Amber Archive Apr 2017: by date

Saturday, 1 April 2017
- [AMBER] How to perform good quality local optimization with Sander danil kutov
- Re: [AMBER] Linkage problem in branched oligosaccharide Manju Sah
- Re: [AMBER] How to perform good quality local optimization with Sander David Case
Sunday, 2 April 2017
- Re: [AMBER] coordinates in restraint mast Thomas Evangelidis
- Re: [AMBER] restarting Amber calculations gives abnormal structures Sadegh Faramarzi Ganjabad
- Re: [AMBER] restarting Amber calculations gives abnormal structures Sadegh Faramarzi Ganjabad
- Re: [AMBER] restarting Amber calculations gives abnormal structures Chris Neale
Monday, 3 April 2017
- [AMBER] mmpbsa - stability calculation Mary Varughese
- Re: [AMBER] mmpbsa - stability calculation David Case
- [AMBER] placing water at specified coordinates with tleap Thomas Evangelidis
- Re: [AMBER] placing water at specified coordinates with tleap David Case
- Re: [AMBER] coordinates in restraint mast Daniel Roe
- [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Ramin Salimi
- Re: [AMBER] restarting Amber calculations gives abnormal structures David Case
- [AMBER] 3 GPUs ? Chris Neale
Tuesday, 4 April 2017
- Re: [AMBER] 3 GPUs ? Andreas Tosstorff
- Re: [AMBER] distance calculations - Protein-RNA Sidhu, Khushwant (Dr.)
- Re: [AMBER] distance calculations - Protein-RNA Bill Ross
- [AMBER] eChemInfo Training and Innovation Course in Drug Design Thomas Exner
- Re: [AMBER] distance calculations - Protein-RNA Daniel Roe
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy David A Case
- [AMBER] mmpbsa- binding energy between ligand-receptor Anna Cebrian Prats
- [AMBER] You won't believe what happens with maximum coordination limits... David Poole
- Re: [AMBER] You won't believe what happens with maximum coordination limits... Hannes Loeffler
- Re: [AMBER] 3 GPUs ? Ross Walker
- [AMBER] Creating a pdb of only certain molecules from a frame Aseel Bala
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Ramin Salimi
- Re: [AMBER] You won't believe what happens with maximum coordination limits... Ben Roberts
- Re: [AMBER] 3 GPUs ? Chris Neale
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Carlos Simmerling
- Re: [AMBER] You won't believe what happens with maximum coordination limits... Marek Maly
- Re: [AMBER] 3 GPUs ? Ross Walker
- Re: [AMBER] 3 GPUs ? Chris Neale
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy David Case
- [AMBER] Atom types for Baaden Hydronium Ion Samaneh Ghassabi Kondalaji
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Ramin Salimi
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Bill Ross
- [AMBER] density plot of Na+ ions using grid Mary Varughese
Wednesday, 5 April 2017
- [AMBER] How to distinguish between water molecules? Markowska
- [AMBER] CPPTRAJ Cluster d00b46022
- Re: [AMBER] How to distinguish between water molecules? Hannes Loeffler
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Ramin Salimi
- [AMBER] ptraj hbonds Mary Varughese
- Re: [AMBER] How to distinguish between water molecules? Markowska
- Re: [AMBER] How to distinguish between water molecules? Hannes Loeffler
- Re: [AMBER] Atom types for Baaden Hydronium Ion David A Case
- Re: [AMBER] How to distinguish between water molecules? David A Case
- Re: [AMBER] How to distinguish between water molecules? Markowska
- [AMBER] Acetonitrile Water Mix Andreas Tosstorff
- Re: [AMBER] How to distinguish between water molecules? Hannes Loeffler
- Re: [AMBER] Acetonitrile Water Mix Marcos Serrou do Amaral
- Re: [AMBER] Acetonitrile Water Mix Andreas Tosstorff
- Re: [AMBER] How to distinguish between water molecules? Markowska
- Re: [AMBER] How to distinguish between water molecules? Jason Swails
- [AMBER] GPU performance Sofia Vasilakaki
- Re: [AMBER] GPU performance Andreas Tosstorff
- Re: [AMBER] Acetonitrile Water Mix David A Case
- Re: [AMBER] Acetonitrile Water Mix Sowmya Indrakumar
- Re: [AMBER] Acetonitrile Water Mix David Cerutti
- [AMBER] Binding site volume calculation Thakur, Abhishek
- Re: [AMBER] Atom types for Baaden Hydronium Ion Samaneh Ghassabi Kondalaji
- Re: [AMBER] Acetonitrile Water Mix Andreas Tosstorff
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Daniel Roe
- Re: [AMBER] ptraj hbonds Daniel Roe
- Re: [AMBER] CPPTRAJ Cluster Daniel Roe
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Bill Ross
- [AMBER] parmed doesn't give any output or error message Sadegh Faramarzi Ganjabad
- Re: [AMBER] Binding site volume calculation David A Case
- Re: [AMBER] Atom types for Baaden Hydronium Ion David A Case
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Charles Lin
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphaelinger
- Re: [AMBER] Atom types for Baaden Hydronium Ion Samaneh Ghassabi Kondalaji
- Re: [AMBER] 3 GPUs ? Ross Walker
- Re: [AMBER] GPU performance Ross Walker
- Re: [AMBER] 3 GPUs ? Chris Neale
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Ramin Salimi
Thursday, 6 April 2017
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Bill Ross
- [AMBER] How to write an frcmod file Andreas Tosstorff
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Bill Ross
- Re: [AMBER] How to write an frcmod file Hannes Loeffler
- Re: [AMBER] You won't believe what happens with maximum coordination limits... David Poole
- [AMBER] Diffusion and permeability coefficients Fabrício Bracht
- Re: [AMBER] Diffusion and permeability coefficients Chris Neale
- Re: [AMBER] Diffusion and permeability coefficients Fabrício Bracht
- [AMBER] GTX 1080 error Jacopo Sgrignani
- Re: [AMBER] GTX 1080 error Paul Westphaelinger
- Re: [AMBER] GTX 1080 error Ross Walker
- [AMBER] Tleap error. Vatsal Purohit
- Re: [AMBER] Tleap error. Scott Brozell
- Re: [AMBER] Tleap error. David A Case
Friday, 7 April 2017
- [AMBER] Periodic box error for restarting simulations with restraints Sadegh Faramarzi Ganjabad
- Re: [AMBER] Acetonitrile Water Mix Marcos Serrou do Amaral
- Re: [AMBER] Periodic box error for restarting simulations with restraints Daniel Roe
- Re: [AMBER] Acetonitrile Water Mix Andreas Tosstorff
- Re: [AMBER] Acetonitrile Water Mix Marcos Serrou do Amaral
- [AMBER] Steered MD using two reaction coordinates Suchetana Gupta
- [AMBER] Query regarding output of 3D-RISM in Amber. Rakesh Srivastava
- Re: [AMBER] Periodic box error for restarting simulations with restraints Sadegh Faramarzi Ganjabad
- Re: [AMBER] Periodic box error for restarting simulations with restraints Bill Ross
- Re: [AMBER] Steered MD using two reaction coordinates Hannes Loeffler
Saturday, 8 April 2017
- [AMBER] cpptraj analysis of two different dsDNA strands. James Kress
- [AMBER] Minimization fails when switching from steepest descent to conjugate gradient Andreas Tosstorff
- Re: [AMBER] Minimization fails when switching from steepest descent to conjugate gradient Elvis Martis
- Re: [AMBER] Minimization fails when switching from steepest descent to conjugate gradient Hai Nguyen
Sunday, 9 April 2017
- Re: [AMBER] cpptraj analysis of two different dsDNA strands. Nhai
- [AMBER] Regarding REMD simulations of Proteins MOHD HOMAIDUR RAHMAN
- Re: [AMBER] cpptraj analysis of two different dsDNA strands. James Kress
- Re: [AMBER] Regarding REMD simulations of Proteins Carlos Simmerling
- Re: [AMBER] Minimization fails when switching from steepest descent to conjugate gradient Chris Moth
- Re: [AMBER] Minimization fails when switching from steepest descent to conjugate gradient Andreas Tosstorff
- Re: [AMBER] Query regarding output of 3D-RISM in Amber. David Case
Monday, 10 April 2017
- Re: [AMBER] Query regarding output of 3D-RISM in Amber. Rakesh Srivastava
- [AMBER] MMPBSA entropy calculation help Mary Varughese
- Re: [AMBER] MMPBSA entropy calculation help David Case
- [AMBER] QM/MM equilibration before SMD in vacuum Samaneh Ghassabi Kondalaji
- Re: [AMBER] QM/MM equilibration before SMD in vacuum Samaneh Ghassabi Kondalaji
- Re: [AMBER] Creating a pdb of only certain molecules from a frame Daniel Roe
- [AMBER] simulation energies are exploding giulia palermo
Tuesday, 11 April 2017
- [AMBER] problem about amber install of MMPBSA.py.mpi 白正亚
- [AMBER] DNA Tutorial B1 - Temperature Drop Johannes Kalliauer
- Re: [AMBER] simulation energies are exploding David Case
- [AMBER] cpptraj creates pdb file it cannot read James Kress
- Re: [AMBER] Periodic box error for restarting simulations with restraints Sadegh Faramarzi Ganjabad
- Re: [AMBER] cpptraj creates pdb file it cannot read Hai Nguyen
- Re: [AMBER] Periodic box error for restarting simulations with restraints Bill Ross
- Re: [AMBER] cpptraj creates pdb file it cannot read James Kress
- Re: [AMBER] cpptraj creates pdb file it cannot read Hai Nguyen
- Re: [AMBER] cpptraj creates pdb file it cannot read James Kress
- Re: [AMBER] cpptraj creates pdb file it cannot read James Kress
- Re: [AMBER] simulation energies are exploding giulia palermo
- Re: [AMBER] cpptraj creates pdb file it cannot read Elka Firmanda
Wednesday, 12 April 2017
- [AMBER] Discrepancy in delta G total and per residues decomposition results in MMPBSA.py mish
- [AMBER] antechamber problem Maura Malinska
- Re: [AMBER] cpptraj creates pdb file it cannot read James Kress
- Re: [AMBER] antechamber problem David Case
- Re: [AMBER] cpptraj creates pdb file it cannot read Hai Nguyen
- Re: [AMBER] antechamber problem Gerald Monard
- Re: [AMBER] cpptraj creates pdb file it cannot read Daniel Roe
- [AMBER] using pmemd.MPI for REMD Kris Feher
- Re: [AMBER] antechamber problem Niel Henriksen
- Re: [AMBER] using pmemd.MPI for REMD Hannes Loeffler
- [AMBER] reorientation in rmsd James Kress
- Re: [AMBER] reorientation in rmsd Bill Ross
- Re: [AMBER] reorientation in rmsd Jason Swails
- Re: [AMBER] reorientation in rmsd James Kress
- Re: [AMBER] reorientation in rmsd David Case
- Re: [AMBER] reorientation in rmsd James Kress
- Re: [AMBER] reorientation in rmsd Andy Watkins
- Re: [AMBER] reorientation in rmsd Andy Watkins
- [AMBER] ERROR in load_lbfgs(): YS=0. 杨满意
- [AMBER] problem with temperature after rst Jorgen Simonsen
- Re: [AMBER] problem with temperature after rst Bill Ross
- Re: [AMBER] problem with temperature after rst Jorgen Simonsen
- Re: [AMBER] problem with temperature after rst Bill Ross
- Re: [AMBER] problem with temperature after rst Bill Ross
- Re: [AMBER] problem with temperature after rst Jorgen Simonsen
- Re: [AMBER] problem with temperature after rst Bill Ross
- Re: [AMBER] problem with temperature after rst Bill Ross
Thursday, 13 April 2017
- Re: [AMBER] antechamber problem Maura Malinska
- [AMBER] AMBER umbrella sampling 吴萌
- Re: [AMBER] using pmemd.MPI for REMD Kris Feher
- Re: [AMBER] using pmemd.MPI for REMD Kris Feher
- Re: [AMBER] ERROR in load_lbfgs(): YS=0. David A Case
- Re: [AMBER] problem with temperature after rst David A Case
- Re: [AMBER] AMBER umbrella sampling Hannes Loeffler
- Re: [AMBER] reorientation in rmsd Jason Swails
- [AMBER] solvateBox for large size of RNA Li, Wen
- Re: [AMBER] solvateBox for large size of RNA David Case
- [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Samaneh Ghassabi Kondalaji
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Hannes Loeffler
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Samaneh Ghassabi Kondalaji
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Hannes Loeffler
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Samaneh Ghassabi Kondalaji
- Re: [AMBER] AMBER umbrella sampling Andreas Tosstorff
- Re: [AMBER] solvateBox for large size of RNA George Giambasu
- [AMBER] Incorrect ligand parameterization using GAFF Emilia Pecora-de-barros
- Re: [AMBER] AMBER umbrella sampling Feng Pan
- Re: [AMBER] Periodic box error for restarting simulations with restraints Sadegh Faramarzi Ganjabad
- Re: [AMBER] Periodic box error for restarting simulations with restraints Chris Neale
- [AMBER] About Tutorial B3 Hadeer ELHabashy
- Re: [AMBER] Incorrect ligand parameterization using GAFF David Case
- Re: [AMBER] About Tutorial B3 David Case
- [AMBER] RES: Incorrect ligand parameterization using GAFF Emilia Pecora-de-barros
- Re: [AMBER] ERROR in load_lbfgs(): YS=0. 杨满意
- [AMBER] Compilation of MPI 3D-RISM issue in amber1 4 Rakesh Srivastava
- Re: [AMBER] Compilation of MPI 3D-RISM issue in amber1 4 Tyler Luchko (Lists)
- Re: [AMBER] Compilation of MPI 3D-RISM issue in amber1 4 Nhai
Friday, 14 April 2017
- Re: [AMBER] Incorrect ligand parameterization using GAFF Hannes Loeffler
- [AMBER] BCC charge for my HEME Thakur, Abhishek
- Re: [AMBER] BCC charge for my HEME Elvis Martis
- Re: [AMBER] BCC charge for my HEME Thakur, Abhishek
- Re: [AMBER] BCC charge for my HEME Elvis Martis
- [AMBER] Format error in frcmod file of HEME Thakur, Abhishek
- Re: [AMBER] Format error in frcmod file of HEME Marcos Serrou do Amaral
- Re: [AMBER] BCC charge for my HEME David Case
- Re: [AMBER] Format error in frcmod file of HEME David Case
- Re: [AMBER] Format error in frcmod file of HEME Thakur, Abhishek
- [AMBER] coordinate bond between them and S and FE Thakur, Abhishek
- Re: [AMBER] coordinate bond between them and S and FE Marcos Serrou do Amaral
- Re: [AMBER] coordinate bond between them and S and FE Thakur, Abhishek
- Re: [AMBER] coordinate bond between them and S and FE Adrian Roitberg
- [AMBER] RES: Incorrect ligand parameterization using GAFF Emilia Pecora-de-barros
- Re: [AMBER] coordinate bond between them and S and FE Andrew Schaub
- Re: [AMBER] AMBER umbrella sampling 吴萌
- [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? nagakumarb.ccamp.res.in
- Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? Bill Ross
- Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? nagakumarb.ccamp.res.in
- Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? Bill Ross
- Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? nagakumarb.ccamp.res.in
- Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? Bill Ross
Saturday, 15 April 2017
- Re: [AMBER] RES: Incorrect ligand parameterization using GAFF Hannes Loeffler
- Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? nagakumarb.ccamp.res.in
- [AMBER] weird asymmetries in solvent box Thomas Charles Pochapsky
- Re: [AMBER] cpptraj creates pdb file it cannot read James Kress
Sunday, 16 April 2017
- Re: [AMBER] Periodic box error for restarting simulations with restraints Sadegh Faramarzi Ganjabad
- Re: [AMBER] cpptraj creates pdb file it cannot read Daniel Roe
- Re: [AMBER] cpptraj creates pdb file it cannot read James Kress
- Re: [AMBER] cpptraj creates pdb file it cannot read Jason Swails
Monday, 17 April 2017
- [AMBER] How to calculate the solvation free energy using Amber? JinpengYang
- Re: [AMBER] How to calculate the solvation free energy using Amber? Bill Ross
- Re: [AMBER] How to calculate the solvation free energy using Amber? hannes.loeffler.stfc.ac.uk
- Re: [AMBER] weird asymmetries in solvent box David Case
- Re: [AMBER] cpptraj creates pdb file it cannot read Daniel Roe
- [AMBER] PCA - concatenating trajectories George Tzotzos
- Re: [AMBER] PCA - concatenating trajectories Adrian Roitberg
- Re: [AMBER] PCA - concatenating trajectories George Tzotzos
- Re: [AMBER] PCA - concatenating trajectories Daniel Roe
- Re: [AMBER] weird asymmetries in solvent box Thomas Pochapsky
- Re: [AMBER] PCA - concatenating trajectories Chris Neale
- Re: [AMBER] PCA - concatenating trajectories George Tzotzos
- Re: [AMBER] weird asymmetries in solvent box David Case
- Re: [AMBER] coordinate bond between them and S and FE Thakur, Abhishek
- Re: [AMBER] coordinate bond between them and S and FE Adrian Roitberg
- Re: [AMBER] coordinate bond between them and S and FE Thakur, Abhishek
- Re: [AMBER] coordinate bond between them and S and FE David Case
- [AMBER] HEME-CYS Thakur, Abhishek
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Samaneh Ghassabi Kondalaji
- Re: [AMBER] HEME-CYS Elvis Martis
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Feng Pan
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Goetz, Andreas
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Samaneh Ghassabi Kondalaji
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Samaneh Ghassabi Kondalaji
- Re: [AMBER] HEME-CYS Thakur, Abhishek
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Goetz, Andreas
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Samaneh Ghassabi Kondalaji
- Re: [AMBER] HEME-CYS Thakur, Abhishek
- Re: [AMBER] cpptraj creates pdb file it cannot read James Kress
- [AMBER] Release of AmberTools17 David Case
- Re: [AMBER] HEME-CYS Elvis Martis
- Re: [AMBER] HEME-CYS Elvis Martis
Tuesday, 18 April 2017
- [AMBER] Adding hydrogens to a ligand jacob wick
- Re: [AMBER] Adding hydrogens to a ligand Bill Ross
- Re: [AMBER] Adding hydrogens to a ligand Hannes Loeffler
- Re: [AMBER] Adding hydrogens to a ligand jacob wick
- [AMBER] Quasi-harmonic entropy calculation ---- Vibrational component of entropy George Tzotzos
- Re: [AMBER] Quasi-harmonic entropy calculation ---- Vibrational component of entropy David Case
- Re: [AMBER] Quasi-harmonic entropy calculation ---- Vibrational component of entropy David Case
- Re: [AMBER] HEME-CYS Elvis Martis
- [AMBER] pmemd.cuda on an Amber Certified High-End workstation Li, Wen
- Re: [AMBER] HEME-CYS Thakur, Abhishek
- Re: [AMBER] pmemd.cuda on an Amber Certified High-End workstation Ross Walker
- [AMBER] Discussion questions regarding PyRED FF development Iqbal, Muhammad Sajid
- Re: [AMBER] pmemd.cuda on an Amber Certified High-End workstation David Case
- [AMBER] Error with MMPSA.py calculation Praneeth Bommisetti
- [AMBER] AmberTools17 + intel17 = bug Hector A. Baldoni
- Re: [AMBER] AmberTools17 + intel17 = bug Hector A. Baldoni
- Re: [AMBER] AmberTools17 + intel17 = bug Daniel Roe
- Re: [AMBER] AmberTools17 + intel17 = bug David Case
- Re: [AMBER] HEME-CYS Elvis Martis
Wednesday, 19 April 2017
- Re: [AMBER] AmberTools17 + intel17 = bug Hector A. Baldoni
- Re: [AMBER] HEME-CYS Thakur, Abhishek
- [AMBER] EVB with RPMD Rob Arbon
- Re: [AMBER] EVB with RPMD David Case
- Re: [AMBER] HEME-CYS Elvis Martis
- Re: [AMBER] HEME-CYS Thakur, Abhishek
- Re: [AMBER] HEME-CYS Elvis Martis
- Re: [AMBER] Release of AmberTools17 James Kress
- Re: [AMBER] weird asymmetries in solvent box Thomas Pochapsky
- Re: [AMBER] Release of AmberTools17 David Case
- Re: [AMBER] Release of AmberTools17 James Kress
- Re: [AMBER] Release of AmberTools17 James Kress
- Re: [AMBER] Release of AmberTools17 Bill Ross
- Re: [AMBER] Error with MMPSA.py calculation Jason Swails
- Re: [AMBER] Release of AmberTools17 James Kress
Thursday, 20 April 2017
- [AMBER] Post MD minimization Manjula Saravanan
- Re: [AMBER] Post MD minimization Bill Ross
- [AMBER] Run NPT in a small periodic box Xiaoliu Zhang
- [AMBER] MMPBSA - error Anna Cebrian Prats
- Re: [AMBER] Post MD minimization David Case
- [AMBER] Membrane Protein Simulation Methodology Gulsevin,Alican
- [AMBER] Recommended LJ parameters for divalent cations used for negatively charged lipid bilayers simulations ? Marek Maly
- Re: [AMBER] MMPBSA - error Ray Luo
- Re: [AMBER] Run NPT in a small periodic box David Case
- [AMBER] 3D-RISM centering 0 Lucia Fusani
- [AMBER] Internal dielectric constant and pmemd Samaneh Ghassabi Kondalaji
- Re: [AMBER] 3D-RISM centering 0 Tyler Luchko (Lists)
- Re: [AMBER] Membrane Protein Simulation Methodology Edson Katekawa
- [AMBER] How to make sure there is bond in my complex Thakur, Abhishek
- Re: [AMBER] How to make sure there is bond in my complex Hai Nguyen
- Re: [AMBER] How to make sure there is bond in my complex Thakur, Abhishek
- Re: [AMBER] How to make sure there is bond in my complex Hai Nguyen
- Re: [AMBER] How to make sure there is bond in my complex Thakur, Abhishek
- Re: [AMBER] pmemd.cuda on an Amber Certified High-End workstation Li, Wen
- [AMBER] Minor bug with updating Amber/AmberTools with Python3 Rohith Mohan
- Re: [AMBER] Minor bug with updating Amber/AmberTools with Python3 Hai Nguyen
- [AMBER] PMEMD should halt with error exit after netcdf write failure Chris Moth
- [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? Guqin Shi
- Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? David Case
- [AMBER] Can't not run cpptraj Khatcharin Siriwong
- Re: [AMBER] Can't not run cpptraj Hai Nguyen
- Re: [AMBER] Can't not run cpptraj Khatcharin Siriwong
- Re: [AMBER] Can't not run cpptraj Gulsevin,Alican
- Re: [AMBER] Can't not run cpptraj Khatcharin Siriwong
- Re: [AMBER] Membrane Protein Simulation Methodology Elvis Martis
Friday, 21 April 2017
- Re: [AMBER] Internal dielectric constant and pmemd David Case
- Re: [AMBER] Internal dielectric constant and pmemd Samaneh Ghassabi Kondalaji
- Re: [AMBER] Internal dielectric constant and pmemd Adrian Roitberg
- Re: [AMBER] Internal dielectric constant and pmemd Samaneh Ghassabi Kondalaji
- Re: [AMBER] Internal dielectric constant and pmemd Adrian Roitberg
- Re: [AMBER] Internal dielectric constant and pmemd Samaneh Ghassabi Kondalaji
- [AMBER] Segmentation fault sylvester kisembo
- Re: [AMBER] Segmentation fault Adrian Roitberg
- Re: [AMBER] Segmentation fault David Case
- Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? Guqin Shi
- Re: [AMBER] Internal dielectric constant and pmemd James Kress
- Re: [AMBER] Internal dielectric constant and pmemd James Kress
- Re: [AMBER] Internal dielectric constant and pmemd Samaneh Ghassabi Kondalaji
- Re: [AMBER] Internal dielectric constant and pmemd James Kress
- [AMBER] residue-based dielectric model in MMGBSA Mrinda Jones
- [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph
- Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph
- Re: [AMBER] Warning message in AmberTools17 upgrade Nhai
- Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph
- Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph
- Re: [AMBER] Warning message in AmberTools17 upgrade Nhai
- Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph
- [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 Mooers, Blaine H.M. (HSC)
- Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph
- Re: [AMBER] Warning message in AmberTools17 upgrade Hai Nguyen
- Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph
- Re: [AMBER] Warning message in AmberTools17 upgrade Hai Nguyen
- Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph
- Re: [AMBER] Internal dielectric constant and pmemd Thomas Cheatham
- Re: [AMBER] Warning message in AmberTools17 upgrade Jason Swails
- Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph
- Re: [AMBER] Internal dielectric constant and pmemd Samaneh Ghassabi Kondalaji
- Re: [AMBER] Segmentation fault sylvester kisembo
- Re: [AMBER] residue-based dielectric model in MMGBSA David Case
- Re: [AMBER] residue-based dielectric model in MMGBSA Thomas Cheatham
- Re: [AMBER] residue-based dielectric model in MMGBSA Thomas Cheatham
- Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 David Case
- Re: [AMBER] Segmentation fault David Case
- Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? David Case
- Re: [AMBER] Warning message in AmberTools17 upgrade Hai Nguyen
- Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? Guqin Shi
Saturday, 22 April 2017
- [AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc Sharon D. Morris
- [AMBER] cpptraj configure may fail in AmberTools17 Hannes Loeffler
- Re: [AMBER] residue-based dielectric model in MMGBSA David Case
- Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? David Case
- Re: [AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc Elvis Martis
- Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? Guqin Shi
- Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 Mooers, Blaine H.M. (HSC)
Sunday, 23 April 2017
- Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 David Case
- Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 Mooers, Blaine H.M. (HSC)
- Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 David Case
- [AMBER] Query regarding convergence issue of 3D-RISM Rakesh Srivastava
Monday, 24 April 2017
- Re: [AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc Elvis Martis
- Re: [AMBER] residue-based dielectric model in MMGBSA Jaime Rubio Martinez
- [AMBER] Query regarding energy calcuation using 3D-RISM Vertika Gautam
- [AMBER] Membrane Protein Simulation Methodology Gulsevin,Alican
- [AMBER] Early-bird and bursary deadline April 30: eChemInfo Training and Innovation Course in Drug Design Thomas Exner
- Re: [AMBER] Query regarding convergence issue of 3D-RISM David Case
- Re: [AMBER] Query regarding energy calcuation using 3D-RISM David Case
- Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph
- Re: [AMBER] Warning message in AmberTools17 upgrade Hai Nguyen
- Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Scott Brozell
- [AMBER] antechamber convergence problem. Vatsal Purohit
- [AMBER] Pairwise energy calculations in cpptraj Aishani Prem
Tuesday, 25 April 2017
- Re: [AMBER] antechamber convergence problem. David Case
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Daniel Roe
- Re: [AMBER] cpptraj configure may fail in AmberTools17 Daniel Roe
- Re: [AMBER] Pairwise energy calculations in cpptraj Daniel Roe
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Scott Brozell
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior David Case
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Scott Brozell
- [AMBER] Stricter convergence Criterion for stretching Ramin Salimi
- Re: [AMBER] Stricter convergence Criterion for stretching Adrian Roitberg
- Re: [AMBER] Stricter convergence Criterion for stretching Ramin Salimi
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Ross Walker
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Daniel Roe
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Nhai
- Re: [AMBER] Stricter convergence Criterion for stretching Ramin Salimi
- [AMBER] Regarding gaussian namelist error Budhathoki, Dipesh
- Re: [AMBER] Regarding gaussian namelist error David Case
- [AMBER] Trouble with simple MD simulation of short peptide and Cu2+ ion Eugene Cha
- Re: [AMBER] Regarding gaussian namelist error Budhathoki, Dipesh
- [AMBER] consult about LEaP in amber 张壮壮
- Re: [AMBER] Trouble with simple MD simulation of short peptide and Cu2+ ion Bill Ross
- Re: [AMBER] Trouble with simple MD simulation of short peptide and Cu2+ ion MOHD HOMAIDUR RAHMAN
- Re: [AMBER] Trouble with simple MD simulation of short peptide and Cu2+ ion Bill Ross
Wednesday, 26 April 2017
- Re: [AMBER] consult about LEaP in amber Elvis Martis
- [AMBER] intra-residue water bridge with cpptraj Joanna Sarzynska
- [AMBER] Release of AmberTools17 binary Hai Nguyen
- Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 Mooers, Blaine H.M. (HSC)
- Re: [AMBER] intra-residue water bridge with cpptraj Daniel Roe
- Re: [AMBER] 3D-RISM centering 0 Lucia Fusani
- [AMBER] Post Doc position in Munich, German required Andreas Tosstorff
- Re: [AMBER] Release of AmberTools17 binary David Case
- [AMBER] barostat=1 error at Stampede Tarsis
- [AMBER] Tutorial - 3 / MM-PBSA Marcelo Andrade Chagas
- Re: [AMBER] Tutorial - 3 / MM-PBSA Hai Nguyen
- Re: [AMBER] barostat=1 error at Stampede Elvis Martis
- Re: [AMBER] barostat=1 error at Stampede Elvis Martis
Thursday, 27 April 2017
- Re: [AMBER] barostat=1 error at Stampede Bill Ross
- [AMBER] Error with 'surf' and acetonitrile-water solvent mixture Marcel Passon
- Re: [AMBER] barostat=1 error at Stampede Ross Walker
- Re: [AMBER] barostat=1 error at Stampede Elvis Martis
- [AMBER] tleap input file that fails following upgrade to AmberTools17 Adams, John E.
- [AMBER] Announcement: Release of DOCK 6.8 Scott Brozell
- [AMBER] Quenstions about Constraints in AMBER Pengfei Li
Friday, 28 April 2017
- Re: [AMBER] Quenstions about Constraints in AMBER Hannes Loeffler
- Re: [AMBER] intra-residue water bridge with cpptraj Joanna Sarzynska
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Scott Brozell
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Adams, John E.
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Hai Nguyen
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Hai Nguyen
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Adams, John E.
- [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber. Miguel Rivera
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Hai Nguyen
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Adams, John E.
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Adams, John E.
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Nhai
- [AMBER] Using AmberTools17 and Amber14 David Adrian Saez San Martin
- Re: [AMBER] Using AmberTools17 and Amber14 Hai Nguyen
Saturday, 29 April 2017
- [AMBER] Too many iterations in routine! in RMSD calculation kungking Hanpaibool
- [AMBER] Restraint in Steered MD/Jarzynski method Ramin Salimi
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 David Case
- Re: [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber. David Case
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Adams, John E.
- [AMBER] Restraint in Steered MD/Jarzynski method Ramin Salimi
- [AMBER] Dftb3 Jacopo Sgrignani
- Re: [AMBER] Dftb3 David Case
Sunday, 30 April 2017
- Re: [AMBER] Restraint in Steered MD/Jarzynski method Hannes Loeffler
- Re: [AMBER] Restraint in Steered MD/Jarzynski method Ramin Salimi
- [AMBER] External electric fields on CUDA enabled PMEMD Neville Bethel
- Re: [AMBER] Quenstions about Constraints in AMBER David Case

Last message date: Sun Apr 30 2017 - 17:30:03 PDT
Archived on: Wed Dec 25 2024 - 05:55:30 PST

Amber Archive Apr 2017 by date