Amber Archive Sep 2018: by date

Friday, 31 August 2018
- [AMBER] KDE analysis, (P) greater than one Mac Kevin Braza
- [AMBER] Constant velocity pulling in SMD M RCC
Saturday, 1 September 2018
- [AMBER] Temperature calculaton by CPPTRAJ Ikuo KURISAKI
- Re: [AMBER] NCSU_SMD for protein-ligand complex pulling M RCC
- [AMBER] Temperature calculaton by CPPTRAJ Ikuo KURISAKI
- [AMBER] Constant pH and Redox Potential MD tutorial Cruzeiro,Vinicius Wilian D
- Re: [AMBER] Temperature calculaton by CPPTRAJ Daniel Roe
- Re: [AMBER] KDE analysis, (P) greater than one Daniel Roe
Sunday, 2 September 2018
- [AMBER] Regarding error in MCPB.py dhaval patel
- [AMBER] Help in COM pulling M RCC
Monday, 3 September 2018
- [AMBER] Subtracting the forces from harmonic restraints Nikolay N. Kuzmich
- Re: [AMBER] Parameters for non-standard residues Anuja Ware
- Re: [AMBER] Normal mode calculation on a truncated system David A Case
- Re: [AMBER] Distance HH TIP3P David A Case
- Re: [AMBER] KDE analysis, (P) greater than one Adrian Roitberg
- Re: [AMBER] Temperature calculaton by CPPTRAJ Ikuo KURISAKI
- Re: [AMBER] cpptraj segmentation fault when using avgout in cluster Charo del Genio
- [AMBER] Format of cpptraj pairwise distance file when clustering Charo del Genio
- [AMBER] parameterizing the covalently bonded ligand hosein geraili
- Re: [AMBER] Format of cpptraj pairwise distance file when clustering Daniel Roe
- [AMBER] Coordinate messed up after tleap set box Simon Kit Sang Chu
- Re: [AMBER] KDE analysis, (P) greater than one Mac Kevin Braza
- [AMBER] Regarding output file in REMD Rajarshi Roy
Tuesday, 4 September 2018
- Re: [AMBER] Format of cpptraj pairwise distance file when clustering Charo del Genio
- Re: [AMBER] Coordinate messed up after tleap set box David A Case
- [AMBER] [david.case.rutgers.edu: Re: Coordinate messed up after tleap set box] David A Case
- Re: [AMBER] Need help regarding calculation of Coordination number from RDF Profile Bharat Manna
- Re: [AMBER] Regarding error in MCPB.py Pengfei Li
- [AMBER] Reg: antechamber net charge calculation -nc Samdani A
- Re: [AMBER] Format of cpptraj pairwise distance file when clustering Daniel Roe
- Re: [AMBER] Coordinate messed up after tleap set box Simon Kit Sang Chu
- [AMBER] GTX-2080 benchmarks Piotr Fajer
- Re: [AMBER] GTX-2080 benchmarks David Cerutti
- Re: [AMBER] Coordinate messed up after tleap set box David A Case
- Re: [AMBER] Reg: antechamber net charge calculation -nc David A Case
- Re: [AMBER] Coordinate messed up after tleap set box Simon Kit Sang Chu
- Re: [AMBER] Format of cpptraj pairwise distance file when clustering Daniel Roe
- [AMBER] RMS is zero Hadi Rahmaninejad
- Re: [AMBER] RMS is zero Stephan Schott
- Re: [AMBER] RMS is zero Hadi Rahmaninejad
Wednesday, 5 September 2018
- [AMBER] Restraining forces for atoms Nikolay N. Kuzmich
- Re: [AMBER] Restraining forces for atoms Bill Ross
- [AMBER] Fwd: Problem with energy minimization sander.MPI maryam azimzadehirani
- Re: [AMBER] Fwd: Problem with energy minimization sander.MPI Bill Ross
- Re: [AMBER] Fwd: Problem with energy minimization sander.MPI maryam azimzadehirani
- Re: [AMBER] Fwd: Problem with energy minimization sander.MPI David A Case
- [AMBER] covalently bonded ligand hosein geraili
- Re: [AMBER] Fwd: Problem with energy minimization sander.MPI maryam azimzadehirani
- Re: [AMBER] KDE analysis, (P) greater than one Jason Swails
Thursday, 6 September 2018
- [AMBER] MCPB.py error (not reading chk file) Sushi Shilpa
- [AMBER] Couldn't find VdW parameters Sushi Shilpa
- Re: [AMBER] Restraining forces for atoms Nikolay N. Kuzmich
- Re: [AMBER] Couldn't find VdW parameters Jason Swails
- [AMBER] Energy uints in mden file and mdout_analyzer.py Meng Wu
- Re: [AMBER] Restraining forces for atoms Bill Ross
- Re: [AMBER] Energy uints in mden file and mdout_analyzer.py David A Case
- Re: [AMBER] Energy uints in mden file and mdout_analyzer.py Meng Wu
Friday, 7 September 2018
- Re: [AMBER] Couldn't find VdW parameters Sushi Shilpa
- [AMBER] parmed pdb to crd Neha Gandhi
- [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster Markowska
- Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster David Cerutti
- Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster Markowska
- Re: [AMBER] parmed pdb to crd Jason Swails
- Re: [AMBER] Energy uints in mden file and mdout_analyzer.py Meng Wu
Saturday, 8 September 2018
- [AMBER] Leap: Nuleotides addition Aravind Ravichandran
- Re: [AMBER] Leap: Nuleotides addition David A Case
- Re: [AMBER] covalently bonded ligand Pengfei Li
- Re: [AMBER] MCPB.py error (not reading chk file) Pengfei Li
- Re: [AMBER] metalParm2.xml or metalParm.xml Pengfei Li
- Re: [AMBER] Arsenous acid (H3AsO3) parameterization Pengfei Li
- Re: [AMBER] Au+++ ion parameter Pengfei Li
- Re: [AMBER] Au+++ ion parameter Pengfei Li
Monday, 10 September 2018
- Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster David A Case
- Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster Ryan Novosielski
- Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster Ross Walker
Tuesday, 11 September 2018
- [AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL 龚乾坤
- Re: [AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL David A Case
- [AMBER] RMS rotate about z-axis only Wesley Michael Botello-Smith
- Re: [AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL 龚乾坤
- [AMBER] Question about configure Ambertool18 on Mac tang.xiaping.outlook.com
- Re: [AMBER] Question about configure Ambertool18 on Mac Bill Ross
- Re: [AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL 龚乾坤
Wednesday, 12 September 2018
- [AMBER] Query for umbrella sampling Saikat Pal
- Re: [AMBER] Question about configure Ambertool18 on Mac tang.xiaping.outlook.com
- Re: [AMBER] Question about configure Ambertool18 on Mac Bill Ross
- Re: [AMBER] Question about configure Ambertool18 on Mac tang.xiaping.outlook.com
- Re: [AMBER] Question about configure Ambertool18 on Mac Bill Ross
- [AMBER] Residue mutation and side chains Benjamin Clausen
- [AMBER] difference of distances using cpptraj in free energy plot Nisha Amarnath Jonniya
- Re: [AMBER] Question about configure Ambertool18 on Mac David A Case
- [AMBER] CPPTRAJ: extracting the restraining forces Nikolay N. Kuzmich
- [AMBER] A confusion about the binding energy calculated by pbsa with implicit membrane model 高振梅
- [AMBER] Amber constraint SMD 李耀
- Re: [AMBER] Residue mutation and side chains Carlos Simmerling
- Re: [AMBER] A confusion about the binding energy calculated by pbsa with implicit membrane model Ray Luo
- Re: [AMBER] difference of distances using cpptraj in free energy plot Daniel Roe
- [AMBER] more about gfortran8.2 and clang9.1: no cpptraj problems here David A Case
- Re: [AMBER] more about gfortran8.2 and clang9.1: no cpptraj problems here Bill Ross
- [AMBER] Query for umbrella sampling Saikat Pal
- Re: [AMBER] more about gfortran8.2 and clang9.1: no cpptraj problems here Bill Ross
- Re: [AMBER] Query for umbrella sampling Bill Ross
- [AMBER] H-bond between the substrate molecule and protein in the MD traj Meng Wu
- Re: [AMBER] H-bond between the substrate molecule and protein in the MD traj Gustaf Olsson
Thursday, 13 September 2018
- [AMBER] Some questions about mmpbsa.py 龚乾坤
- Re: [AMBER] Residue mutation and side chains Benjamin Clausen
- Re: [AMBER] Residue mutation and side chains Bill Ross
- Re: [AMBER] difference of distances using cpptraj in free energy plot Nisha Amarnath Jonniya
- [AMBER] Compression of CDF coordinate files to gzip AMBER18. DHEERAJ CHITARA
- Re: [AMBER] Some questions about mmpbsa.py David A Case
- Re: [AMBER] Compression of CDF coordinate files to gzip AMBER18. David A Case
- Re: [AMBER] H-bond between the substrate molecule and protein in the MD traj Daniel Roe
- [AMBER] Distance based energy calculation MOHD HOMAIDUR RAHMAN
- Re: [AMBER] Residue mutation and side chains Carlos Simmerling
- [AMBER] How to calculate Coordination number from RDF Profile using CPPTRAJ ? Bharat Manna
- [AMBER] a error about MMPBSA.PY 龚乾坤
Friday, 14 September 2018
- [AMBER] Query regarding the number of cores for running sander.MPI Leena Aggarwal
- Re: [AMBER] Query regarding the number of cores for running sander.MPI Stephan Schott
- [AMBER] Question about Amber. Asier Zorrilla
- Re: [AMBER] Question about Amber. Carlos Simmerling
- Re: [AMBER] Question about Amber. Adrian Roitberg
- Re: [AMBER] a error about MMPBSA.PY David A Case
- Re: [AMBER] Question about Amber. David A Case
- [AMBER] A confusion about the binding energy calculated by pbsa with implicit membrane model 高振梅
- [AMBER] Error in umbrella sampling Saikat Pal
- Re: [AMBER] RMS rotate about z-axis only Hai Nguyen
- [AMBER] Protein "jumping" during SMD run Cory Ayres
- Re: [AMBER] Error in umbrella sampling Bill Ross
- [AMBER] rdf in one dimmension Hadi Rahmaninejad
- Re: [AMBER] Protein "jumping" during SMD run Carlos Simmerling
- Re: [AMBER] rdf in one dimmension Tom Kurtzman
- Re: [AMBER] rdf in one dimmension Tom Kurtzman
Saturday, 15 September 2018
- [AMBER] why not free QM software？ Albert
- Re: [AMBER] why not free QM software？ Charles-Alexandre Mattelaer
- [AMBER] Newbie question about installing AmberTool18 in Linux (VirtualBox) leifepeterson.sbcglobal.net
- [AMBER] Installing fortran in Ubuntu-64 for Sander leifepeterson.sbcglobal.net
- Re: [AMBER] Installing fortran in Ubuntu-64 for Sander Dwight McGee
- [AMBER] RESOLVED: Installing fortran in Ubuntu-64 for Sander leifepeterson.sbcglobal.net
- [AMBER] Sander 01_Min.out error leifepeterson.sbcglobal.net
- [AMBER] RESOLVED: peek_ewald_inpcrd: Box info not found in inpcrd leifepeterson.sbcglobal.net
- [AMBER] unwrap problem in the liquid water dynamics trajectory analysis jinfeng liu
Sunday, 16 September 2018
- [AMBER] Clustering_distance_metric_option_general_rule Antonio Amber Carlesso
- Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis Matias Machado
- Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis Matias Machado
- Re: [AMBER] How to calculate Coordination number from RDF Profile using CPPTRAJ ? Matias Machado
- Re: [AMBER] RESOLVED: peek_ewald_inpcrd: Box info not found in inpcrd Matias Machado
- [AMBER] Adding 12_6_4 LJ parameters in prmtop file Deepika Sardana
- Re: [AMBER] why not free QM software？ Gustavo Seabra
- Re: [AMBER] why not free QM software？ Albert
- [AMBER] AMBER Alanine tutorial (different outputs from AMBER15 and AMBER18) leifepeterson.sbcglobal.net
- Re: [AMBER] why not free QM software？ Gustavo Seabra
- Re: [AMBER] AMBER Alanine tutorial (different outputs from AMBER15 and AMBER18) Matias Machado
- Re: [AMBER] Newbie question about installing AmberTool18 in Linux (VirtualBox) Hai Nguyen
- Re: [AMBER] rdf in one dimmension Hadi Rahmaninejad
- Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis David A Case
- Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis jinfeng liu
- Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis jinfeng liu
- [AMBER] Options for nonpolar solvation free energy calculation with mm_pbsa.pl 龚乾坤
Monday, 17 September 2018
- Re: [AMBER] Question about Amber. Asier Zorrilla
- Re: [AMBER] Question about Amber. Bill Ross
- Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis Daniel Roe
- Re: [AMBER] rdf in one dimmension Daniel Roe
- [AMBER] RESOLVED: AMBER Alanine tutorial (need to replace .mdcrd with .nc) leifepeterson.sbcglobal.net
- [AMBER] test errors of amber18 Lei Zhao
- [AMBER] pbsa:cannot match namelist object name mprob 高振梅
- Re: [AMBER] Error in umbrella sampling Saikat Pal
- Re: [AMBER] Error in umbrella sampling David A Case
- Re: [AMBER] pbsa:cannot match namelist object name mprob Ray Luo
- Re: [AMBER] Error in umbrella sampling Saikat Pal
- [AMBER] Contact Map Sourav Purohit
- Re: [AMBER] rdf in one dimmension Tom Kurtzman
- [AMBER] Amber16 cuda compiling error senal dinuka
- Re: [AMBER] Amber16 cuda compiling error David Cerutti
- Re: [AMBER] Amber16 cuda compiling error senal dinuka
- Re: [AMBER] Amber16 cuda compiling error David Cerutti
- [AMBER] Amber Installation Error Yuthika Dholey
Tuesday, 18 September 2018
- Re: [AMBER] Amber16 cuda compiling error David Case
- Re: [AMBER] Amber Installation Error David Case
- Re: [AMBER] Error in umbrella sampling Saikat Pal
- [AMBER] Regarding nastruct command in cpptraj Rajarshi Roy
- [AMBER] atomic fluctuation vs residue Avirup Ghosh
- [AMBER] Problem in testing the Zinc enzyme example using MCPB.py Alex Schwartz
- [AMBER] Fwd: Distance based energy calculation MOHD HOMAIDUR RAHMAN
Wednesday, 19 September 2018
- [AMBER] Unknown keyword Sushi Shilpa
- Re: [AMBER] Unknown keyword Bill Ross
- [AMBER] Problem with stripping with a condition Hadi Rahmaninejad
Thursday, 20 September 2018
- [AMBER] Running GIST calculation in parallel M RCC
- [AMBER] Amber on GPU emanuele falbo
- Re: [AMBER] Amber on GPU David A Case
- Re: [AMBER] Amber on GPU emanuele falbo
- Re: [AMBER] QM/MM Thermodynamic Integration emanuele falbo
- [AMBER] Temperature RMS, ntslim limit Nikolay N. Kuzmich
- Re: [AMBER] Problem with stripping with a condition Daniel Roe
- Re: [AMBER] Contact Map Daniel Roe
- Re: [AMBER] Regarding nastruct command in cpptraj Daniel Roe
- Re: [AMBER] atomic fluctuation vs residue Daniel Roe
- Re: [AMBER] Temperature RMS, ntslim limit Matias Machado
- Re: [AMBER] Distance based energy calculation Daniel Roe
- Re: [AMBER] Clustering_distance_metric_option_general_rule Daniel Roe
- Re: [AMBER] RMS rotate about z-axis only Daniel Roe
- Re: [AMBER] Running GIST calculation in parallel Daniel Roe
- Re: [AMBER] CPPTRAJ: extracting the restraining forces Daniel Roe
- Re: [AMBER] Clustering_distance_metric_option_general_rule Christina Bergonzo
- Re: [AMBER] Contact Map Sourav Purohit
- Re: [AMBER] QM/MM Thermodynamic Integration Goetz, Andreas
Friday, 21 September 2018
- Re: [AMBER] Regarding nastruct command in cpptraj Rajarshi Roy
Thursday, 20 September 2018
- [AMBER] Seeking clarification regarding Calculation of Linear Interaction Energy (lie) Bharat Manna
- Re: [AMBER] How to calculate Coordination number from RDF Profile using CPPTRAJ ? Bharat Manna
Friday, 21 September 2018
- Re: [AMBER] AMBER ntslim limit Nikolay N. Kuzmich
- Re: [AMBER] AMBER ntslim limit Bill Ross
- [AMBER] cuda 10 support Waqas Takkar
- Re: [AMBER] Question about Amber. Asier Zorrilla
- [AMBER] Query on 2DRMSD Saikat Pal
- Re: [AMBER] AMBER ntslim limit Matias Machado
- [AMBER] setting of different concentration of Nacl Nisha Amarnath Jonniya
- Re: [AMBER] setting of different concentration of Nacl Matias Machado
- Re: [AMBER] setting of different concentration of Nacl Stephan Schott
- Re: [AMBER] Running GIST calculation in parallel M RCC
- Re: [AMBER] setting of different concentration of Nacl Matias Machado
- Re: [AMBER] setting of different concentration of Nacl Stephan Schott
- Re: [AMBER] cuda 10 support David Cerutti
- Re: [AMBER] Regarding nastruct command in cpptraj Daniel Roe
- Re: [AMBER] Regarding nastruct command in cpptraj Rajarshi Roy
- Re: [AMBER] Running GIST calculation in parallel Daniel Roe
- Re: [AMBER] Running GIST calculation in parallel Matias Machado
- Re: [AMBER] Running GIST calculation in parallel Tom Kurtzman
- Re: [AMBER] Query on 2DRMSD Thomas Cheatham
Saturday, 22 September 2018
- Re: [AMBER] Problem in testing the Zinc enzyme example using MCPB.py Pengfei Li
- Re: [AMBER] Adding 12_6_4 LJ parameters in prmtop file Pengfei Li
- Re: [AMBER] Adding 12_6_4 LJ parameters in prmtop file Pengfei Li
Sunday, 23 September 2018
- Re: [AMBER] Running GIST calculation in parallel Matias Machado
- [AMBER] Critical Isoform selectivity in MD M RCC
Monday, 24 September 2018
- [AMBER] Error while creating topology file(HMassRepartition) in parmed Aravind Ravichandran
- Re: [AMBER] Options for nonpolar solvation free energy calculation with mm_pbsa.pl David A Case
- Re: [AMBER] Error while creating topology file(HMassRepartition) in parmed David A Case
- Re: [AMBER] Error while creating topology file(HMassRepartition) in parmed David A Case
- [AMBER] SMD free energy inferred from work Ruth Helena Tichauer
- Re: [AMBER] SMD free energy inferred from work Feng Pan
- Re: [AMBER] Contact Map Daniel Roe
- Re: [AMBER] Contact Map Daniel Roe
- [AMBER] nVidia Webinar: Achievable Free Energy Calculations through GPU-Accelerated AMBER accuratefreeenergy.gmail.com
- Re: [AMBER] SMD free energy inferred from work Ruth Helena Tichauer
- Re: [AMBER] Error while creating topology file(HMassRepartition) in parmed David Case
Tuesday, 25 September 2018
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphälinger
- [AMBER] PBC error. Amber force field in NAMD M RCC
- Re: [AMBER] PBC error. Amber force field in NAMD Eric Lang
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 James Kress
- [AMBER] Calculating residence times with cpptraj Stefan Ivanov
- [AMBER] Reducing memory usage in lifetime analyses Gustaf Olsson
Wednesday, 26 September 2018
- [AMBER] Problem with antechamber/acdoctor Sarah Fegan - UKRI STFC
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphälinger
- Re: [AMBER] Calculating residence times with cpptraj Daniel Roe
- Re: [AMBER] Reducing memory usage in lifetime analyses Daniel Roe
Thursday, 27 September 2018
- Re: [AMBER] Re-scaling masses and kinetic energy in TI calculations David Case
- Re: [AMBER] Critical Isoform selectivity in MD David Case
- [AMBER] Counter Ions in X-Ray structure. Keiran Corbett
- Re: [AMBER] test errors of amber18 David Case
- Re: [AMBER] Re-scaling masses and kinetic energy in TI calculations Tom Kurtzman
- Re: [AMBER] Counter Ions in X-Ray structure. David Case
- [AMBER] annoying elapsed time in mdout of amber18 Song-Ho Chong
- [AMBER] Umbrella sampling scripts emanuele falbo
- Re: [AMBER] Umbrella sampling scripts Marcos Serrou do Amaral
- Re: [AMBER] Umbrella sampling scripts emanuele falbo
- Re: [AMBER] Counter Ions in X-Ray structure. Keiran Corbett
- Re: [AMBER] Umbrella sampling scripts emanuele falbo
- Re: [AMBER] Counter Ions in X-Ray structure. Keiran Corbett
- Re: [AMBER] Umbrella sampling scripts Marcos Serrou do Amaral
- Re: [AMBER] Counter Ions in X-Ray structure. Matias Machado
- [AMBER] NVIDIA GPU RTX 2080 / RTX 2080 Ti Alain Chaumont
- Re: [AMBER] NVIDIA GPU RTX 2080 / RTX 2080 Ti David Cerutti
- Re: [AMBER] Counter Ions in X-Ray structure. Matias Machado
- Re: [AMBER] Umbrella sampling scripts emanuele falbo
- Re: [AMBER] annoying elapsed time in mdout of amber18 David Case
- Re: [AMBER] Counter Ions in X-Ray structure. David Case
- Re: [AMBER] Clustering_distance_metric_option_general_rule Antonio Amber Carlesso
- Re: [AMBER] annoying elapsed time in mdout of amber18 Song-Ho Chong
Friday, 28 September 2018
- Re: [AMBER] annoying elapsed time in mdout of amber18 Song-Ho Chong
- Re: [AMBER] Reducing memory usage in lifetime analyses Gustaf Olsson
- [AMBER] Problems with MPI compilation gb_force.F90 Ruben Ramos Horta
- Re: [AMBER] Problems with MPI compilation gb_force.F90 David Case
- Re: [AMBER] Problems with MPI compilation gb_force.F90 James Kress
- Re: [AMBER] annoying elapsed time in mdout of amber18 James Kress
- Re: [AMBER] annoying elapsed time in mdout of amber18 Song-Ho Chong
Saturday, 29 September 2018
- [AMBER] How to computing peptide partial charges with antechamber? yulongsun.nwpu.edu.cn
- Re: [AMBER] How to computing peptide partial charges with antechamber? David Case

Last message date: Sat Sep 29 2018 - 11:00:03 PDT
Archived on: Sun Nov 24 2024 - 05:55:55 PST

Amber Archive Sep 2018 by date