Amber Archive Jun 2016: by date

Tuesday, 31 May 2016
- Re: [AMBER] cpptraj clustering based on ligand cavity Neha Gandhi
- [AMBER] rdf or watershell Neha Gandhi
- [AMBER] QMS-QMMM Odin Zeus
Wednesday, 1 June 2016
- [AMBER] radial (rdf) computation time Neha Gandhi
- Re: [AMBER] QMS-QMMM Adrian Roitberg
- Re: [AMBER] radial (rdf) computation time Daniel Roe
- Re: [AMBER] cpptraj clustering based on ligand cavity Daniel Roe
- Re: [AMBER] rdf or watershell Daniel Roe
- [AMBER] FW: MMPBSA.py issue with complex prmtop file Kalenkiewicz, Andrew (NIH/NICHD) [F]
- Re: [AMBER] FW: MMPBSA.py issue with complex prmtop file Hai Nguyen
- Re: [AMBER] FW: MMPBSA.py issue with complex prmtop file Hai Nguyen
- [AMBER] Amber Cpptraj troubleshoot Angelina Malagodi
- Re: [AMBER] Amber Cpptraj troubleshoot Hai Nguyen
- Re: [AMBER] Amber Cpptraj troubleshoot Daniel Roe
- Re: [AMBER] Amber Cpptraj troubleshoot Angelina Malagodi
- Re: [AMBER] Amber Cpptraj troubleshoot Angelina Malagodi
- Re: [AMBER] Amber Cpptraj troubleshoot Hai Nguyen
- Re: [AMBER] Amber Cpptraj troubleshoot Hai Nguyen
- Re: [AMBER] Amber Cpptraj troubleshoot David A Case
- [AMBER] mmgbsa calculation chemjxn
- [AMBER] parmchk and parmchk2 segmentation fault Neha Gandhi
- Re: [AMBER] parmchk and parmchk2 segmentation fault David A Case
- Re: [AMBER] radial (rdf) computation time Neha Gandhi
Thursday, 2 June 2016
- [AMBER] Unreadable rst7 Elisa Pieri
- Re: [AMBER] Unreadable rst7 Bill Ross
- Re: [AMBER] Unreadable rst7 Elisa Pieri
- Re: [AMBER] Unreadable rst7 Bill Ross
- Re: [AMBER] Unreadable rst7 Bill Ross
- Re: [AMBER] Unreadable rst7 Elisa Pieri
- Re: [AMBER] mmgbsa calculation Jason Swails
- Re: [AMBER] Unreadable rst7 Jason Swails
- Re: [AMBER] Unreadable rst7 David A Case
- Re: [AMBER] Unreadable rst7 Elisa Pieri
- Re: [AMBER] Unreadable rst7 Jason Swails
- Re: [AMBER] radial (rdf) computation time Daniel Roe
- [AMBER] mmpbsa analys Ziba Bahadori
- Re: [AMBER] mmpbsa analys Jason Swails
- Re: [AMBER] Replacing water with a H2O2 and restart the simulation Morteza Chehel Amirani
- Re: [AMBER] mdl file for 1d-rism Jingyi Yan
- Re: [AMBER] Replacing water with a H2O2 and restart the simulation Bill Ross
Friday, 3 June 2016
- [AMBER] Some problems about heme 163邮箱
- [AMBER] iwrap and mmpbsa Mary Varughese
- [AMBER] re imaging doubt Mary Varughese
- [AMBER] Amber16 won't install Gulsevin,Alican
- Re: [AMBER] Some problems about heme Vaibhav Dixit
- Re: [AMBER] re imaging doubt Hai Nguyen
- Re: [AMBER] Amber16 won't install Hai Nguyen
- Re: [AMBER] Amber16 won't install Hai Nguyen
- Re: [AMBER] Amber16 won't install Gulsevin,Alican
- Re: [AMBER] Amber16 won't install Hai Nguyen
- [AMBER] proper box size to calculate binding enthalpy of host-guest in explicit solvent Budhathoki, Dipesh
- Re: [AMBER] Amber16 won't install Gulsevin,Alican
- Re: [AMBER] Amber16 won't install Hai Nguyen
- Re: [AMBER] iwrap and mmpbsa Jason Swails
- Re: [AMBER] GAFF2 setup Igor Marques
- Re: [AMBER] Some problems about heme David A Case
- [AMBER] TI calculation with ligand dimer Hu, Yuan
- [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 mmaestre
Saturday, 4 June 2016
- Re: [AMBER] TI calculation with ligand dimer Hannes Loeffler
- [AMBER] Principle Component Analysis (PCA) in cpptraj Himanshu Joshi
- [AMBER] Some problems about Heme 163邮箱
- Re: [AMBER] Some problems about Heme Vaibhav Dixit
- [AMBER] mmpbsa problem Ziba Bahadori
- Re: [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 Mark Abraham
- Re: [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 Ross Walker
- Re: [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 Mark Abraham
- Re: [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 Ross Walker
- [AMBER] Ambertools16 test failed for leap zoran matovic
- Re: [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 mmaestre
- Re: [AMBER] Some problems about Heme David A Case
- Re: [AMBER] Ambertools16 test failed for leap David A Case
- Re: [AMBER] Ambertools16 test failed for leap zmatovic.kg.ac.rs
Sunday, 5 June 2016
- [AMBER] pulling a zn ion with SMD Fabian gmail
- Re: [AMBER] pulling a zn ion with SMD Himanshu Joshi
- [AMBER] [Amber] Build parameters on HEME-Fe-HIS system 163邮箱
- Re: [AMBER] Principle Component Analysis (PCA) in cpptraj Daniel Roe
- [AMBER] Protein - ligand tutorials - reg arthivenkat2.gmail.com
- Re: [AMBER] Principle Component Analysis (PCA) in cpptraj Himanshu Joshi
- Re: [AMBER] Principle Component Analysis (PCA) in cpptraj Himanshu Joshi
- Re: [AMBER] Principle Component Analysis (PCA) in cpptraj Daniel Roe
- Re: [AMBER] Protein - ligand tutorials - reg Hai Nguyen
- Re: [AMBER] Protein - ligand tutorials - reg David A Case
- [AMBER] proper box size to calculate binding enthalpy of host-guest in explicit solvent Budhathoki, Dipesh
- [AMBER] test 4096wat mmaestre
- Re: [AMBER] test 4096wat Charles Lin
- Re: [AMBER] test 4096wat Charles Lin
Monday, 6 June 2016
- [AMBER] Issue of AMBER 2016 with CUDA Huian Li
- [AMBER] restarting a run Thomas Pochapsky
- [AMBER] cpinutil.py problem Elisa Pieri
- Re: [AMBER] Some problems about Heme Lachele Foley
- Re: [AMBER] cpinutil.py problem Jason Swails
- Re: [AMBER] cpinutil.py problem Elisa Pieri
- Re: [AMBER] cpinutil.py problem Elisa Pieri
- Re: [AMBER] TI calculation with ligand dimer Hu, Yuan
- Re: [AMBER] Issue of AMBER 2016 with CUDA David A Case
- Re: [AMBER] restarting a run David A Case
- Re: [AMBER] restarting a run Thomas Pochapsky
- Re: [AMBER] proper box size to calculate binding enthalpy of host-guest Budhathoki, Dipesh
- Re: [AMBER] Clustering of MD trajectories: ptraj, cpptraj Daniel Roe
- Re: [AMBER] proper box size to calculate binding enthalpy of host-guest Niel Henriksen
- [AMBER] setMolecules failed Damiano Spadoni
- Re: [AMBER] setMolecules failed Daniel Roe
- Re: [AMBER] proper box size to calculate binding enthalpy of host-guest Budhathoki, Dipesh
- Re: [AMBER] proper box size to calculate binding enthalpy of host-guest Niel Henriksen
- Re: [AMBER] proper box size to calculate binding enthalpy of host-guest Budhathoki, Dipesh
Tuesday, 7 June 2016
- Re: [AMBER] restarting a run David A Case
- Re: [AMBER] setMolecules failed David A Case
- [AMBER] cpptraj reading a reference coordinate for analyses Neha Gandhi
- Re: [AMBER] pulling a zn ion with SMD Fabian gmail
- Re: [AMBER] setMolecules failed Damiano Spadoni
- [AMBER] Amber14 & Cuda 7.5 Nikolay N. Kuzmich
- Re: [AMBER] restarting a run Thomas Pochapsky
- Re: [AMBER] Amber14 & Cuda 7.5 Irfan Alibay
- Re: [AMBER] setMolecules failed Jason Swails
- Re: [AMBER] cpptraj reading a reference coordinate for analyses Daniel Roe
- Re: [AMBER] Issue of AMBER 2016 with CUDA Huian Li
- Re: [AMBER] setMolecules failed David A Case
- Re: [AMBER] setMolecules failed Jason Swails
- Re: [AMBER] Some problems about Heme Pengfei Li
- Re: [AMBER] Issue of AMBER 2016 with CUDA Jason Swails
- [AMBER] Umbrella sampling with two degrees of freedom Airy Sanjeev
- Re: [AMBER] Umbrella sampling with two degrees of freedom Feng Pan
- Re: [AMBER] Umbrella sampling with two degrees of freedom David Cerutti
- [AMBER] Energy decomposition in MM/GBSA mish
Wednesday, 8 June 2016
- [AMBER] neuraminic acid mmaestre
- Re: [AMBER] neuraminic acid Lachele Foley
- Re: [AMBER] neuraminic acid mmaestre
- [AMBER] Error while trying to upgrade AmberTools 15 Nikolay N. Kuzmich
- Re: [AMBER] Error while trying to upgrade AmberTools 15 Jason Swails
- [AMBER] MD simulations with jar=1 and more than one nmropt restraint James Murdock
- Re: [AMBER] Umbrella sampling with two degrees of freedom Carlos Simmerling
- [AMBER] How to define COM group of atoms greater than 1024 atoms when nmropt=1 and pmemd.cuda.MPI Shuntaro Chiba
- Re: [AMBER] MD simulations with jar=1 and more than one nmropt restraint Feng Pan
- [AMBER] Umbrella Sampling Airy Sanjeev
- Re: [AMBER] Umbrella Sampling David Cerutti
- Re: [AMBER] Umbrella Sampling Carlos Simmerling
- [AMBER] Dismal QM/MM Efficiency Nisler, Collin R.
- Re: [AMBER] Dismal QM/MM Efficiency Adrian Roitberg
- Re: [AMBER] Dismal QM/MM Efficiency Dr. Andreas W. Goetz
- Re: [AMBER] Dismal QM/MM Efficiency Nisler, Collin R.
- Re: [AMBER] Dismal QM/MM Efficiency Nisler, Collin R.
- Re: [AMBER] Dismal QM/MM Efficiency Jason Swails
- [AMBER] hanging test mdgx/1p7e for installation to 'long' path Kenneth Hoste
- Re: [AMBER] Dismal QM/MM Efficiency Dr. Andreas W. Goetz
- Re: [AMBER] hanging test mdgx/1p7e for installation to 'long' path David Cerutti
- [AMBER] Principal Component Analysis Kat G
- [AMBER] buffer OR buffer_xyz_list in setBox command mish
- Re: [AMBER] Principal Component Analysis Jason Swails
- [AMBER] energy decomposition Sanjib Paul
Thursday, 9 June 2016
- [AMBER] INDIGO-DataCloud Newsletter, May 2016 galileo.galile22.yahoo.com
- [AMBER] THF parametrization Norbert GARNIER
- Re: [AMBER] energy decomposition David A Case
- [AMBER] PCA error not Lara rajam
- Re: [AMBER] PCA error not Daniel Roe
- [AMBER] RMSD for the backbone atoms of residues Aishani Prem
- Re: [AMBER] RMSD for the backbone atoms of residues Daniel Roe
- Re: [AMBER] RMSD for the backbone atoms of residues Aishani Prem
- Re: [AMBER] RMSD for the backbone atoms of residues Daniel Roe
- Re: [AMBER] RMSD for the backbone atoms of residues Aishani Prem
- Re: [AMBER] RMSD for the backbone atoms of residues Hai Nguyen
- [AMBER] QM/MM MD problem Debodyuti Dutta
- [AMBER] Issue with with the nocenter in tLeap Sushil Mishra
Friday, 10 June 2016
- Re: [AMBER] RMSD for the backbone atoms of residues Dr. Anselm Horn
- Re: [AMBER] hanging test mdgx/1p7e for installation to 'long' path Kenneth Hoste
- [AMBER] FF14SB implementation Miroslav Krepl
- [AMBER] Error in tleap for the atom type of OCT1 and OCT2 of glutamic acid at C-terminal Shreeramesh
- Re: [AMBER] RMSD for the backbone atoms of residues Daniel Roe
- [AMBER] addition of hydrogen to unionised the -COO group Martina Devi
- [AMBER] Regarding error in MMPBSA MOHD HOMAIDUR RAHMAN
- [AMBER] radial distribution function tails for liquids using GAFF conor parks
Saturday, 11 June 2016
- [AMBER] Free energy decomposition of QM/MM-GBSA Allen Zou
- Re: [AMBER] Error in tleap for the atom type of OCT1 and OCT2 of glutamic acid at C-terminal David A Case
- Re: [AMBER] addition of hydrogen to unionised the -COO group David A Case
- Re: [AMBER] radial distribution function tails for liquids using GAFF David A Case
- Re: [AMBER] addition of hydrogen to unionised the -COO group Martina Devi
- Re: [AMBER] radial distribution function tails for liquids using GAFF Conor Parks
- Re: [AMBER] addition of hydrogen to unionised the -COO group David A Case
Sunday, 12 June 2016
- [AMBER] Help me with double ambiguous noe.map files!!! PLEASE tanfei777.sina.cn
- Re: [AMBER] Help me with double ambiguous noe.map files!!! PLEASE David A Case
- [AMBER] Problem in Calculating Rotational diffusion ATUL KUMAR
- Re: [AMBER] Problem in Calculating Rotational diffusion Daniel Roe
- [AMBER] 回复：Re: Help me with double ambiguous noe.map files!!! PLEASE tanfei777.sina.cn
- [AMBER] Can I turn off group coordinate averaging? tanfei777.sina.cn
- Re: [AMBER] Problem in Calculating Rotational diffusion ATUL KUMAR
Monday, 13 June 2016
- [AMBER] problems with building sulfo sialil-lacnac mmaestre
- Re: [AMBER] Error in tleap for the atom type of OCT1 and OCT2 of glutamic acid at C-terminal Shreeramesh
- [AMBER] umbrella sampling with two degrees of freedom Airy Sanjeev
- [AMBER] Choose reference frame for rmsd Jean-Patrick Francoia
- Re: [AMBER] Choose reference frame for rmsd Daniel Roe
- Re: [AMBER] Error in tleap for the atom type of OCT1 and OCT2 of glutamic acid at C-terminal Daniel Roe
- Re: [AMBER] Problem in Calculating Rotational diffusion Daniel Roe
- [AMBER] umbrella sampling long axex problem Airy Sanjeev
- Re: [AMBER] Help me with double ambiguous noe.map files!!! PLEASE Duggan, Brendan
- [AMBER] Radial Distribution Function Angelina Malagodi
- Re: [AMBER] Radial Distribution Function Daniel Roe
- Re: [AMBER] Radial Distribution Function Angelina Malagodi
- Re: [AMBER] Can I turn off group coordinate averaging? David A Case
- Re: [AMBER] Radial Distribution Function Daniel Roe
- Re: [AMBER] Radial Distribution Function Angelina Malagodi
- Re: [AMBER] Radial Distribution Function Hai Nguyen
- Re: [AMBER] Radial Distribution Function Angelina Malagodi
- Re: [AMBER] Radial Distribution Function Daniel Roe
- Re: [AMBER] Choose reference frame for rmsd Jean-Patrick Francoia
- [AMBER] 回复：Re: Help me with double ambiguous noe.map files!!! PLEASE tanfei777.sina.cn
- [AMBER] Fwd: eChemInfo Workshop on Rational Drug Design in Milano Thomas Exner
- Re: [AMBER] addition of hydrogen to unionised the -COO group Martina Devi
Tuesday, 14 June 2016
- [AMBER] antechamber error message Martina Devi
- [AMBER] Errors in my installation Abdul-Rashid Iii Sampaco
- [AMBER] Problem: Do not receive mails from Amber list but Amber digest SHAILESH KUMAR
- [AMBER] Difference between radius of gyration and max radius of gyration Jean-Patrick Francoia
- Re: [AMBER] Errors in my installation Marcelo Andrade Chagas
- Re: [AMBER] antechamber error message David A Case
- Re: [AMBER] Errors in my installation David A Case
- Re: [AMBER] FF14SB implementation David A Case
- Re: [AMBER] FF14SB implementation Vlad Cojocaru
- Re: [AMBER] FF14SB implementation Miroslav Krepl
- Re: [AMBER] FF14SB implementation Carlos Simmerling
- Re: [AMBER] FF14SB implementation Vlad Cojocaru
- Re: [AMBER] FF14SB implementation Carlos Simmerling
- Re: [AMBER] Errors in my installation Hai Nguyen
- Re: [AMBER] Difference between radius of gyration and max radius of gyration Daniel Roe
- Re: [AMBER] antechamber error message Martina Devi
- Re: [AMBER] Difference between radius of gyration and max radius of gyration Jean-Patrick Francoia
- Re: [AMBER] antechamber error message David A Case
- Re: [AMBER] Problem: Do not receive mails from Amber list but Amber digest Ross Walker
- [AMBER] [ANN] Release of NGLView for interactive trajectory visualization in Jupyter notebooks. Hai Nguyen
- Re: [AMBER] Problem: Do not receive mails from Amber list but Amber digest SHAILESH KUMAR
- [AMBER] amber16 pmemd cuda rst file Neha Gandhi
- Re: [AMBER] amber16 pmemd cuda rst file Daniel Roe
- Re: [AMBER] amber16 pmemd cuda rst file Neha Gandhi
- Re: [AMBER] amber16 pmemd cuda rst file Daniel Roe
- Re: [AMBER] Errors in my installation Abdul-Rashid Iii Sampaco
- [AMBER] Visualizing QM/MM Simulations Nisler, Collin R.
- [AMBER] Density File Wong Li Zhe
- Re: [AMBER] Visualizing QM/MM Simulations Dr. Andreas W. Goetz
- Re: [AMBER] Errors in my installation Hai Nguyen
- Re: [AMBER] Errors in my installation Abdul-Rashid Iii Sampaco
- Re: [AMBER] Errors in my installation Hai Nguyen
- Re: [AMBER] Free energy decomposition of QM/MM-GBSA Jason Swails
- Re: [AMBER] Errors in my installation Abdul-Rashid Iii Sampaco
- Re: [AMBER] Errors in my installation Hai Nguyen
- Re: [AMBER] Errors in my installation koushik kasavajhala
- Re: [AMBER] Errors in my installation Abdul-Rashid Iii Sampaco
- Re: [AMBER] Errors in my installation Abdul-Rashid Iii Sampaco
- [AMBER] Reminder: Training and Innovation Course in Drug Design Thomas Exner
Wednesday, 15 June 2016
- [AMBER] Lipidorder/No output Batuhan Kav
- Re: [AMBER] Lipidorder/No output Hannes Loeffler
- Re: [AMBER] Lipidorder/No output Batuhan Kav
- Re: [AMBER] Lipidorder/No output Hannes Loeffler
- Re: [AMBER] Density File David A Case
- Re: [AMBER] Lipidorder/No output Batuhan Kav
- Re: [AMBER] Lipidorder/No output Hannes Loeffler
- Re: [AMBER] Lipidorder/No output Batuhan Kav
- Re: [AMBER] Lipidorder/No output Hannes Loeffler
- Re: [AMBER] Lipidorder/No output Daniel Roe
- Re: [AMBER] amber16 pmemd cuda rst file Daniel Roe
- [AMBER] ABOUT the GaMD patch for Amber14 Yeng-Tseng Wang
- Re: [AMBER] ABOUT the GaMD patch for Amber14 Ross Walker
- Re: [AMBER] ABOUT the GaMD patch for Amber14 Yeng-Tseng Wang
- Re: [AMBER] ABOUT the GaMD patch for Amber14 Neha Gandhi
- [AMBER] Which of charge methods in antechamber are appropriate? Atila Petrosian
- Re: [AMBER] Which of charge methods in antechamber are appropriate? Gustavo Seabra
- [AMBER] Imaging problem? colvin
- [AMBER] QMMM-MD Odin Zeus
Thursday, 16 June 2016
- [AMBER] mmpbsa doubt Mary Varughese
- [AMBER] extremely slow cluster analysis with cpptraj Michael Shokhen
- Re: [AMBER] Imaging problem? Dr. Anselm Horn
- Re: [AMBER] QMMM-MD David A Case
- Re: [AMBER] QMMM-MD Adrian Roitberg
- [AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR
- Re: [AMBER] extremely slow cluster analysis with cpptraj Daniel Roe
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Hai Nguyen
- Re: [AMBER] QMMM-MD Gustavo Seabra
- [AMBER] Entropy normal mode error George Tzotzos
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Hai Nguyen
- Re: [AMBER] Entropy normal mode error SHAILESH KUMAR
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Hai Nguyen
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR
Friday, 17 June 2016
- Re: [AMBER] Imaging problem? colvin
- Re: [AMBER] Imaging problem? colvin
- [AMBER] script for calculation of dihedral angle frequency Sehrish Naz Aijaz
- [AMBER] Une demande d'aide avec GAFF ( 2 ) Chloe Renard
- [AMBER] NMR restraints on GPU (asterisks in output) Miroslav Krepl
- Re: [AMBER] amber16 pmemd cuda rst file Marc van der Kamp
- Re: [AMBER] energy decomposition Sanjib Paul
- Re: [AMBER] amber16 pmemd cuda rst file Hannes Loeffler
- Re: [AMBER] Imaging problem? Dr. Anselm Horn
- Re: [AMBER] Imaging problem? Carlos Simmerling
- Re: [AMBER] script for calculation of dihedral angle frequency David A Case
- Re: [AMBER] Une demande d'aide avec GAFF ( 2 ) David A Case
- Re: [AMBER] amber16 pmemd cuda rst file David A Case
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Daniel Roe
Saturday, 18 June 2016
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR
- [AMBER] volmap: densities too low Jean-Patrick Francoia
- Re: [AMBER] volmap: densities too low Jason Swails
- [AMBER] GIST calculation Sanjib Paul
- Re: [AMBER] amber16 pmemd cuda rst file David A Case
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Daniel Roe
Monday, 20 June 2016
- Re: [AMBER] volmap: densities too low Jean-Patrick Francoia
- Re: [AMBER] amber16 pmemd cuda rst file Hannes Loeffler
- Re: [AMBER] Une demande d'aide avec GAFF ( 2 ) Chloe Renard
- Re: [AMBER] volmap: densities too low Jason Swails
- [AMBER] Saving the coordinates during a simulation Aishani Prem
- Re: [AMBER] Saving the coordinates during a simulation Daniel Roe
- Re: [AMBER] Saving the coordinates during a simulation Cruzeiro,Vinicius Wilian D
- Re: [AMBER] amber16 pmemd cuda rst file David A Case
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Daniel Roe
Tuesday, 21 June 2016
- [AMBER] Bad atom type: FE when calculating free energy using mmpbsa 163邮箱
- [AMBER] Stripping waters from trajectory on a distance-based criteria Alessandro Contini
- Re: [AMBER] Bad atom type: FE when calculating free energy using mmpbsa David A Case
- Re: [AMBER] NMR restraints on GPU (asterisks in output) David A Case
- Re: [AMBER] GAFF2 setup David A Case
- [AMBER] Principle component analysis: percentage contribution of eigenvectors Hirdesh Kumar
- Re: [AMBER] Stripping waters from trajectory on a distance-based criteria Daniel Roe
- Re: [AMBER] Principle component analysis: percentage contribution of eigenvectors Daniel Roe
- [AMBER] Amber16+CUDA8.0 pmemd.cuda worked, and then stopped working, saying "cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" Zack Scholl
- [AMBER] Problem analysing output with process_mdout.perl script Ruth Helena Tichauer
- [AMBER] Problem with PCA projection Kat G
- [AMBER] Amber16 and CUDA8.0 pmemd.cuda worked, and then stopped working, saying "cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" Zack Scholl
- Re: [AMBER] Problem with PCA projection Daniel Roe
- Re: [AMBER] Problem analysing output with process_mdout.perl script David A Case
- Re: [AMBER] mdl file for 1d-rism Tyler Luchko (Lists)
- [AMBER] Problem with PCA projection (cont) Kat G
- Re: [AMBER] Problem with PCA projection (cont) Daniel Roe
- [AMBER] AMBER support for gtx1080 Anton Perera
- [AMBER] Query regarding dihedral angles Sehrish Naz Aijaz
- Re: [AMBER] Query regarding dihedral angles Hai Nguyen
Wednesday, 22 June 2016
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR
- Re: [AMBER] AMBER support for gtx1080 Charles Lin
- Re: [AMBER] Query regarding dihedral angles Carlos Simmerling
- Re: [AMBER] Stripping waters from trajectory on a distance-based criteria Alessandro Contini
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Daniel Roe
- [AMBER] convergence criteria in enhanced md techniques Neha Gandhi
- Re: [AMBER] convergence criteria in enhanced md techniques Daniel Roe
- Re: [AMBER] Problem analysing output with process_mdout.perl script Ruth Helena Tichauer
- Re: [AMBER] Problem analysing output with process_mdout.perl script Hai Nguyen
- [AMBER] RESP charges amir sadeghi
- Re: [AMBER] Issue with with the nocenter in tLeap David A Case
- Re: [AMBER] Issue with with the nocenter in tLeap Sushil Mishra
- Re: [AMBER] RESP charges FyD
Thursday, 23 June 2016
- [AMBER] MMPBSA.PY Error :LengthError: length mismatch in energy vectors 徐明远
- [AMBER] Running pmemd.MPI across the nodes Himanshu Joshi
- [AMBER] MMPBSA.py nmode output problem Xiao-Lei Wang
- Re: [AMBER] MMPBSA.py nmode output problem Daniel Roe
- Re: [AMBER] Running pmemd.MPI across the nodes Daniel Roe
- Re: [AMBER] MMPBSA.PY Error :LengthError: length mismatch in energy vectors Daniel Roe
- [AMBER] measures of data reliability in Steered MD Asmita Gupta
- Re: [AMBER] measures of data reliability in Steered MD Adrian Roitberg
- Re: [AMBER] AMBER support for gtx1080 Zack Scholl
- [AMBER] Error in MMPBSA Shreeramesh
- Re: [AMBER] MMPBSA.py nmode output problem Xiao-Lei Wang
- Re: [AMBER] Issue with with the nocenter in tLeap Daniel Roe
- Re: [AMBER] Problem analysing output with process_mdout.perl script Ruth Helena Tichauer
- [AMBER] Error in MCPB.py Fabrício Bracht
- Re: [AMBER] Error in MMPBSA Jason Swails
- Re: [AMBER] Error in MCPB.py Marcelo Andrade Chagas
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Daniel Roe
- Re: [AMBER] Error in MCPB.py Fabrício Bracht
- [AMBER] Amber16 + GTX1080 - working well Beavil, Andrew
- Re: [AMBER] Error in MCPB.py Pengfei Li
- Re: [AMBER] Issue with with the nocenter in tLeap Sushil Mishra
Friday, 24 June 2016
- [AMBER] cpptraj analysis of water in cavity Michael Shokhen
- Re: [AMBER] SHAKE Error bharat gupta
- [AMBER] HYDROGEN BONDING ANALYSIS chemjxn
- Re: [AMBER] Amber16 + GTX1080 - working well Ross Walker
- Re: [AMBER] SHAKE Error David A Case
- Re: [AMBER] HYDROGEN BONDING ANALYSIS Hai Nguyen
- Re: [AMBER] cpptraj analysis of water in cavity Daniel Roe
- Re: [AMBER] Issue with with the nocenter in tLeap Daniel Roe
- [AMBER] How to compare protein dynamics in free and bound-ligands states with cpptraj Kat G
- Re: [AMBER] How to compare protein dynamics in free and bound-ligands states with cpptraj Adrian Roitberg
Saturday, 25 June 2016
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Daniel Roe
- [AMBER] solvent equilibration Shilpa Gupta
- Re: [AMBER] solvent equilibration Bill Ross
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR
- Re: [AMBER] solvent equilibration Hector A. Baldoni
- [AMBER] Fw: Ziba Bahadori
- [AMBER] Mmpbsa problem Ziba Bahadori
Sunday, 26 June 2016
- [AMBER] Regarding run.rst file generation Vishal Nemaysh
- Re: [AMBER] AMBER Digest, Vol 1616, Issue 1 bharat gupta
- Re: [AMBER] solvent equilibration David A Case
- Re: [AMBER] Regarding run.rst file generation David A Case
- [AMBER] Problem with SHAKE in water molecule David A Case
- [AMBER] can we sample ligand conformation in Amber Albert
- Re: [AMBER] can we sample ligand conformation in Amber Ilyas Yildirim
- Re: [AMBER] can we sample ligand conformation in Amber Carlos Simmerling
- Re: [AMBER] can we sample ligand conformation in Amber Albert
- Re: [AMBER] AMBER Digest, Vol 1618, Issue 1 bharat gupta
Monday, 27 June 2016
- [AMBER] Thermodynamic Integration with QM/MM Hamiltonian Xiangyu Jia
- Re: [AMBER] can we sample ligand conformation in Amber Albert
- [AMBER] Distorted and clumped structures after cpptraj average structure calculation Prayagraj Fandilolu
- Re: [AMBER] Distorted and clumped structures after cpptraj average structure calculation Dr. Anselm Horn
- Re: [AMBER] Thermodynamic Integration with QM/MM Hamiltonian David A Case
- Re: [AMBER] Distorted and clumped structures after cpptraj average structure calculation David A Case
- Re: [AMBER] AMBER Digest, Vol 1618, Issue 1 bharat gupta
- Re: [AMBER] Thermodynamic Integration with QM/MM Hamiltonian Xiangyu Jia
- [AMBER] MCPB Fabrício Bracht
- Re: [AMBER] Thermodynamic Integration with QM/MM Hamiltonian Dr. Andreas W. Goetz
- Re: [AMBER] SHAKE Error bharat gupta
- Re: [AMBER] SHAKE Error David A Case
- [AMBER] problem:hydrogen bonding analysis contain water molecular chemjxn
Tuesday, 28 June 2016
- [AMBER] charge of aminoacids in an special pH Atila Petrosian
- Re: [AMBER] charge of aminoacids in an special pH Marc van der Kamp
- Re: [AMBER] QM/MM - SCF converge error bharat gupta
- [AMBER] Hidden parameters for tleap Lea Natalia Toledo Carvajal
- Re: [AMBER] QM/MM - SCF converge error David A Case
- Re: [AMBER] problem:hydrogen bonding analysis contain water molecular Daniel Roe
- Re: [AMBER] Hidden parameters for tleap David A Case
- Re: [AMBER] MCPB Pengfei Li
- [AMBER] prepin to mol2 Martina Devi
- [AMBER] convert mol2 to prepin Martina Devi
- Re: [AMBER] prepin to mol2 David A Case
- [AMBER] difference in ptraj for ambertools-12 and 15 Thakur, Abhishek
- [AMBER] Error: [cluster] Not all arguments handled: [ pdb ] Thakur, Abhishek
- Re: [AMBER] Error: [cluster] Not all arguments handled: [ pdb ] Hai Nguyen
- Re: [AMBER] Error: [cluster] Not all arguments handled: [ pdb ] Thakur, Abhishek
- [AMBER] the meaning of NONBON in frcmod Zhenyu Meng
- Re: [AMBER] the meaning of NONBON in frcmod David Cerutti
- [AMBER] equilibration problem esther nehu
- [AMBER] Fwd: equilibration problem esther nehu
Wednesday, 29 June 2016
- [AMBER] Does Amber14 work with CUDA higher than 6.5? Karolina Markowska
- Re: [AMBER] the meaning of NONBON in frcmod Zhenyu Meng
- Re: [AMBER] QM/MM simulation bharat gupta
- Re: [AMBER] Slow performance of Amber12 on cluster bharat gupta
- Re: [AMBER] QM/MM simulation Marc van der Kamp
- Re: [AMBER] the meaning of NONBON in frcmod David Cerutti
- Re: [AMBER] the meaning of NONBON in frcmod David Cerutti
- [AMBER] RMSD PLot ankita mehta
- Re: [AMBER] the meaning of NONBON in frcmod Zhenyu Meng
- [AMBER] Using Gromcas trajectories with CPPTRAJ anu chandra
- Re: [AMBER] 9. Hidden parameters for tleap Lea Natalia Toledo Carvajal
- Re: [AMBER] the meaning of NONBON in frcmod zoran matovic
- [AMBER] TIP3PFBOX: water model Shilpa Gupta
- Re: [AMBER] RMSD PLot Gustavo Seabra
- Re: [AMBER] QM/MM simulation Gustavo Seabra
- Re: [AMBER] Slow performance of Amber12 on cluster Gustavo Seabra
- Re: [AMBER] RMSD PLot Thiago Lipinski Paes
- Re: [AMBER] Using Gromcas trajectories with CPPTRAJ Daniel Roe
- Re: [AMBER] TIP3PFBOX: water model Thakur, Abhishek
- Re: [AMBER] Does Amber14 work with CUDA higher than 6.5? Thakur, Abhishek
- Re: [AMBER] TIP3PFBOX: water model Christina Bergonzo
- [AMBER] Advice for Implicit Solvent MD with Nucleic Acids Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] equilibration problem Thakur, Abhishek
- Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids Carlos Simmerling
- [AMBER] Structural refinement of the protein complexed with metalo-ions James Starlight
- Re: [AMBER] prepin to mol2 FyD
- [AMBER] convert mol2 to pdb Martina Devi
- Re: [AMBER] convert mol2 to pdb Hai Nguyen
- Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] convert mol2 to pdb Martina Devi
- Re: [AMBER] equilibration problem esther nehu
- Re: [AMBER] convert mol2 to pdb Gerald Monard
- Re: [AMBER] convert mol2 to pdb Hai Nguyen
- Re: [AMBER] equilibration problem Thakur, Abhishek
- Re: [AMBER] convert mol2 to pdb Martina Devi
- Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids Carlos Simmerling
- Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids Nhai
- Re: [AMBER] equilibration problem esther nehu
- Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] equilibration problem Thakur, Abhishek
- Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids Nhai
- Re: [AMBER] equilibration problem esther nehu
- Re: [AMBER] Does Amber14 work with CUDA higher than 6.5? Ross Walker
- Re: [AMBER] MCPB Fabrício Bracht
- Re: [AMBER] equilibration problem Thakur, Abhishek
- Re: [AMBER] equilibration problem esther nehu
- Re: [AMBER] MCPB Fabrício Bracht
- Re: [AMBER] MCPB Marcelo Andrade Chagas
- Re: [AMBER] Using Gromcas trajectories with CPPTRAJ Nhai
- [AMBER] Ambertools16 error compiling Esteban Gabriel Vega Hissi
- Re: [AMBER] Ambertools16 error compiling Hai Nguyen
- Re: [AMBER] Does Amber14 work with CUDA higher than 6.5? Markowska
- Re: [AMBER] MCPB Fabrício Bracht
- [AMBER] Library errors while using NAB on Amber16 Slava Chushak
- Re: [AMBER] Amber16 + GTX1080 - working well Zack Scholl
- [AMBER] cutoff and switching Bisignano, Paola
- Re: [AMBER] cutoff and switching Ross Walker
- Re: [AMBER] cutoff and switching Bisignano, Paola
- Re: [AMBER] cutoff and switching Bisignano, Paola
- Re: [AMBER] Library errors while using NAB on Amber16 David A Case
- Re: [AMBER] RMSD PLot ankita mehta
- Re: [AMBER] RMSD PLot Hai Nguyen
- Re: [AMBER] convert mol2 to pdb FyD
- Re: [AMBER] convert mol2 to pdb FyD
- Re: [AMBER] convert mol2 to pdb Hai Nguyen
Thursday, 30 June 2016
- [AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt Jose Manuel Gally
- Re: [AMBER] Structural refinement of the protein complexed with metalo-ions James Starlight
- Re: [AMBER] the meaning of NONBON in frcmod Zhenyu Meng
- Re: [AMBER] Structural refinement of the protein complexed withmetalo-ions zoran matovic
- Re: [AMBER] Structural refinement of the protein complexed with metalo-ions David A Case
- Re: [AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt David A Case
- Re: [AMBER] 9. Hidden parameters for tleap David A Case
- [AMBER] compiling reduce with gcc6 David A Case
- Re: [AMBER] Structural refinement of the protein complexed with metalo-ions James Starlight
- [AMBER] one more point about gcc6 David A Case
- [AMBER] addAtomType problem Lea Natalia Toledo Carvajal
- [AMBER] how to calculate the correlation function for first water shell? Parviz Seifpanahi Shabane
- Re: [AMBER] Structural refinement of the protein complexed with metalo-ions Pengfei Li
- Re: [AMBER] MCPB Pengfei Li
- Re: [AMBER] MCPB Pengfei Li
- Re: [AMBER] addAtomType problem zoran matovic
- [AMBER] Regarding ho parameter in gaff MOHD HOMAIDUR RAHMAN
- [AMBER] GB-neck2 MD with nucleic acids Kasprzak, Wojciech (NIH/NCI) [C]
- [AMBER] bad atom type decomp Bruno Falcone
- Re: [AMBER] GB-neck2 MD with nucleic acids Hai Nguyen
- Re: [AMBER] GB-neck2 MD with nucleic acids Carlos Simmerling
- Re: [AMBER] GB-neck2 MD with nucleic acids Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] GB-neck2 MD with nucleic acids Hai Nguyen
- Re: [AMBER] Progress with testing GB-neck2 MD with nucleic acids Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] Progress with testing GB-neck2 MD with nucleic acids Hai Nguyen
- Re: [AMBER] Progress with testing GB-neck2 MD with nucleic acids Carlos Simmerling
- Re: [AMBER] bad atom type decomp Hai Nguyen
- Re: [AMBER] how to calculate the correlation function for first water shell? Hai Nguyen

Last message date: Thu Jun 30 2016 - 19:30:03 PDT
Archived on: Wed Apr 24 2024 - 05:55:21 PDT

Amber Archive Jun 2016 by date