanol and acetone using free energy methods? (Sat Mar 30 2019 - 14:47:07 PDT)
- Re: [AMBER] Jar pulling (Fri Mar 15 2019 - 07:15:17 PDT)
- Re: [AMBER] CUDA COM distance restraint (v18 with patch.7 applied) (Sun Mar 10 2019 - 12:10:57 PDT)
Sundar
- Re: [AMBER] distance restraint (Thu Mar 07 2019 - 06:29:09 PST)
- Re: [AMBER] distance restraint (Wed Mar 06 2019 - 07:57:38 PST)
Sunita Patel
- Re: [AMBER] distance restraint (Thu Mar 07 2019 - 20:12:15 PST)
- Re: [AMBER] distance restraint (Wed Mar 06 2019 - 19:58:55 PST)
- [AMBER] distance restraint (Sat Mar 02 2019 - 04:00:15 PST)
- Re: [AMBER] Atom type of Calcium (Fri Mar 01 2019 - 23:26:23 PST)
Szymon Żaczek
- Re: [AMBER] AMBER 18 error in QM region of QMMM (Tue Mar 26 2019 - 02:45:10 PDT)
Thomas Evangelidis
- Re: [AMBER] write equilibrium bond lengths, angles and dihedrals from a ligand structure file to a frcmod file (Sun Mar 10 2019 - 03:49:56 PDT)
- [AMBER] write equilibrium bond lengths, angles and dihedrals from a ligand structure file to a frcmod file (Fri Mar 08 2019 - 10:08:14 PST)
Träg, Johannes
- Re: [AMBER] gaff2 parameters of c3-c3-os-c3 (Mon Mar 18 2019 - 03:41:46 PDT)
- [AMBER] gaff2 parameters of c3-c3-os-c3 (Fri Mar 15 2019 - 08:21:05 PDT)
- [AMBER] parameters for cc and cd (Wed Mar 13 2019 - 10:27:19 PDT)
Vikram Dalal
- [AMBER] Query about protein DNA MD (Fri Mar 08 2019 - 09:29:34 PST)
- [AMBER] Help regarding protein DNA MD in AMBER (Thu Mar 07 2019 - 03:25:19 PST)
Wesley Michael Botello-Smith
- Re: [AMBER] MMPBSA (Sat Mar 30 2019 - 12:58:42 PDT)
- Re: [AMBER] MMPBSA (Sat Mar 30 2019 - 12:43:38 PDT)
Xiaocong Wang
- Re: [AMBER] [error] The system has extended beyond the extent of the virtual box (Sun Mar 03 2019 - 02:17:15 PST)
- [AMBER] [error] The system has extended beyond the extent of the virtual box (Sun Mar 03 2019 - 00:37:41 PST)
Xiaoyu Wang
- [AMBER] Restraint and ambmask syntax issue (Fri Mar 15 2019 - 11:36:13 PDT)
xmgign.126.com
- [AMBER] How can I generate of force field parameter for nano-material? (Sun Mar 03 2019 - 22:00:57 PST)
zaid kamal
- [AMBER] Message-ID: <20190301134103.u232i6wjibdt4cav@godel.rutgers.edu> (Mon Mar 04 2019 - 00:37:49 PST)
Zhonghua Xia
- Re: [AMBER] Error in Minimization (Fri Mar 15 2019 - 09:48:21 PDT)
- Re: [AMBER] Error in Minimization (Fri Mar 15 2019 - 08:37:48 PDT)
- [AMBER] Error in Minimization (Fri Mar 08 2019 - 01:18:57 PST)
李耀
- [AMBER] Amber18: Adaptively Biased MD (Metadynalmics) (Thu Mar 21 2019 - 08:49:56 PDT)
- [AMBER] Amber18: cv_min and cv_max for periodic cv in ABMD (Wed Mar 20 2019 - 09:25:26 PDT)
- [AMBER] Amber18 STSM (Sat Mar 16 2019 - 06:38:45 PDT)
郭昱
- [AMBER] how to make sure .prmtop is the same for NEB calculation when using explicit solvent? (Sun Mar 03 2019 - 19:06:08 PST)
高含露
- [AMBER] nmode_com.96 (Wed Mar 13 2019 - 01:24:58 PDT)
강무석
- [AMBER] Job terminated during TI calculation in pmemd.cuda (Wed Mar 13 2019 - 01:13:42 PDT)

Amber Archive Mar 2019 by author