Amber Archive Feb 2019 by thread
- [AMBER] MCPB.py and ambmask for IRON Prasanth G, Research Scholar (Fri Feb 01 2019 - 01:58:13 PST)
- Re: [AMBER] PCA Analyze mode evec.pev Shirin Jamshidi (Fri Feb 01 2019 - 04:12:17 PST)
- [AMBER] Adding an atom to a residue by parmed mish (Fri Feb 01 2019 - 07:46:40 PST)
- [AMBER] QMMM differences between AMBER PM3 and Orca PM3 GiovanniMaria Piccini (Fri Feb 01 2019 - 08:55:57 PST)
- [AMBER] mpi installation problem Prabir Khatua (Fri Feb 01 2019 - 11:02:42 PST)
- Re: [AMBER] Problem regarding RMSD Daniel Roe (Fri Feb 01 2019 - 12:48:30 PST)
- [AMBER] vdw radii of sodium ion in GAFF Qasim Pars (Fri Feb 01 2019 - 16:34:55 PST)
- [AMBER] merging molecules Stefano Guglielmo (Sat Feb 02 2019 - 09:10:11 PST)
- [AMBER] MCPB.py & error: coordinates number in fchk file are not consistent with the atom number Prasanth G, Research Scholar (Mon Feb 04 2019 - 05:43:32 PST)
- [AMBER] RMSD of single residue, fit to main structure Rosellen, Martin (Mon Feb 04 2019 - 06:33:18 PST)
- [AMBER] NaN in QM-MMPBSA results Sundar (Mon Feb 04 2019 - 11:13:57 PST)
- [AMBER] Wham analysis on amber18 (pmemd.cuda) output file mish (Tue Feb 05 2019 - 03:05:32 PST)
- [AMBER] Cpptraj hist command Pablo Palomino (Tue Feb 05 2019 - 03:23:22 PST)
- [AMBER] pairwise command in cpptraj Leena Aggarwal (Tue Feb 05 2019 - 04:27:22 PST)
- [AMBER] Graphs Keiran Corbett (Tue Feb 05 2019 - 05:56:06 PST)
- [AMBER] Ca in Amber14 vs Amber18 Keiran Corbett (Tue Feb 05 2019 - 06:07:53 PST)
- [AMBER] hbonds solute with residue Rosellen, Martin (Tue Feb 05 2019 - 06:29:26 PST)
- [AMBER] cpptraj MYRIAN TORRES RICO (Tue Feb 05 2019 - 06:51:05 PST)
- Re: [AMBER] MCPB.py error with HEME containing protein Pengfei Li (Tue Feb 05 2019 - 08:00:19 PST)
- Re: [AMBER] MCPB.py Error Pengfei Li (Tue Feb 05 2019 - 09:03:59 PST)
- [AMBER] Use of LIE command in cpptraj error Debarati DasGupta (Tue Feb 05 2019 - 12:28:50 PST)
- [AMBER] chamber problem Prabir Khatua (Tue Feb 05 2019 - 13:46:38 PST)
- [AMBER] Creating PRMTOP and INPCRD in Amber 16 Fulbabu Sk (Wed Feb 06 2019 - 01:30:55 PST)
- Re: [AMBER] FW: Building topology of a molecule with Antechamber David A Case (Wed Feb 06 2019 - 04:56:02 PST)
- [AMBER] Change simulation box size Anthony Cruz-Balberdy (Wed Feb 06 2019 - 05:24:24 PST)
- [AMBER] RESP charges for atoms/molecules which not included gaff, gaff2, exc..? Erdem Yeler (Wed Feb 06 2019 - 05:49:32 PST)
- [AMBER] mmpbsa error Mehreen Ghufran (Wed Feb 06 2019 - 08:19:55 PST)
- [AMBER] The 3D-RISM-PC+ information for each atoms Eugene huh (Wed Feb 06 2019 - 23:49:04 PST)
- [AMBER] FW: Running Tempered + Hamiltonian replica exchange using pmemd.cuda.MPI BLUNTZER Marie (Thu Feb 07 2019 - 03:28:17 PST)
- [AMBER] Regarding constant pH MD Saikat Pal (Fri Feb 08 2019 - 07:29:38 PST)
- [AMBER] amber installation problem Rimon Riju (Fri Feb 08 2019 - 23:19:03 PST)
- [AMBER] Convert prmtop to PSF file in Cpptraj Fulbabu Sk (Sat Feb 09 2019 - 12:39:50 PST)
- [AMBER] 1D-RISM: *.xvv generation error Eugene huh (Mon Feb 11 2019 - 01:31:43 PST)
- [AMBER] Behavior of MSD at different collision frequency values Abdullah Bin Faheem (Mon Feb 11 2019 - 02:13:07 PST)
- [AMBER] Planarity of bound versus unbound ligand Tye Martin (Mon Feb 11 2019 - 12:36:42 PST)
- [AMBER] charmm psf to amber prmtop conversion problem Prabir Khatua (Mon Feb 11 2019 - 13:09:31 PST)
- [AMBER] Atom type of Calcium Sunita Patel (Mon Feb 11 2019 - 23:22:24 PST)
- [AMBER] Restart file is not formed until the simulation finishes Chetna Tyagi (Tue Feb 12 2019 - 02:55:30 PST)
- [AMBER] MM-GBSA for protein-sugar complex James Starlight (Tue Feb 12 2019 - 07:30:10 PST)
- [AMBER] Cpptraj: PC1 and PC1 as function of residue number calculation Fulbabu Sk (Tue Feb 12 2019 - 11:30:42 PST)
- [AMBER] Interpreting QM MMPBSA results Sundar (Tue Feb 12 2019 - 14:50:25 PST)
- [AMBER] cpptraj PCA error Alen Ahmetovic (Tue Feb 12 2019 - 16:27:22 PST)
- [AMBER] Regarding population of hydrogen bond MOHD HOMAIDUR RAHMAN (Tue Feb 12 2019 - 17:24:14 PST)
- [AMBER] Amber installation on Ubuntu 18.04 Rajarshi Roy (Tue Feb 12 2019 - 20:32:32 PST)
- [AMBER] Amber18 TI on K10 - any known problem? Thomas Fox (Wed Feb 13 2019 - 04:06:28 PST)
- [AMBER] gromacs .top file error fateme haghighi (Wed Feb 13 2019 - 06:52:06 PST)
- [AMBER] A few issues Paul, Austin (Wed Feb 13 2019 - 06:55:12 PST)
- [AMBER] reference.frc file from MMPBSA calculations Sundar (Wed Feb 13 2019 - 10:02:55 PST)
- [AMBER] NMR restraints in AmberTools? Istvan Kolossvary (Wed Feb 13 2019 - 15:34:45 PST)
- [AMBER] Dihedral configuration entropy Lod King (Wed Feb 13 2019 - 16:02:50 PST)
- [AMBER] Calculation of Entropy using MMPBSA AMBER 18 DHEERAJ CHITARA (Wed Feb 13 2019 - 21:43:48 PST)
- [AMBER] MMPBSA Nisha Amarnath Jonniya (Wed Feb 13 2019 - 23:06:08 PST)
- [AMBER] making force fields files from topology Hadi Rahmaninejad (Thu Feb 14 2019 - 07:31:45 PST)
- [AMBER] MBAR from TI on pmemd Hosein Geraili Daronkola (Thu Feb 14 2019 - 08:36:17 PST)
- Re: [AMBER] OpenMPI 4.0.0 support Stephan Schott (Thu Feb 14 2019 - 16:54:02 PST)
- [AMBER] Dihedral configuration entropy Lod King (Thu Feb 14 2019 - 17:48:27 PST)
- [AMBER] Generating spherical macro-ion in amber ATUL KUMAR (Thu Feb 14 2019 - 23:20:18 PST)
- [AMBER] MBAR from TI on pmemd Hosein Geraili Daronkola (Fri Feb 15 2019 - 00:38:46 PST)
- [AMBER] xleap "impose" and addAtomtypes command for paramfit gen_conformers.sh Erdem Yeler (Sat Feb 16 2019 - 20:54:52 PST)
- [AMBER] peptide-bilayer MD simulation analysis golshan bakrani (Sun Feb 17 2019 - 21:50:35 PST)
- [AMBER] Speed-up calculation of Entropy with MMPBSA James Starlight (Mon Feb 18 2019 - 01:34:22 PST)
- [AMBER] Umbrella Sampling and WHAM analysis mish (Mon Feb 18 2019 - 03:29:31 PST)
- [AMBER] MBAR from TI on pmemd Hosein Geraili Daronkola (Mon Feb 18 2019 - 04:57:17 PST)
- [AMBER] ChamberParm objects are not supported by this action Hadi Rahmaninejad (Mon Feb 18 2019 - 09:13:22 PST)
- [AMBER] puckering coordinates MYRIAN TORRES RICO (Mon Feb 18 2019 - 09:54:13 PST)
- Re: [AMBER] Speed-up calculation of Entropy with MMPBSA (James Starlight) David Minh (Mon Feb 18 2019 - 12:22:08 PST)
- [AMBER] ff99SBi force field in Amber Advanced Tutorial A22 Michiel de Hoon (Mon Feb 18 2019 - 18:30:06 PST)
- [AMBER] Problem during parallel installation Sunita Patel (Tue Feb 19 2019 - 07:05:49 PST)
- [AMBER] Bad atom type i Keiran Corbett (Tue Feb 19 2019 - 02:04:52 PST)
- [AMBER] puckering MYRIAN TORRES RICO (Tue Feb 19 2019 - 07:23:43 PST)
- [AMBER] gas phase TI Hosein Geraili Daronkola (Tue Feb 19 2019 - 07:37:39 PST)
- [AMBER] gas phase TI Hosein Geraili Daronkola (Tue Feb 19 2019 - 07:42:00 PST)
- [AMBER] gas phase TI Hosein Geraili Daronkola (Tue Feb 19 2019 - 07:52:58 PST)
- [AMBER] gas phase TI Hosein Geraili Daronkola (Tue Feb 19 2019 - 08:06:54 PST)
- [AMBER] MMPBSA Calculation Error: Order of protein and ligand M RCC (Tue Feb 19 2019 - 09:17:07 PST)
- [AMBER] Silica in antechamber Hadi Rahmaninejad (Tue Feb 19 2019 - 09:46:42 PST)
- [AMBER] Protein_plus_ADP_plus_Mg2+_preparation_general_rule Antonio Amber Carlesso (Tue Feb 19 2019 - 10:57:26 PST)
- [AMBER] Ovito visualization Shayna Hilburg (Tue Feb 19 2019 - 12:48:46 PST)
- [AMBER] Suggestions for Analysis Souvik Dey (Tue Feb 19 2019 - 15:49:27 PST)
- [AMBER] MMGBSA Angew Chemie (Tue Feb 19 2019 - 20:21:34 PST)
- [AMBER] overestimate hydrogen bonding distance Niko Prasetyo (Wed Feb 20 2019 - 01:36:40 PST)
- [AMBER] puckering coordinates MYRIAN TORRES RICO (Wed Feb 20 2019 - 03:17:48 PST)
- [AMBER] Bond breakage modelling Ali Khodayari (Wed Feb 20 2019 - 05:04:13 PST)
- [AMBER] puckering coordinates MYRIAN TORRES RICO (Wed Feb 20 2019 - 06:22:34 PST)
- [AMBER] Amber14 installation issue Alexey Orlov (Wed Feb 20 2019 - 09:56:56 PST)
- [AMBER] XMIN internal output suppressed Istvan Kolossvary (Wed Feb 20 2019 - 15:45:51 PST)
- [AMBER] Can cpptraj multidihedral use nonbonded atoms? Michael F. Bruist (Wed Feb 20 2019 - 15:48:29 PST)
- [AMBER] About clusterdihedral Gilberto Pereira (Thu Feb 21 2019 - 01:06:47 PST)
- [AMBER] Error and sudden halt in equilibration senal dinuka (Thu Feb 21 2019 - 03:00:00 PST)
- [AMBER] Problem in running pmemd.cuda ATUL KUMAR (Thu Feb 21 2019 - 03:00:03 PST)
- [AMBER] Reference energies in CpHMD (constant pH MD) for HIP Rodrigo Pérez Cossio (Thu Feb 21 2019 - 16:16:48 PST)
- [AMBER] Does NVIDIA RTX 2080 Ti support Amber16 with cuda-8? M RCC (Fri Feb 22 2019 - 00:20:29 PST)
- [AMBER] puckering coordinates MYRIAN TORRES RICO (Fri Feb 22 2019 - 01:40:41 PST)
- [AMBER] MBAR from TI on pmemd Hosein Geraili Daronkola (Fri Feb 22 2019 - 02:33:31 PST)
- [AMBER] Dihedral Kb Value when IDIVF=1 Erdem Yeler (Fri Feb 22 2019 - 03:17:57 PST)
- [AMBER] QM/MM - gaussian interface query Abhilash J (Sat Feb 23 2019 - 04:02:31 PST)
- [AMBER] Potential bug in sander/LMOD Istvan Kolossvary (Sun Feb 24 2019 - 14:29:11 PST)
- [AMBER] Protein-ligand simulation and help w.r.t files for carrying out simulation Prasanth G, Research Scholar (Mon Feb 25 2019 - 04:53:34 PST)
- [AMBER] pytraj distance image Antoine MARION (Mon Feb 25 2019 - 07:53:56 PST)
- [AMBER] Nothing returned in aMD simulation of membrane protein Meng Wu (Mon Feb 25 2019 - 21:42:52 PST)
- [AMBER] confusion of choosing force field Sasthi Charan Mandal (Tue Feb 26 2019 - 04:54:13 PST)
- [AMBER] Changing ligand coordinates D. Yousefi (Tue Feb 26 2019 - 05:29:04 PST)
- [AMBER] command from ambertools tutorial does not working Sasthi Charan Mandal (Tue Feb 26 2019 - 09:29:30 PST)
- [AMBER] protein function Hosein Geraili Daronkola (Tue Feb 26 2019 - 10:30:12 PST)
- [AMBER] Error in generating the residue topology for non-standard amino acid residues RITUPARNA ROY (Wed Feb 27 2019 - 06:48:10 PST)
- [AMBER] antechamber error Chang Woon Jang (Wed Feb 27 2019 - 09:38:14 PST)
- [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? Feng, Zimin (Wed Feb 27 2019 - 12:25:02 PST)
- [AMBER] CPPTRAJ Center of Mass binning Debarati DasGupta (Wed Feb 27 2019 - 12:49:54 PST)
- [AMBER] CPPTRAJ grid unknown command Debarati DasGupta (Wed Feb 27 2019 - 14:11:54 PST)
- [AMBER] Two dimensional replica exchange MD: Success rate Stephan Eismann (Wed Feb 27 2019 - 17:30:20 PST)
- [AMBER] alchemical_analysis Hosein Geraili Daronkola (Thu Feb 28 2019 - 08:24:01 PST)
- Last message date: Thu Feb 28 2019 - 16:00:03 PST
- Archived on: Mon Nov 25 2024 - 05:55:40 PST
