Amber Archive Dec 2014: by date

Sunday, 30 November 2014
- Re: [AMBER] hydophobicity Mary Varughese
- Re: [AMBER] Monitoring pi-cationic interaction asdda asa
- Re: [AMBER] installing amber12 in GPU Vijay Achari
Monday, 1 December 2014
- [AMBER] LEaP Error Aronica, Pietro
- Re: [AMBER] Problem with triangular point in parameter file David A Case
- Re: [AMBER] LEaP Error David A Case
- Re: [AMBER] installing amber12 in GPU Ross Walker
- [AMBER] tleap segmentation fault George Tzotzos
- Re: [AMBER] tleap segmentation fault Daniel Roe
- Re: [AMBER] tleap segmentation fault George Tzotzos
- Re: [AMBER] tleap segmentation fault Jason Swails
- Re: [AMBER] tleap segmentation fault George Tzotzos
- Re: [AMBER] tleap segmentation fault Daniel Roe
- Re: [AMBER] LEaP Error Aronica, Pietro
- Re: [AMBER] LEaP Error Aronica, Pietro
- Re: [AMBER] LEaP Error Daniel Roe
- Re: [AMBER] LEaP Error Daniel Roe
- Re: [AMBER] Problem with triangular point in parameter file Jorgen Simonsen
- [AMBER] Problems with amber14 intallation in parallel Dailin Li
- [AMBER] Ambertools14 Installation Appears to Reset Edward Kalkreuter
- Re: [AMBER] Ambertools14 Installation Appears to Reset Jason Swails
- Re: [AMBER] Problems with amber14 intallation in parallel Daniel Roe
- Re: [AMBER] TI and FEW Nadine Homeyer
Tuesday, 2 December 2014
- [AMBER] bug in "natural language" system to define nmropt restraints: generalized distance coordinate Marc van der Kamp
- [AMBER] accelerated MD set up Asmita Gupta
- Re: [AMBER] accelerated MD set up Vlad Cojocaru
- Re: [AMBER] Problem with triangular point in parameter file David A Case
- Re: [AMBER] accelerated MD set up Asmita Gupta
- [AMBER] how to retain the MG++ coordination geometry during simulation BERGY
- Re: [AMBER] how to retain the MG++ coordination geometry during simulation Ken Merz
- Re: [AMBER] how to retain the MG++ coordination geometry during simulation Marc van der Kamp
- [AMBER] On the significant dG error in the MMGBSA results.dat James Starlight
- Re: [AMBER] how to retain the MG++ coordination geometry during simulation BERGY
- [AMBER] Linker Attached to DNA Brittany Boykin
- Re: [AMBER] On the significant dG error in the MMGBSA results.dat Aron Broom
- Re: [AMBER] Linker Attached to DNA chandan patel
- [AMBER] DMPC lipids are slightly charged in lipid14? Matthew Harrigan
- Re: [AMBER] DMPC lipids are slightly charged in lipid14? Gould, Ian R
- Re: [AMBER] Linker Attached to DNA FyD
Wednesday, 3 December 2014
- Re: [AMBER] On the significant dG error in the MMGBSA results.dat James Starlight
- [AMBER] MMGBSA.py cpptraj - autoimaging issue de Manzanos Guinot, Angela
- Re: [AMBER] MMGBSA.py cpptraj - autoimaging issue de Manzanos Guinot, Angela
- Re: [AMBER] MMGBSA.py cpptraj - autoimaging issue Jason Swails
- Re: [AMBER] On the significant dG error in the MMGBSA results.dat Aron Broom
- Re: [AMBER] MMGBSA.py cpptraj - autoimaging issue Daniel Roe
- [AMBER] B-factor values George Tzotzos
- Re: [AMBER] B-factor values Jason Swails
- [AMBER] Help regarding error in top n crd generation Ruchika Bhat
Thursday, 4 December 2014
- Re: [AMBER] Help regarding error in top n crd generation Ayesha Fatima
- Re: [AMBER] Help regarding error in top n crd generation Ruchika Bhat
- Re: [AMBER] Help regarding error in top n crd generation David A Case
- [AMBER] How to calculate energy change between two conformations Kshatresh Dutta Dubey
- [AMBER] Docking with Dock6 Wong, Sook (NIH/NCATS) [V]
- Re: [AMBER] Docking with Dock6 Aldo Segura
- Re: [AMBER] Docking with Dock6 David A Case
- Re: [AMBER] Docking with Dock6 Wong, Sook (NIH/NCATS) [V]
- [AMBER] Monitoring GPU voltage Kenneth Lam
- Re: [AMBER] How to calculate energy change between two conformations Jason Swails
- Re: [AMBER] Monitoring GPU voltage Tru Huynh
- Re: [AMBER] Monitoring GPU voltage Kenneth Lam
- Re: [AMBER] Monitoring GPU voltage Jason Swails
- Re: [AMBER] How to calculate energy change between two conformations Kshatresh Dutta Dubey
- Re: [AMBER] Monitoring GPU voltage Kenneth Lam
- Re: [AMBER] How to calculate energy change between two conformations Jason Swails
- Re: [AMBER] How to calculate energy change between two conformations Kshatresh Dutta Dubey
- Re: [AMBER] Monitoring GPU voltage Ross Walker
- Re: [AMBER] Monitoring GPU voltage Kenneth Lam
- [AMBER] xleap segmentation fault when removing residues Mickey Richards
- [AMBER] TINKER and SANDER minimization (AMOEBA force field) 양지현
- Re: [AMBER] TINKER and SANDER minimization (AMOEBA force field) David A Case
- Re: [AMBER] Monitoring GPU voltage Ross Walker
- Re: [AMBER] CHAMBER error Abhishek TYAGI
- [AMBER] closeness Sylvester Tumusiime
- Re: [AMBER] closeness Daniel Roe
Friday, 5 December 2014
- [AMBER] MMGBSA.py - issues with molsurf de Manzanos Guinot, Angela
- [AMBER] Problems with implicit solvent Carlo Guardiani
- Re: [AMBER] On the significant dG error in the MMGBSA results.dat James Starlight
- Re: [AMBER] closeness Sylvester Tumusiime
- Re: [AMBER] Problems with implicit solvent Carlos Simmerling
- Re: [AMBER] problem with unknown compiler: gnu Narendar Kolimi
- Re: [AMBER] closeness David A Case
- Re: [AMBER] problem with unknown compiler: gnu David A Case
- Re: [AMBER] On the significant dG error in the MMGBSA results.dat Jason Swails
- [AMBER] Alignment before calculation? Soumendranath Bhakat
- Re: [AMBER] On the significant dG error in the MMGBSA results.dat Aron Broom
- Re: [AMBER] MMGBSA.py - issues with molsurf Daniel Roe
- Re: [AMBER] closeness Daniel Roe
- Re: [AMBER] Alignment before calculation? Daniel Roe
- Re: [AMBER] problem with unknown compiler: gnu Narendar Kolimi
- Re: [AMBER] problem with unknown compiler: gnu Jason Swails
- [AMBER] error creating mol2 files Anupam Goel
- Re: [AMBER] problem with unknown compiler: gnu Narendar Kolimi
- Re: [AMBER] MMGBSA.py - issues with molsurf Marcus Arieno
- Re: [AMBER] error creating mol2 files Aldo Segura
- Re: [AMBER] error creating mol2 files Anupam Goel
- Re: [AMBER] error creating mol2 files Aldo Segura
- Re: [AMBER] closeness Sylvester Tumusiime
- Re: [AMBER] error creating mol2 files Anupam Goel
- Re: [AMBER] error creating mol2 files Anupam Goel
- Re: [AMBER] error creating mol2 files hannes.loeffler.stfc.ac.uk
- Re: [AMBER] closeness Sylvester Tumusiime
- Re: [AMBER] closeness Daniel Roe
- Re: [AMBER] error creating mol2 files Aldo Segura
- Re: [AMBER] error creating mol2 files David A Case
- Re: [AMBER] error creating mol2 files Anupam Goel
- Re: [AMBER] error creating mol2 files Aldo Segura
- Re: [AMBER] error creating mol2 files Anupam Goel
- Re: [AMBER] Monitoring GPU voltage Kenneth Lam
- Re: [AMBER] closeness Sylvester Tumusiime
Saturday, 6 December 2014
- [AMBER] Can i combine the result given by sander and pmemd together wangmt
- Re: [AMBER] Can i combine the result given by sander and pmemd together YC Sun
- Re: [AMBER] error creating mol2 files FyD
- Re: [AMBER] closeness David A Case
- Re: [AMBER] Can i combine the result given by sander and pmemd together David A Case
- [AMBER] Use of special characters * and ? in ambermask Emilio Lence
- [AMBER] Problems with amber14 intallation in parallel Dailin Li
Sunday, 7 December 2014
- [AMBER] acetate params for mtkpp Francesco Pietra
- Re: [AMBER] acetate params for mtkpp Francesco Pietra
- Re: [AMBER] Problems with amber14 intallation in parallel Jason Swails
- Re: [AMBER] acetate params for mtkpp Jason Swails
Monday, 8 December 2014
- Re: [AMBER] On the significant dG error in the MMGBSA results.dat James Starlight
- [AMBER] ERROR USING tleap ROOPALI VERMA
- [AMBER] Calculating of charge MOHD HOMAIDUR RAHMAN
- Re: [AMBER] ERROR USING tleap David A Case
- Re: [AMBER] Calculating of charge David A Case
- [AMBER] single strand DNA Urszula Uciechowska
- Re: [AMBER] single strand DNA Carlos Simmerling
- [AMBER] Problem with AMBER mail list wangmt
- [AMBER] help in calculating diffusion coefficient Robin Jain
- Re: [AMBER] Problems with amber14 intallation in parallel Jason Swails
- Re: [AMBER] Problem with AMBER mail list David A Case
- Re: [AMBER] help in calculating diffusion coefficient David A Case
- Re: [AMBER] MMPBSA.py bad atom type Jason Swails
- [AMBER] Wrong bond types in Antechamber MOL2 Denis Schmidt
- Re: [AMBER] Problem with AMBER mail list Jason Swails
- Re: [AMBER] Instructions on How to install Amber on Suse Linux Jin Zhang
- Re: [AMBER] acetate params for mtkpp Francesco Pietra
- [AMBER] analyze.x error when dealing with the system containing ions in tinker Ya Gao
- Re: [AMBER] Instructions on How to install Amber on Suse Linux Daniel Roe
- Re: [AMBER] analyze.x error when dealing with the system containing ions in tinker Jason Swails
- [AMBER] Lipid 14 PDB format Romero, Raquel
- Re: [AMBER] Instructions on How to install Amber on Suse Linux Aldo Segura
- [AMBER] selecting the best docking pose with MM/PBSA Thomas Evangelidis
- [AMBER] Software announcement: Release of PUPIL 3.0 Joan Torras
- Re: [AMBER] analyze.x error when dealing with the system containing ions in tinker David A Case
- [AMBER] sander.PUPIL compile error 汪盛
- Re: [AMBER] ERROR USING tleap Hai Nguyen
- Re: [AMBER] analyze.x error when dealing with the system containing ions in tinker Ya Gao
- Re: [AMBER] analyze.x error when dealing with the system containing ions in tinker Ya Gao
- [AMBER] questions about bcc charge 徐晓庶
- [AMBER] Antechamber problem Atila Petrosian
- Re: [AMBER] Antechamber problem hannes.loeffler.stfc.ac.uk
- Re: [AMBER] On the significant dG error in the MMGBSA results.dat James Starlight
- Re: [AMBER] Software announcement: Release of PUPIL 3.0 hannes.loeffler.stfc.ac.uk
- Re: [AMBER] questions about bcc charge hannes.loeffler.stfc.ac.uk
Tuesday, 9 December 2014
- Re: [AMBER] ERROR USING tleap ROOPALI VERMA
- [AMBER] Empirical force fields: release of R.E.D. Server Dev./PyRED Nov. 2014 FyD
- Re: [AMBER] Software announcement: Release of PUPIL 3.0 Torras, Joan
- Re: [AMBER] Software announcement: Release of PUPIL 3.0 Marc van der Kamp
- Re: [AMBER] Software announcement: Release of PUPIL 3.0 Torras, Joan
- Re: [AMBER] Wrong bond types in Antechamber MOL2 Hannes Loeffler
- Re: [AMBER] Wrong bond types in Antechamber MOL2 Denis Schmidt
- Re: [AMBER] Wrong bond types in Antechamber MOL2 Hannes Loeffler
- Re: [AMBER] Antechamber problem Jason Swails
- Re: [AMBER] ERROR USING tleap Jason Swails
- Re: [AMBER] ERROR USING tleap David A Case
- [AMBER] Query about MMPBSA.py de Manzanos Guinot, Angela
- Re: [AMBER] Query about MMPBSA.py Jason Swails
- Re: [AMBER] selecting the best docking pose with MM/PBSA Ray Luo, Ph.D.
- [AMBER] getting the input files for antechamber Ahmet yıldırım
- [AMBER] AmberTools suppose program Yu Chen
- [AMBER] Add MgCl2 salts Haining Liu
- Re: [AMBER] selecting the best docking pose with MM/PBSA Thomas Evangelidis
- Re: [AMBER] AmberTools suppose program Chris Moth
- [AMBER] TLEAP issues Wong, Sook (NIH/NCATS) [V]
- Re: [AMBER] Monitoring GPU voltage Tru Huynh
- Re: [AMBER] selecting the best docking pose with MM/PBSA Ray Luo, Ph.D.
- Re: [AMBER] TLEAP issues Jason Swails
- Re: [AMBER] Add MgCl2 salts Jason Swails
- Re: [AMBER] AmberTools suppose program David A Case
- Re: [AMBER] Add MgCl2 salts David A Case
- Re: [AMBER] TLEAP issues David A Case
- [AMBER] switch digest model to normal fjliu
- Re: [AMBER] AmberTools suppose program Yu Chen
Wednesday, 10 December 2014
- [AMBER] Failure to restart H-REMD Carlo Guardiani
- [AMBER] another segfault with sander14 and TI/softcore Hannes Loeffler
- Re: [AMBER] Query about MMPBSA.py de Manzanos Guinot, Angela
- Re: [AMBER] Query about MMPBSA.py Jason Swails
- Re: [AMBER] Failure to restart H-REMD Jason Swails
- [AMBER] Amber12 parallel installation error Kanin Wichapong
- Re: [AMBER] Amber12 parallel installation error Jason Swails
- Re: [AMBER] TLEAP issues Aldo Segura
- Re: [AMBER] Failure to restart H-REMD Carlo Guardiani
- [AMBER] PM6-DH+ simulation problem Marcos Serrou do Amaral
- [AMBER] Information on ff12polA and ff12polL Manikanthan Bhavaraju
- [AMBER] MMPBSA-ERROR for firstmolecule-dna Abhishek TYAGI
- [AMBER] Is BUG in cpptraj of version 14?? Chris Gao
Thursday, 11 December 2014
- [AMBER] steered MD based on PCA Guillaume Roellinger
- Re: [AMBER] Information on ff12polA and ff12polL David A Case
- Re: [AMBER] Amber12 parallel installation error David A Case
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Jason Swails
- Re: [AMBER] Free energy landscape Carlos Simmerling
- Re: [AMBER] Is BUG in cpptraj of version 14?? Daniel Roe
- [AMBER] Generate pmf of small molecule membrane insertion wmsmith
- Re: [AMBER] PM6-DH+ simulation problem Andreas Goetz
Friday, 12 December 2014
- [AMBER] Problem with simulation of protein-DNA complex Aditya Sarkar
- [AMBER] script to convert the Gromacs topology to Amber topology? Ravi Tripathi
- [AMBER] MM-PBSA (addions) Atila Petrosian
- [AMBER] AmberTools14/Amber10 Francesco Pietra
- Re: [AMBER] AmberTools14/Amber10 aksbmbg_s.caluniv.ac.in
- Re: [AMBER] AmberTools14/Amber10 aksbmbg_s.caluniv.ac.in
- [AMBER] change the mode of my AMBER mail list from digest to normal fjliu
- Re: [AMBER] change the mode of my AMBER mail list from digest to normal aksbmbg_s.caluniv.ac.in
- Re: [AMBER] AmberTools14/Amber10 Jason Swails
- Re: [AMBER] MM-PBSA (addions) Jason Swails
- [AMBER] MM-PBSA (addions) Atila Petrosian
- Re: [AMBER] script to convert the Gromacs topology to Amber topology? Jason Swails
- Re: [AMBER] PM6-DH+ simulation problem Marcos Serrou do Amaral
- Re: [AMBER] Problem with simulation of protein-DNA complex Daniel Roe
- Re: [AMBER] AmberTools14/Amber10 Francesco Pietra
- Re: [AMBER] AmberTools14/Amber10 Francesco Pietra
- Re: [AMBER] change the mode of my AMBER mail list from digest to normal Ross Walker
- Re: [AMBER] change the mode of my AMBER mail list from digest to normal fjliu
- Re: [AMBER] Problem with simulation of protein-DNA complex Aditya Sarkar
- [AMBER] conversion of AMBER trajectory to Gromacs trajectory Robin Jain
- Re: [AMBER] conversion of AMBER trajectory to Gromacs trajectory aksbmbg_s.caluniv.ac.in
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Abhishek TYAGI
Saturday, 13 December 2014
- [AMBER] Generation of 3D structure of polypeptides with modified amino acids Suman Chakrabarty
- [AMBER] 8Mureabox URE residue unknown CHAMI F.
- Re: [AMBER] Problem with simulation of protein-DNA complex Jason Swails
- Re: [AMBER] conversion of AMBER trajectory to Gromacs trajectory Jason Swails
- Re: [AMBER] Generation of 3D structure of polypeptides with modified amino acids Jason Swails
- Re: [AMBER] 8Mureabox URE residue unknown Jason Swails
- Re: [AMBER] conversion of AMBER trajectory to Gromacs trajectory Daniel Roe
- [AMBER] PCA 2dprojection with xtal data and energy information BERGY
- Re: [AMBER] PCA 2dprojection with xtal data and energy information Daniel Roe
- [AMBER] "Unit 18 Error on OPEN: logfile" kurisaki
- Re: [AMBER] "Unit 18 Error on OPEN: logfile" kurisaki
- Re: [AMBER] "Unit 18 Error on OPEN: logfile" kurisaki
- Re: [AMBER] PCA 2dprojection with xtal data and energy information BERGY
- Re: [AMBER] PCA 2dprojection with xtal data and energy information Daniel Roe
Sunday, 14 December 2014
- [AMBER] production run for diffusion constant Robin Jain
- Re: [AMBER] production run for diffusion constant Daniel Roe
- [AMBER] Looking for AMBER FF12SB for CHARMM Zhang, Sixue
- [AMBER] Glycan-protein h-bond ptraj maryam azimzadehirani
- [AMBER] Error in Box Dimension 杨川
- Re: [AMBER] Glycan-protein h-bond ptraj Daniel Roe
- Re: [AMBER] Error in Box Dimension Daniel Roe
- Re: [AMBER] Glycan-protein h-bond ptraj maryam azimzadehirani
Monday, 15 December 2014
- Re: [AMBER] Glycan-protein h-bond ptraj Daniel Roe
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Abhishek TYAGI
- Re: [AMBER] Problem with simulation of protein-DNA complex Aditya Sarkar
- [AMBER] Optimization under restraint atoms using ibelly option Akihiro Yamane
- Re: [AMBER] Problem with simulation of protein-DNA complex Daniel Roe
- [AMBER] gas phase, nonperiodic system with AMOEBA ff in AMBER Lawrenz, Morgan
- [AMBER] Missing psi dihedral at cationic N-terminus of protein/peptide? nealec
- [AMBER] error while saving prmtop and inpcrd Anupam Goel
- Re: [AMBER] gas phase, nonperiodic system with AMOEBA ff in AMBER Jason Swails
- Re: [AMBER] gas phase, nonperiodic system with AMOEBA ff in AMBER Lawrenz, Morgan
- Re: [AMBER] error while saving prmtop and inpcrd David A Case
- Re: [AMBER] Optimization under restraint atoms using ibelly option David A Case
- [AMBER] Analyzing multiple trajectories in cpptraj Gard Nelson
- Re: [AMBER] Analyzing multiple trajectories in cpptraj Daniel Roe
- [AMBER] Different convergence in pmemd.cuda against CPU Hiromasa WATANABE
- Re: [AMBER] Error in Box Dimension 杨川
- Re: [AMBER] Different convergence in pmemd.cuda against CPU Ross Walker
- Re: [AMBER] Different convergence in pmemd.cuda against CPU Hiromasa WATANABE
- [AMBER] How to analyze REMD results Wang Moye
Tuesday, 16 December 2014
- [AMBER] Fwd: RED-III.52-Tools stopped to work suddenly. Zeinab Emami
- [AMBER] Amber 12 on K20 GPUs -- how am I doing? Baker D.J.
- Re: [AMBER] Error in Box Dimension David A Case
- [AMBER] phosphoserine parameters Jacopo Sgrignani
- Re: [AMBER] phosphoserine parameters Christina Bergonzo
- Re: [AMBER] phosphoserine parameters David A Case
- Re: [AMBER] Analyzing multiple trajectories in cpptraj Gard Nelson
- Re: [AMBER] Analyzing multiple trajectories in cpptraj Daniel Roe
- Re: [AMBER] Fwd: RED-III.52-Tools stopped to work suddenly. FyD
- Re: [AMBER] Amber 12 on K20 GPUs -- how am I doing? Ross Walker
- Re: [AMBER] Different convergence in pmemd.cuda against CPU Ross Walker
- [AMBER] clustering problem in ambertool14 Mahendra B Thapa
- Re: [AMBER] clustering problem in ambertool14 Daniel Roe
- Re: [AMBER] PCA 2dprojection with xtal data and energy information BERGY
- Re: [AMBER] PCA 2dprojection with xtal data and energy information Daniel Roe
- [AMBER] excluding atom sets from MMPB/GB-SA calculations Hallel Freedman
- Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Hallel Freedman
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Abhishek TYAGI
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Jason Swails
- Re: [AMBER] PCA 2dprojection with xtal data and energy information BERGY
- [AMBER] TiMergeError fjliu
- Re: [AMBER] TiMergeError hannes.loeffler.stfc.ac.uk
- Re: [AMBER] TiMergeError fjliu
- Re: [AMBER] subscribe amber wliu
Wednesday, 17 December 2014
- Re: [AMBER] TiMergeError hannes.loeffler.stfc.ac.uk
- [AMBER] error in parallel installation of Amber 12 with AmberTools13 Robin Jain
- Re: [AMBER] TiMergeError Hannes Loeffler
- Re: [AMBER] Fwd: RED-III.52-Tools stopped to work suddenly. Zeinab Emami
- Re: [AMBER] error in parallel installation of Amber 12 with AmberTools13 aksbmbg_s.caluniv.ac.in
- Re: [AMBER] TiMergeError fjliu
- Re: [AMBER] TiMergeError Hannes Loeffler
- Re: [AMBER] error in parallel installation of Amber 12 with AmberTools13 David A Case
- Re: [AMBER] another segfault with sander14 and TI/softcore David A Case
- Re: [AMBER] another segfault with sander14 and TI/softcore Hannes Loeffler
- Re: [AMBER] subscribe amber Jason Swails
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Ray Luo, Ph.D.
- Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Ray Luo, Ph.D.
- Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Hallel Freedman
- Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Jason Swails
- Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Hallel Freedman
- Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Jason Swails
- [AMBER] error running equilibration (wall clock called) Anupam Goel
- Re: [AMBER] error running equilibration (wall clock called) David A Case
- Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Hallel Freedman
- Re: [AMBER] error running equilibration (wall clock called) Anupam Goel
- [AMBER] leap crashes and set: Improper number of arguments! Francesco Pietra
- [AMBER] Fwd: leap crashes and set: Improper number of arguments! Francesco Pietra
- Re: [AMBER] Fwd: leap crashes and set: Improper number of arguments! Bill Ross
- Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Jason Swails
- Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Hallel Freedman
Thursday, 18 December 2014
- Re: [AMBER] Optimization under restraint atoms using ibelly option Akihiro Yamane
- [AMBER] help in calculation of diffusion coefficient Robin Jain
- [AMBER] installing error Amber 12 Error Houcemeddine Othman
- Re: [AMBER] installing error Amber 12 Error Daniel Roe
- Re: [AMBER] help in calculation of diffusion coefficient Daniel Roe
- [AMBER] help on the AMBER Tutorial B0 Dabing Chen
- Re: [AMBER] help on the AMBER Tutorial B0 Daniel Roe
- Re: [AMBER] how can i use acpype yaser
- Re: [AMBER] how can i use acpype David A Case
- Re: [AMBER] how can i use acpype Yaser Hosseini
- [AMBER] unclear leap crashing Francesco Pietra
- Re: [AMBER] how can i use acpype Jason Swails
- [AMBER] Improper torsions in NMA Ganesh Kamath
- [AMBER] pseudo F-statistic (pSF) Jonathan Gough
Friday, 19 December 2014
- Re: [AMBER] how can i use acpype Yaser Hosseini
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Abhishek TYAGI
- [AMBER] error in install amber Yaser Hosseini
- Re: [AMBER] unclear leap crashing FyD
- [AMBER] Free Energy Workshop, Münster, March 9-11, 2015 Vlad Cojocaru
- Re: [AMBER] unclear leap crashing David A Case
- Re: [AMBER] Improper torsions in NMA David A Case
- Re: [AMBER] error in install amber David A Case
- Re: [AMBER] how can i use acpype Jason Swails
- Re: [AMBER] pseudo F-statistic (pSF) Daniel Roe
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Ray Luo, Ph.D.
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Jason Swails
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Ray Luo, Ph.D.
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Daniel Roe
- Re: [AMBER] Improper torsions in NMA Ganesh Kamath
- Re: [AMBER] unclear leap crashing Francesco Pietra
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Ray Luo, Ph.D.
Saturday, 20 December 2014
- Re: [AMBER] Improper torsions in NMA David A Case
- [AMBER] Fwd: unclear leap crashing Francesco Pietra
- Re: [AMBER] unclear leap crashing Francesco Pietra
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Abhishek TYAGI
Sunday, 21 December 2014
- [AMBER] Hydrogen charge site and Oxygen V-site displacement Sylvester Tumusiime
- [AMBER] Error in pmemd.amoeba.MPI run Ya Gao
- [AMBER] pmemd.MPI fails to run Fabian Glaser
- Re: [AMBER] Error in pmemd.amoeba.MPI run Jason Swails
- Re: [AMBER] pmemd.MPI fails to run Jason Swails
- [AMBER] pmemd.MPI fails Fabian Glaser
- [AMBER] error in acpype Yaser Hosseini
- Re: [AMBER] error in install amber Yaser Hosseini
- [AMBER] Singe point QM/MM energy using Gaussian interface Bence Hégely
- Re: [AMBER] error in install amber Jason Swails
- Re: [AMBER] Singe point QM/MM energy using Gaussian interface Jason Swails
- Re: [AMBER] error in install amber Alan
- [AMBER] How to analyze REMD results Wang Moye
- Re: [AMBER] How to analyze REMD results Carlos Simmerling
- [AMBER] NVE simulation Robin Jain
- Re: [AMBER] NVE simulation Daniel Roe
- Re: [AMBER] Different convergence in pmemd.cuda against CPU Hiromasa WATANABE
- [AMBER] Laccase studies of 2013 mmaestre.gate.sinica.edu.tw
Monday, 22 December 2014
- Re: [AMBER] Hydrogen charge site and Oxygen V-site displacement David A Case
- Re: [AMBER] Fwd: unclear leap crashing David A Case
- Re: [AMBER] Missing psi dihedral at cationic N-terminus of protein/peptide? David A Case
- [AMBER] target dynamics problem antonio.coluccia.uniroma1.it
- Re: [AMBER] target dynamics problem Carlos Simmerling
- Re: [AMBER] target dynamics problem antonio.coluccia.uniroma1.it
- Re: [AMBER] target dynamics problem Carlos Simmerling
- Re: [AMBER] target dynamics problem antonio.coluccia.uniroma1.it
- [AMBER] antechamber script Ahmet yıldırım
- Re: [AMBER] NVE simulation George M Giambasu
- Re: [AMBER] antechamber script Bill Ross
- Re: [AMBER] antechamber script Marc van der Kamp
- Re: [AMBER] target dynamics problem Jason Swails
- Re: [AMBER] target dynamics problem Carlos Simmerling
- Re: [AMBER] antechamber script Ahmet yıldırım
- Re: [AMBER] antechamber script hannes.loeffler.stfc.ac.uk
- Re: [AMBER] antechamber script Nhai
- [AMBER] Umbrella sampling for molecules moving Helen Lvy
- Re: [AMBER] antechamber script David A Case
- Re: [AMBER] antechamber script Ahmet yıldırım
- Re: [AMBER] Umbrella sampling for molecules moving Carlos Simmerling
- Re: [AMBER] Missing psi dihedral at cationic N-terminus of protein/peptide? Carlos Simmerling
- Re: [AMBER] pseudo F-statistic (pSF) Jonathan Gough
- Re: [AMBER] pseudo F-statistic (pSF) Daniel Roe
- Re: [AMBER] pseudo F-statistic (pSF) Jonathan Gough
- Re: [AMBER] Hydrogen charge site and Oxygen V-site displacement Sylvester Tumusiime
Tuesday, 23 December 2014
- [AMBER] Parameter could not be saved Harmeet Kaur
- Re: [AMBER] Parameter could not be saved Soumendranath Bhakat
- [AMBER] a problem in MM-GBSA calculation 朱亚莉
- Re: [AMBER] a problem in MM-GBSA calculation Carlos Simmerling
- Re: [AMBER] Parameter could not be saved Jason Swails
- Re: [AMBER] Parameter could not be saved Kshatresh Dutta Dubey
- [AMBER] ifqnt chemjxn
- Re: [AMBER] a problem in MM-GBSA calculation Jinfeng Huang
- Re: [AMBER] a problem in MM-GBSA calculation Jason Swails
- Re: [AMBER] ifqnt Jason Swails
- Re: [AMBER] ifqnt chemjxn.126.com
- [AMBER] Errors during Adding hydrogen atoms to the PDB file（MCPB program） wjli
- [AMBER] 回复： Errors during Adding hydrogen atoms to the PDB file（MCPB program） wjli
- Re: [AMBER] ifqnt Jason Swails
- Re: [AMBER] ifqnt chemjxn.126.com
Wednesday, 24 December 2014
- Re: [AMBER] ifqnt Kshatresh Dutta Dubey
- Re: [AMBER] ifqnt Jason Swails
- Re: [AMBER] ifqnt Jason Swails
- Re: [AMBER] Forcefield for DNA Nihal Korkmaz
Thursday, 25 December 2014
- [AMBER] WHAM tolerance Sun
- [AMBER] conversion of amber outputs to gromacs shahab shariati
- [AMBER] conversion of amber outputs to gromacs shahab shariati
Friday, 26 December 2014
- Re: [AMBER] conversion of amber outputs to gromacs Kshatresh Dutta Dubey
- [AMBER] conversion of amber outputs to gromacs shahab shariati
- [AMBER] charmmlipid2amber.py Jacopo Sgrignani
- Re: [AMBER] conversion of amber outputs to gromacs Jason Swails
- [AMBER] Amber 14 Performance and Other Questions Novosielski, Ryan
- Re: [AMBER] Amber 14 Performance and Other Questions Ross Walker
- Re: [AMBER] conversion of amber outputs to gromacs Sarah Witzke
Saturday, 27 December 2014
- [AMBER] lipid conversion Jacopo Sgrignani
- Re: [AMBER] lipid conversion Sarah Witzke
- Re: [AMBER] lipid conversion Jacopo Sgrignani
- Re: [AMBER] lipid conversion Jonathan Gough
- [AMBER] Error during Adding Fragment（about MCPB ） wjli
- [AMBER] Enthalpy calculation of protein. Abhilash J
Sunday, 28 December 2014
- [AMBER] amber force field 王珍
- Re: [AMBER] Enthalpy calculation of protein. David A Case
- Re: [AMBER] Enthalpy calculation of protein. Abhilash J
- Re: [AMBER] pmemd.MPI fails to run Fabian Glaser
- Re: [AMBER] pmemd.MPI fails to run Ryan Novosielski
- Re: [AMBER] pmemd.MPI fails to run Ross Walker
- Re: [AMBER] pmemd.MPI fails to run Fabian
- Re: [AMBER] pmemd.MPI fails to run Thomas Cheatham
- Re: [AMBER] pmemd.MPI fails to run Fabian Gmail
- Re: [AMBER] Enthalpy calculation of protein. David A Case
- Re: [AMBER] pmemd.MPI fails to run Bill Ross
- Re: [AMBER] Enthalpy calculation of protein. aneesh cna
- Re: [AMBER] Enthalpy calculation of protein. Abhilash J
- [AMBER] Total energy of system is positive MOHD HOMAIDUR RAHMAN
Monday, 29 December 2014
- Re: [AMBER] pmemd.MPI fails to run Fabian Glaser
- Re: [AMBER] pmemd.MPI fails to run Jason Swails
- [AMBER] convergence problem in antechamber with Ambertools14 Rebeca García Fandiño
- [AMBER] Fwd: pmemd.MPI fails to run Fabian Glaser
- [AMBER] TI calculation using pmemd wangmt
- Re: [AMBER] Fwd: pmemd.MPI fails to run Ross Walker
- Re: [AMBER] Total energy of system is positive Jason Swails
- Re: [AMBER] amber force field pavel.banas.upol.cz
- Re: [AMBER] TI calculation using pmemd hannes.loeffler.stfc.ac.uk
- Re: [AMBER] Total energy of system is positive MOHD HOMAIDUR RAHMAN
- [AMBER] rms fit Sylvester Tumusiime
- [AMBER] Peter Kollman lectureship, Jan 8 David A Case
- Re: [AMBER] Total energy of system is positive Adrian Roitberg
- Re: [AMBER] Total energy of system is positive Jason Swails
- [AMBER] Imaging membrane proteins Parker de Waal
- Re: [AMBER] convergence problem in antechamber with Ambertools14 David A Case
- Re: [AMBER] rms fit David A Case
- Re: [AMBER] Imaging membrane proteins David A Case
- Re: [AMBER] Total energy of system is positive MOHD HOMAIDUR RAHMAN
- Re: [AMBER] Total energy of system is positive Jason Swails
Tuesday, 30 December 2014
- Re: [AMBER] convergence problem in antechamber with Ambertools14 Rebeca García Fandiño
- Re: [AMBER] amber force field Jiri Sponer
- Re: [AMBER] Peter Kollman lectureship, Jan 8 Gustavo Seabra
- [AMBER] Need help in SMD Kshatresh Dutta Dubey
- [AMBER] amber14 CUDA GPU for workstation? Michael Shokhen
- Re: [AMBER] amber14 CUDA GPU for workstation? Ross Walker
- Re: [AMBER] rms fit Sylvester Tumusiime
- Re: [AMBER] amber14 CUDA GPU for workstation? Michael Shokhen
- Re: [AMBER] amber14 CUDA GPU for workstation? Adrian Roitberg
- Re: [AMBER] amber14 CUDA GPU for workstation? Michael Shokhen
- Re: [AMBER] amber14 CUDA GPU for workstation? Ross Walker
- Re: [AMBER] Peter Kollman lectureship, Jan 8 David A Case
- Re: [AMBER] amber14 CUDA GPU for workstation? Jason Swails
- Re: [AMBER] Need help in SMD Jason Swails
- Re: [AMBER] WHAM tolerance Jason Swails
Wednesday, 31 December 2014
- [AMBER] Need help in Targeted MD Pallavi Mohanty
- Re: [AMBER] Need help in SMD Kshatresh Dutta Dubey
- Re: [AMBER] Need help in Targeted MD David A Case
- Re: [AMBER] Need help in Targeted MD Carlos Simmerling
- [AMBER] Solvation free energy using soft core potential Teerapong Pirojsirikul

Last message date: Wed Dec 31 2014 - 17:30:03 PST
Archived on: Mon Apr 22 2024 - 05:54:56 PDT

Amber Archive Dec 2014 by date