Amber Archive May 2018: by date

Monday, 30 April 2018
- Re: [AMBER] QM/MM minimization issue using sander (AMBER 18) Goetz, Andreas
Tuesday, 1 May 2018
- Re: [AMBER] QM/MM minimization issue using sander (AMBER 18) Abhilash J
- [AMBER] Computing interaction energies from trajectory Aravind Ravichandran
- Re: [AMBER] Cremer Pucker values using Pytraj Vivek Bharadwaj
- Re: [AMBER] QM/MM minimization issue using sander (AMBER 18) Abhilash J
- [AMBER] Using infe = 1, &pmd, and pmemd.cuda (AMBER16) Lenz, Stefan
- [AMBER] CPPTRAJ Ensemble Keyword: "Too Many Open Files" Jason Ku Wang
- Re: [AMBER] Boost not linking when compiling on Mac Gustaf Olsson
Wednesday, 2 May 2018
- [AMBER] GPU benchmark - Amber18 Hadházi Ádám
- [AMBER] update ambertools Tousif Hossen
- [AMBER] update Ambertools Tousif Hossen
- [AMBER] PhD/Junior position, AMBER sims DNA/RNA Jiri Sponer
- Re: [AMBER] Boost not linking when compiling on Mac David A Case
- Re: [AMBER] GPU benchmark - Amber18 David A Case
- Re: [AMBER] update ambertools David A Case
- Re: [AMBER] Boost not linking when compiling on Mac Gustaf Olsson
- [AMBER] How to extract frames with particular hydrogen bonds only Stejskal, Lenka
- Re: [AMBER] update ambertools Kevin Keane
- Re: [AMBER] .rst and .mdcrd file outputted in ascii David A Case
- Re: [AMBER] Using infe = 1, &pmd, and pmemd.cuda (AMBER16) Feng Pan
- [AMBER] need QMMM interface for TURBOMOLE 陈金峰
- Re: [AMBER] Boost not linking when compiling on Mac Scott Brozell
Thursday, 3 May 2018
- [AMBER] Multiple temperature groups I Lőrincz
- [AMBER] input files from AmberTools 16/17 run on Amber14 pmemd.cuda engine problem Chetna Tyagi
- Re: [AMBER] CPPTRAJ Ensemble Keyword: "Too Many Open Files" Daniel Roe
- Re: [AMBER] input files from AmberTools 16/17 run on Amber14 pmemd.cuda engine problem Gustaf Olsson
- Re: [AMBER] input files from AmberTools 16/17 run on Amber14 pmemd.cuda engine problem Daniel Roe
- Re: [AMBER] input files from AmberTools 16/17 run on Amber14 pmemd.cuda engine problem Chetna Tyagi
- Re: [AMBER] How to extract frames with particular hydrogen bonds only Daniel Roe
- Re: [AMBER] Configure CUDA issues Kadir Ozcan
- Re: [AMBER] Configure CUDA issues David A Case
- Re: [AMBER] AMBER Digest, Vol 2280, Issue 1 Kadir Ozcan
Friday, 4 May 2018
- [AMBER] calculation of cavity water Tousif Hossen
- [AMBER] Problem in distance restraint Kshatresh Dutta Dubey
- Re: [AMBER] Simulation does not restart from restart file written in previous step. Abhilash J
- Re: [AMBER] AMBER Digest, Vol 2280, Issue 1 David A Case
- [AMBER] Setting initial velocities diego.soler.uam.es
- Re: [AMBER] Problem in distance restraint David A Case
- Re: [AMBER] calculation of cavity water Kenneth Huang
- Re: [AMBER] calculation of cavity water Leena Aggarwal
Saturday, 5 May 2018
- [AMBER] SGLD Piotr Fajer
- Re: [AMBER] SGLD David A Case
- Re: [AMBER] SGLD Piotr Fajer
- Re: [AMBER] calculation of cavity water Tousif Hossen
- [AMBER] Poly amino acid helix form topology files roja rahmani
Sunday, 6 May 2018
- [AMBER] nativecontacts command in CPPTRAJ Ruth Helena Tichauer
- Re: [AMBER] nativecontacts command in CPPTRAJ Andreas Tosstorff
- Re: [AMBER] Poly amino acid helix form topology files Carlos Simmerling
- Re: [AMBER] Poly amino acid helix form topology files roja rahmani
- Re: [AMBER] Poly amino acid helix form topology files Carlos Simmerling
- Re: [AMBER] Poly amino acid helix form topology files roja rahmani
- Re: [AMBER] calculation of cavity water Kenneth Huang
- Re: [AMBER] calculation of cavity water Kenneth Huang
- Re: [AMBER] nativecontacts command in CPPTRAJ Ruth Helena Tichauer
- Re: [AMBER] nativecontacts command in CPPTRAJ Sowmya Indrakumar
- Re: [AMBER] nativecontacts command in CPPTRAJ Ruth Helena Tichauer
- Re: [AMBER] nativecontacts command in CPPTRAJ Sowmya Indrakumar
- Re: [AMBER] calculation of cavity water Tousif Hossen
Monday, 7 May 2018
- Re: [AMBER] Poly amino acid helix form topology files ABEL Stephane
- Re: [AMBER] Poly amino acid helix form topology files roja rahmani
- Re: [AMBER] Poly amino acid helix form topology files ABEL Stephane
- Re: [AMBER] need QMMM interface for TURBOMOLE David A Case
- Re: [AMBER] Poly amino acid helix form topology files Carlos Simmerling
- Re: [AMBER] calculation of cavity water Tousif Hossen
- Re: [AMBER] calculation of cavity water Kenneth Huang
- [AMBER] PC modes per residue from existing evecs file? Kenneth Huang
- Re: [AMBER] calculation of cavity water Tousif Hossen
- Re: [AMBER] calculation of cavity water Tom Kurtzman
- Re: [AMBER] need QMMM interface for TURBOMOLE Goetz, Andreas
- Re: [AMBER] calculation of cavity water Tousif Hossen
- [AMBER] Amber 18 Thermodynamic integration question David Wifling
- [AMBER] Advice on SMD QM/MM for Cyanogenic Glucoside senal dinuka
Tuesday, 8 May 2018
- [AMBER] GBNSR6 with MMPBSA.py Jose Manuel Granadino Roldán
- Re: [AMBER] need QMMM interface for TURBOMOLE Antoine MARION
- [AMBER] MMPBSA.py.MPI and matching topology files a problem Kasprzak, Wojciech (NIH/NCI) [C]
- [AMBER] Parametrization: consistency with gaff force field Alechania Misturini
- Re: [AMBER] need QMMM interface for TURBOMOLE Scott Brozell
- [AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory Chris Neale
- Re: [AMBER] Setting initial velocities Hai Nguyen
- Re: [AMBER] Setting initial velocities Hai Nguyen
- [AMBER] what are the benefits of cuda9 vs. 8 with amber 18? Chris Neale
- [AMBER] Extracting infromation from topology file anu chandra
- Re: [AMBER] Extracting infromation from topology file Hai Nguyen
- [AMBER] Query related to the Umbrella sampling method Saikat Pal
Wednesday, 9 May 2018
- [AMBER] adding NME and ACE terminals roja rahmani
- Re: [AMBER] adding NME and ACE terminals Juan Eiros
- [AMBER] Different outputs of external electric field Meng Wu
- [AMBER] Error: No data sets selected - Problem or not? Gustaf Olsson
- Re: [AMBER] adding NME and ACE terminals roja rahmani
- Re: [AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory David A Case
- Re: [AMBER] adding NME and ACE terminals roja rahmani
- Re: [AMBER] Error: No data sets selected - Problem or not? Daniel Roe
- Re: [AMBER] need QMMM interface for TURBOMOLE Holger Kruse
- Re: [AMBER] Setting initial velocities David A Case
- Re: [AMBER] Error: No data sets selected - Problem or not? Gustaf Olsson
- Re: [AMBER] what are the benefits of cuda9 vs. 8 with amber 18? David A Case
- Re: [AMBER] Different outputs of external electric field David A Case
- Re: [AMBER] adding NME and ACE terminals David A Case
- Re: [AMBER] Amber 18 Thermodynamic integration question David A Case
- Re: [AMBER] what are the benefits of cuda9 vs. 8 with amber 18? Chris Neale
- Re: [AMBER] adding NME and ACE terminals roja rahmani
- Re: [AMBER] adding NME and ACE terminals ABEL Stephane
- Re: [AMBER] adding NME and ACE terminals roja rahmani
- Re: [AMBER] adding NME and ACE terminals ABEL Stephane
- Re: [AMBER] Multiple temperature groups David A Case
- Re: [AMBER] Different outputs of external electric field Meng Wu
Thursday, 10 May 2018
- Re: [AMBER] Different outputs of external electric field David A Case
- Re: [AMBER] Different outputs of external electric field David A Case
- [AMBER] QM/MM issue with boron containing compound (AMBER16) Bodee Nutho
- [AMBER] MMPBSA.py execution error Jose Manuel Granadino Roldán
- Re: [AMBER] MMPBSA.py execution error Daniel Roe
- Re: [AMBER] QM/MM issue with boron containing compound (AMBER16) David A Case
- Re: [AMBER] MMPBSA.py execution error David A Case
- Re: [AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory Chris Neale
- Re: [AMBER] MMPBSA.py execution error Hai Nguyen
- Re: [AMBER] QM/MM issue with boron containing compound (AMBER16) Bodee Nutho
- [AMBER] Angle calculation between three amino acids maryam azimzadehirani
Friday, 11 May 2018
- Re: [AMBER] MMPBSA.py execution error Jose Manuel Granadino Roldán
- Re: [AMBER] Angle calculation between three amino acids Daniel Roe
- Re: [AMBER] Angle calculation between three amino acids maryam azimzadehirani
- [AMBER] MMPBSA.py.MPI: questions about output warnings and discrepancies Kasprzak, Wojciech (NIH/NCI) [C]
- [AMBER] TMD : Doubts regarding TGTMDFRC Aravind Ravichandran
Saturday, 12 May 2018
- [AMBER] change the charge of the chlorine ion Saikat Pal
- Re: [AMBER] change the charge of the chlorine ion David A Case
- Re: [AMBER] TMD : Doubts regarding TGTMDFRC Carlos Simmerling
- [AMBER] lipid MSD values for lipid 14 FF Chitrak Gupta
Sunday, 13 May 2018
- Re: [AMBER] Novice Question: MD Visualisation in VMD Horn, Anselm
- Re: [AMBER] Novice Question: MD Visualisation in VMD David A Case
- Re: [AMBER] Novice Question: MD Visualisation in VMD James Kress
- [AMBER] lipid 14 MSD with OPC water Chitrak Gupta
- Re: [AMBER] change the charge of the chlorine ion Saikat Pal
- Re: [AMBER] TMD : Doubts regarding TGTMDFRC Aravind Ravichandran
Monday, 14 May 2018
- [AMBER] tleap error 'FATAL: Atom .R<NMET 1>.A<CAY 20> does not have a type' Midhun K Madhu
- [AMBER] combining trajectories with different parameter files Chetna Tyagi
- Re: [AMBER] tleap error 'FATAL: Atom .R<NMET 1>.A<CAY 20> does not have a type' David A Case
- Re: [AMBER] combining trajectories with different parameter files David A Case
- Re: [AMBER] TMD : Doubts regarding TGTMDFRC Carlos Simmerling
- Re: [AMBER] combining trajectories with different parameter files Chetna Tyagi
- Re: [AMBER] combining trajectories with different parameter files Daniel Roe
- [AMBER] GUI for TI setup Hadházi Ádám
- [AMBER] autoimage problem Ming Tang
- Re: [AMBER] Parametrization: consistency with gaff force field David A Case
- Re: [AMBER] GUI for TI setup Charles Lin
- Re: [AMBER] GUI for TI setup James Kress
- [AMBER] NetCDF error: NetCDF: Not a valid ID Midhun K Madhu
- [AMBER] Creating a Gold surface library file Timothy Cholko
- Re: [AMBER] Creating a Gold surface library file David A Case
- [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters. with pmemd.cuda David Sáez
- Re: [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters. with pmemd.cuda David Adrian Saez San Martin
Tuesday, 15 May 2018
- Re: [AMBER] Parametrization: consistency with gaff force field Alechania Misturini
- Re: [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters. with pmemd.cuda David A Case
- [AMBER] MMPBSA.py - PrmtopError: Inconsistent charge definition for atom Rodrigo Galindo-Murillo
- [AMBER] Electrostatic potential calculation Meng Wu
- [AMBER] pmemd.MPI compatible for REMD simulation IN AMBER package Saikat Pal
Wednesday, 16 May 2018
- Re: [AMBER] pmemd.MPI compatible for REMD simulation IN AMBER package Cruzeiro,Vinicius Wilian D
- Re: [AMBER] MMPBSA.py - PrmtopError: Inconsistent charge definition for atom David A Case
- Re: [AMBER] autoimage problem David A Case
- Re: [AMBER] autoimage problem Daniel Roe
- [AMBER] I: help please giuseppe gatti
- [AMBER] MMPBSA energy decomposition Yuxin Xie
- [AMBER] Reservoir REMD using GPUs Hurst, Travis C (MU-Student)
Thursday, 17 May 2018
- [AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version). DHEERAJ CHITARA
- [AMBER] MD stops due to the distortion of a molecule Sergey Samsonov
- [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" PRITI ROY
- [AMBER] DFT method for calculating amino acids partial charges in AMBER99 roja rahmani
- Re: [AMBER] DFT method for calculating amino acids partial charges in AMBER99 FyD
- Re: [AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version). Carlos Simmerling
- Re: [AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version). DHEERAJ CHITARA
- Re: [AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version). David A Case
- [AMBER] Reg. generating empty frcmod file for ligand molecule DHEERAJ CHITARA
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" Leena Aggarwal
- Re: [AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version). DHEERAJ CHITARA
- Re: [AMBER] MD stops due to the distortion of a molecule David A Case
- Re: [AMBER] Reg. generating empty frcmod file for ligand molecule Aashish Bhatt
- Re: [AMBER] Reg. generating empty frcmod file for ligand molecule DHEERAJ CHITARA
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" PRITI ROY
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" Leena Aggarwal
- [AMBER] GPU questions 陈金峰
- Re: [AMBER] GPU questions Daniel Roe
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" Tyler Luchko (Lists)
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" David A Case
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" PRITI ROY
- Re: [AMBER] Creating a Gold surface library file Timothy Cholko
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" Leena Aggarwal
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" PRITI ROY
- Re: [AMBER] MD stops due to the distortion of a molecule Sergey Samsonov
- Re: [AMBER] Electrostatic potential calculation Meng Wu
Friday, 18 May 2018
- [AMBER] Parametrization of Small Molecules Johannes Loeffler
- [AMBER] [cpptraj] Angle between atom and two centroids Eiros Zamora, Juan
- Re: [AMBER] Creating a Gold surface library file David A Case
- Re: [AMBER] Parametrization of Small Molecules David A Case
- Re: [AMBER] [cpptraj] Angle between atom and two centroids David A Case
- Re: [AMBER] [cpptraj] Angle between atom and two centroids Daniel Roe
- Re: [AMBER] DFT method for calculating amino acids partial charges in AMBER99 David A Case
- Re: [AMBER] I: help please David A Case
- [AMBER] Facing problem to generate ala10_chir.dat in REMD tutorial Saikat Pal
- Re: [AMBER] DFT method for calculating amino acids partial charges in AMBER99 roja rahmani
- Re: [AMBER] NetCDF error: NetCDF: Not a valid ID David A Case
- Re: [AMBER] Facing problem to generate ala10_chir.dat in REMD tutorial David A Case
- Re: [AMBER] Electrostatic potential calculation Daniel Roe
- [AMBER] QMMM surface scan 陈金峰
- Re: [AMBER] Creating a Gold surface library file Timothy Cholko
Saturday, 19 May 2018
- [AMBER] Amber16 pmemd.cuda.MPI simulation can drop a frame with an inopportune node crash Chris Neale
- Re: [AMBER] Amber16 pmemd.cuda.MPI simulation can drop a frame with an inopportune node crash David Cerutti
- Re: [AMBER] Creating a Gold surface library file David A Case
- Re: [AMBER] Amber16 pmemd.cuda.MPI simulation can drop a frame with an inopportune node crash Chris Neale
Sunday, 20 May 2018
- [AMBER] Restart From Check point File Midhun K Madhu
- Re: [AMBER] Restart From Check point File Stephan Schott
Monday, 21 May 2018
- [AMBER] Total Energy Decomposition daniele selli
- [AMBER] info grafic about MD Rosellen, Martin
- [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model Sadegh Faramarzi Ganjabad
- Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model Karla Galdamez
- Re: [AMBER] Restart From Check point File Midhun K Madhu
Tuesday, 22 May 2018
- Re: [AMBER] Total Energy Decomposition David A Case
- Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model David A Case
- Re: [AMBER] Restart From Check point File Stephan Schott
- Re: [AMBER] nativecontacts command in CPPTRAJ Ruth Helena Tichauer
- Re: [AMBER] nativecontacts command in CPPTRAJ Daniel Roe
- [AMBER] 1x PCI-E Riser card for MD/TI? Hadházi Ádám
- [AMBER] Possible memory leak with LMOD Charo del Genio
- [AMBER] Scabilility of the code in cpus Ana Luisa Novo de Oliveira
- [AMBER] Hydrogen Bond Occupancy Jerrano Bowleg
- Re: [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters. with pmemd.cuda David A Case
- Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model David A Case
- [AMBER] R: Re: SHAKEH: Extra bond between hydrogen atoms of TIP3 water model Sadegh Faramarzi Ganjabad
- Re: [AMBER] Possible memory leak with LMOD David A Case
- Re: [AMBER] Scabilility of the code in cpus David A Case
- Re: [AMBER] 1x PCI-E Riser card for MD/TI? Ross Walker
- Re: [AMBER] 1x PCI-E Riser card for MD/TI? Hadházi Ádám
- Re: [AMBER] Creating a Gold surface library file Timothy Cholko
- Re: [AMBER] R: Re: SHAKEH: Extra bond between hydrogen atoms of TIP3 water model David A Case
- Re: [AMBER] Creating a Gold surface library file David A Case
- Re: [AMBER] Hydrogen Bond Occupancy David A Case
- [AMBER] VMD window Karla Galdamez
- Re: [AMBER] VMD window Gustaf Olsson
- Re: [AMBER] Hydrogen Bond Occupancy Gustaf Olsson
- Re: [AMBER] VMD window Karla Galdamez
Wednesday, 23 May 2018
- Re: [AMBER] VMD window Gustaf Olsson
- Re: [AMBER] nativecontacts command in CPPTRAJ Ruth Helena Tichauer
- Re: [AMBER] nativecontacts command in CPPTRAJ Andreas Tosstorff
- [AMBER] update_amber URL time out problem Meng Wu
- Re: [AMBER] nativecontacts command in CPPTRAJ Ruth Helena Tichauer
- [AMBER] S-S bond roja rahmani
- Re: [AMBER] Total Energy Decomposition daniele selli
- Re: [AMBER] update_amber URL time out problem David A Case
- Re: [AMBER] Hydrogen Bond Occupancy Jerrano Bowleg
- Re: [AMBER] VMD window Karla Galdamez
- Re: [AMBER] nativecontacts command in CPPTRAJ Ruth Helena Tichauer
- [AMBER] Use of Amber12 and 14 on the same simulation JoAnne Babula
- Re: [AMBER] Possible memory leak with LMOD Charo del Genio
- [AMBER] parmed/chamber verify including CMAP corrections David Sáez
- Re: [AMBER] parmed/chamber verify including CMAP corrections Robin Betz
- Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model Sadegh Faramarzi Ganjabad
- [AMBER] Amber 18 manual shows TI as not supported in pmemd.cuda Patricio German Barletta Roldan
- [AMBER] pmemd.MPI won't work in Amber 18 Hai Long
- Re: [AMBER] update_amber URL time out problem Meng Wu
- Re: [AMBER] S-S bond FyD
- Re: [AMBER] S-S bond roja rahmani
Thursday, 24 May 2018
- [AMBER] optimization of QM zone in QM/MM-GBSA calculations. mish
- [AMBER] Error in using pdb4amber command senal dinuka
- Re: [AMBER] Use of Amber12 and 14 on the same simulation David A Case
- Re: [AMBER] Possible memory leak with LMOD David A Case
- Re: [AMBER] Amber 18 manual shows TI as not supported in pmemd.cuda David A Case
- Re: [AMBER] pmemd.MPI won't work in Amber 18 David A Case
- Re: [AMBER] eCheminfo Milano July 16-29, Training and Innovation Course in Drug Design 2018, bursary and early-bird deadline ending soon Thomas Exner
- Re: [AMBER] update_amber URL time out problem David A Case
- Re: [AMBER] optimization of QM zone in QM/MM-GBSA calculations. David A Case
- Re: [AMBER] Error in using pdb4amber command David A Case
- Re: [AMBER] Error in using pdb4amber command senal dinuka
- [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Markowska
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Gustaf Olsson
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Carlos Simmerling
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Gustaf Olsson
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Markowska
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Carlos Simmerling
- Re: [AMBER] Error in using pdb4amber command Aashish Bhatt
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Markowska
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Kshatresh Dutta Dubey
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Carlos Simmerling
- [AMBER] Plotting phi-psi plots with free energy scale Chetna Tyagi
- Re: [AMBER] Plotting phi-psi plots with free energy scale Carlos Simmerling
- [AMBER] How to evaluate the impact of PH on protein structures by Amber Lei Zhao
- [AMBER] AMBER TI more examples Omoto, Kiyoyuki
- Re: [AMBER] pmemd.MPI won't work in Amber 18 Hai Long
- Re: [AMBER] pmemd.MPI won't work in Amber 18 Ross Walker
Friday, 25 May 2018
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Markowska
- Re: [AMBER] Reservoir REMD using GPUs Carlos Simmerling
- [AMBER] ABMD with multiple walkers Qinghua Liao
- [AMBER] CUDA v9.0 with AMBER16 Question Korey M Reid
Saturday, 26 May 2018
- [AMBER] Using multiple CPU threads senal dinuka
- Re: [AMBER] CUDA v9.0 with AMBER16 Question David A Case
- Re: [AMBER] Using multiple CPU threads David A Case
- Re: [AMBER] ABMD with multiple walkers Feng Pan
- [AMBER] Troubleshooting SHAKE problems in minimization Alen Ahmetovic
Sunday, 27 May 2018
- Re: [AMBER] Troubleshooting SHAKE problems in minimization David A Case
- Re: [AMBER] ABMD with multiple walkers Qinghua Liao
- Re: [AMBER] ABMD with multiple walkers Feng Pan
Monday, 28 May 2018
- [AMBER] DEADLINE EXTENDED: Call for Papers, GCC 2018, 14th German Conference on Chemoinformatics Stefan.Guessregen.sanofi.com
- [AMBER] error in rst file during Minimization Subrata Paul
- Re: [AMBER] ABMD with multiple walkers Qinghua Liao
- Re: [AMBER] error in rst file during Minimization Stephan Schott
- Re: [AMBER] error in rst file during Minimization Subrata Paul
- Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model Sadegh Faramarzi Ganjabad
- [AMBER] AMBER NFE SMD calculation with new collective variable georg.kuenze.vanderbilt.edu
- Re: [AMBER] ABMD with multiple walkers Feng Pan
- [AMBER] AMBER: trouble while running constant pH simulation 李耀
Tuesday, 29 May 2018
- Re: [AMBER] ABMD with multiple walkers Qinghua Liao
- Re: [AMBER] AMBER: trouble while running constant pH simulation 李耀
- Re: [AMBER] AMBER: trouble while running constant pH simulation Cruzeiro,Vinicius Wilian D
- Re: [AMBER] AMBER TI more examples David A Case
- Re: [AMBER] Reservoir REMD using GPUs Hurst, Travis C (MU-Student)
- [AMBER] Automatic patching failed! senal dinuka
- Re: [AMBER] Automatic patching failed! Charles Lin
- Re: [AMBER] Automatic patching failed! senal dinuka
- [AMBER] Request of help on Leap PDB preparation error "atom does not have a type" 符哲瀚
- Re: [AMBER] Automatic patching failed! Charles Lin
- Re: [AMBER] Request of help on Leap PDB preparation error "atom does not have a type" Gustaf Olsson
- [AMBER] sander failed with prmtop complex.top! Urszula Uciechowska
Wednesday, 30 May 2018
- Re: [AMBER] Automatic patching failed! senal dinuka
- [AMBER] TI for side chain mutation in dimer protein Josephine la sala
- Re: [AMBER] eCheminfo Oxford, UK Training and Innovation Course in Drug Design 2018, first announcement Thomas Exner
- [AMBER] problems with MCPY.py step 2 Cristián Ferretti
- Re: [AMBER] Request of help on Leap PDB preparation error "atom does not have a type" Carlos Simmerling
- Re: [AMBER] Automatic patching failed! David A Case
- Re: [AMBER] Request of help on Leap PDB preparation error "atom does not have a type" David A Case
- [AMBER] TiMergeError: Cannot have dihedral cross through softcore region Jissy Akkarapattiakal Kuriappan
- [AMBER] TI for side chain mutation in dimer protein Josephine la sala
- Re: [AMBER] AMBER: trouble while running constant pH simulation > (Cruzeiro, Vinicius Wilian D) 李耀
- Re: [AMBER] AMBER: trouble while running constant pH simulation > (Cruzeiro, Vinicius Wilian D) Cruzeiro,Vinicius Wilian D
- [AMBER] Conda Installation error andreas.tosstorff.cup.uni-muenchen.de
- Re: [AMBER] AMBER NFE SMD calculation with new collective variable Feng Pan
- Re: [AMBER] Problem with g++ compiler with boost (AmberTools18) Matias Machado
- [AMBER] Dimension Box visualization Aashish Bhatt
Thursday, 31 May 2018
- Re: [AMBER] Problem with g++ compiler with boost (AmberTools18) David A Case
- Re: [AMBER] Dimension Box visualization David A Case
- Re: [AMBER] Dimension Box visualization Matias Machado
- Re: [AMBER] Problem with g++ compiler with boost (AmberTools18) Matias Machado
- [AMBER] Ubuntu 18 Sepideh Jafari
- Re: [AMBER] Ubuntu 18 David A Case
- Re: [AMBER] Conda Installation error Hai Nguyen
- Re: [AMBER] Ubuntu 18 Sepideh Jafari
- Re: [AMBER] Ubuntu 18 Scott Brozell
- Re: [AMBER] Conda Installation error Scott Brozell
- Re: [AMBER] Conda Installation error Hai Nguyen
- Re: [AMBER] Conda Installation error Scott Brozell
- [AMBER] Initial configuration of ADP and ion simulation using AMBER. Abhilash J
- Re: [AMBER] Possible memory leak with LMOD David A Case
- Re: [AMBER] Reservoir REMD using GPUs koushik kasavajhala

Last message date: Thu May 31 2018 - 13:00:03 PDT
Archived on: Wed Oct 29 2025 - 05:55:45 PDT

Amber Archive May 2018 by date