Amber Archive Oct 2019: by date

Monday, 30 September 2019
- Re: [AMBER] Installaiton of pmemd for Amber16 Ryoichi Utsumi
- Re: [AMBER] Amber18 installation Sunita Patel
Tuesday, 1 October 2019
- Re: [AMBER] How to incorporate new lipid molecules through packmol-memgen Chetna Tyagi
- [AMBER] netcdf: issue with timestamp Sarath Dantu (Staff)
- [AMBER] Is there any standard set of parameters to build the topology Iron Sulfur clusters? David Sáez
- Re: [AMBER] DNA methylation parameters Zhendong Li
- [AMBER] I add Ions to the system and they don't show up!!! Parviz Seifpanahi Shabane
- [AMBER] regarding amber licensed version and free version. Seketoulie Keretsu
- Re: [AMBER] regarding amber licensed version and free version. Carlos Simmerling
- Re: [AMBER] netcdf: issue with timestamp Daniel Roe
- Re: [AMBER] I add Ions to the system and they don't show up!!! Daniel Roe
- [AMBER] Thermodynamic integration Debarati DasGupta
- [AMBER] ABMD COM_DISTANCE Help Kyle Ghaby
- [AMBER] CPPTRAJ parameter file error Rui Chen
- Re: [AMBER] I add Ions to the system and they don't show up!!! David Case
Wednesday, 2 October 2019
- [AMBER] seek help for mmpbsa 石娜
- Re: [AMBER] seek help for mmpbsa Liao
- Re: [AMBER] CPPTRAJ parameter file error Daniel Roe
- [AMBER] WHere do I modify the charge of a standard residue? David Sáez
- Re: [AMBER] I add Ions to the system and they don't show up!!! Parviz Seifpanahi Shabane
- [AMBER] restraining a peptide to devoid of any secondary structure Vlad Cojocaru
- [AMBER] Error during the test of amber 18 installation Sunita Patel
- Re: [AMBER] CPPTRAJ parameter file error Rui Chen
- Re: [AMBER] ABMD COM_DISTANCE Help Feng Pan
- Re: [AMBER] Thermodynamic integration Charles Lin
- Re: [AMBER] ABMD COM_DISTANCE Help Kyle Ghaby
- [AMBER] Gtx 16-series Charles-Alexandre Mattelaer
- Re: [AMBER] WHere do I modify the charge of a standard residue? David Case
- Re: [AMBER] Error during the test of amber 18 installation David Case
- Re: [AMBER] CPPTRAJ parameter file error Rui Chen
- Re: [AMBER] I add Ions to the system and they don't show up!!! Bill Ross
- [AMBER] ERROR: NaNs found in input coordinates. HOCHEOL LIM
Thursday, 3 October 2019
- [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop Swagata Halder
- Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop Bill Ross
- Re: [AMBER] ERROR: NaNs found in input coordinates. Daniel Roe
- Re: [AMBER] CPPTRAJ parameter file error Daniel Roe
- Re: [AMBER] Thermodynamic integration Debarati DasGupta
- Re: [AMBER] Thermodynamic integration Sadaf Rani
- Re: [AMBER] ABMD COM_DISTANCE Help Feng Pan
- Re: [AMBER] Thermodynamic integration Charles Lin
- Re: [AMBER] Thermodynamic integration Charles Lin
- Re: [AMBER] ABMD COM_DISTANCE Help Kyle Ghaby
- Re: [AMBER] ABMD COM_DISTANCE Help Feng Pan
- Re: [AMBER] Gtx 16-series Gerardo Zerbetto De Palma
- Re: [AMBER] Thermodynamic integration Debarati DasGupta
- Re: [AMBER] Error during the test of amber 18 installation Daniel Roe
- Re: [AMBER] Thermodynamic integration Charles Lin
- Re: [AMBER] Rotational/torsion energy Daniel Roe
- Re: [AMBER] Thermodynamic integration David Case
- [AMBER] Amber Installation Problem on Mac Fanglue Ni
- Re: [AMBER] Amber Installation Problem on Mac Ray Luo
- Re: [AMBER] Rotational/torsion energy Gustaf Olsson
- Re: [AMBER] Amber Installation Problem on Mac Gustaf Olsson
- Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop Swagata Halder
- Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop Bill Ross
Friday, 4 October 2019
- Re: [AMBER] Error during the test of amber 18 installation Sunita Patel
- Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop Jiri Sponer
- [AMBER] CHARMM-GUI now supports Amber Paul Westphälinger
- [AMBER] Calculate MMGBSA keeping water in binding site Rosellen, Martin
- Re: [AMBER] Calculate MMGBSA keeping water in binding site Carlos Simmerling
- Re: [AMBER] Amber Installation Problem on Mac David A Case
- Re: [AMBER] Amber Installation Problem on Mac: update David A Case
- Re: [AMBER] I add Ions to the system and they don't show up!!! Parviz Seifpanahi Shabane
- Re: [AMBER] CPPTRAJ parameter file error Rui Chen
- Re: [AMBER] Amber Installation Problem on Mac: me too Mooers, Blaine H.M. (HSC)
Saturday, 5 October 2019
- [AMBER] About STOP PMEMD Terminated Abnormally! HOCHEOL LIM
- Re: [AMBER] About STOP PMEMD Terminated Abnormally! David Case
- Re: [AMBER] Calculate MMGBSA keeping water in binding site Rosellen, Martin
- Re: [AMBER] RTX 2080 slower then 1080 Ti with pmemd 18 ? Charles-Alexandre Mattelaer
Sunday, 6 October 2019
- [AMBER] tleap hangs when tries to read new residue Dawid das
- Re: [AMBER] tleap hangs when tries to read new residue Bill Ross
- Re: [AMBER] tleap hangs when tries to read new residue Bill Ross
- Re: [AMBER] RTX 2080 slower then 1080 Ti with pmemd 18 ? Ross Walker
- Re: [AMBER] RTX 2080 slower then 1080 Ti with pmemd 18 ? Charles-Alexandre Mattelaer
Monday, 7 October 2019
- [AMBER] hydroxyapatite force field parameters Tal Duanias
- [AMBER] Force extension curve from ASMD Aravind R
- [AMBER] How can I use modified GAFF? 조준범
- Re: [AMBER] How can I use modified GAFF? Bill Ross
- Re: [AMBER] How can I use modified GAFF? Bill Ross
- Re: [AMBER] tleap hangs when tries to read new residue Dawid das
- Re: [AMBER] tleap hangs when tries to read new residue Bill Ross
- [AMBER] Error using MCPB.py Hafiz Saqib Ali
- Re: [AMBER] Error during the test of amber 18 installation Sunita Patel
- Re: [AMBER] tleap hangs when tries to read new residue David A Case
- Re: [AMBER] Error during the test of amber 18 installation David A Case
- Re: [AMBER] Error during the test of amber 18 installation David A Case
- Re: [AMBER] tleap hangs when tries to read new residue Dawid das
- Re: [AMBER] hydroxyapatite force field parameters Pengfei Li
- Re: [AMBER] Error using MCPB.py Pengfei Li
- Re: [AMBER] CPPTRAJ parameter file error Daniel Roe
- [AMBER] mmpbsa MYRIAN TORRES RICO
- Re: [AMBER] hydroxyapatite force field parameters Tal Duanias
- [AMBER] cpptraj.MPI error Debarati DasGupta
- Re: [AMBER] cpptraj.MPI error Daniel Roe
- Re: [AMBER] tleap hangs when tries to read new residue Matias Machado
- Re: [AMBER] tleap hangs when tries to read new residue Dawid das
- [AMBER] Question about ff14SB and parameter files Nate Guerin
- Re: [AMBER] Question about ff14SB and parameter files Carlos Simmerling
- Re: [AMBER] CPPTRAJ parameter file error Rui Chen
- [AMBER] H - bond tools shivangi agarwal
- Re: [AMBER] H - bond tools Elvis Martis
- Re: [AMBER] H - bond tools shivangi agarwal
Tuesday, 8 October 2019
- [AMBER] Imaging issue Hira Jabeen
- Re: [AMBER] Imaging issue David A Case
- [AMBER] Gaff v2.1 Force Field for n4 chaumont
- [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Dawid das
- [AMBER] amber99sb-disp forcefield in Amber Prithvi Raj Pandey
- Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Carlos Simmerling
- Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Dawid das
- Re: [AMBER] amber99sb-disp forcefield in Amber Carlos Simmerling
- Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Carlos Simmerling
- Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Dawid das
- Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Carlos Simmerling
- Re: [AMBER] amber99sb-disp forcefield in Amber Supriyo Bhattacharya
- [AMBER] Problem in MMPBSA analysis 崔佳文
Wednesday, 9 October 2019
- Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Dawid das
- Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Bill Ross
- Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Dawid das
- [AMBER] Error during the test of amber 18 installation Sunita Patel
- [AMBER] "Could not import Amber Python modules!" error sunyeping
- Re: [AMBER] "Could not import Amber Python modules!" error Hai Nguyen
- Re: [AMBER] "Could not import Amber Python modules!" error Anthony Cruz-Balberdy
- Re: [AMBER] "Could not import Amber Python modules!" error sunyeping
- Re: [AMBER] "Could not import Amber Python modules!" error Mijiddorj B
- Re: [AMBER] "Could not import Amber Python modules!" error David A Case
- Re: [AMBER] Gaff v2.1 Force Field for n4 Junmei Wang
- Re: [AMBER] Thermodynamic integration Debarati DasGupta
- Re: [AMBER] CPPTRAJ parameter file error Rui Chen
Thursday, 10 October 2019
- [AMBER] mmpbsa MYRIAN TORRES RICO
- Re: [AMBER] Thermodynamic integration Sadaf Rani
- Re: [AMBER] Thermodynamic integration Charles Lin
- [AMBER] tleap changes order of atoms in the parm file Dawid das
- Re: [AMBER] tleap changes order of atoms in the parm file Bill Ross
- Re: [AMBER] CPPTRAJ parameter file error Daniel Roe
- Re: [AMBER] tleap changes order of atoms in the parm file Dawid das
- Re: [AMBER] Thermodynamic integration Sadaf Rani
- Re: [AMBER] tleap changes order of atoms in the parm file Bill Ross
- Re: [AMBER] H - bond tools Daniel Roe
- Re: [AMBER] tleap changes order of atoms in the parm file Dawid das
- [AMBER] Generating the parameters of a peptide sequence consisting of non-standard amino-acid RITUPARNA ROY
- [AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber Miroslav Suruzhon
- Re: [AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber Elvis Martis
- Re: [AMBER] Error during the test of amber 18 installation Daniel Roe
- Re: [AMBER] tleap changes order of atoms in the parm file David A Case
- Re: [AMBER] Calculate MMGBSA keeping water in binding site Carlos Simmerling
- Re: [AMBER] tleap changes order of atoms in the parm file Bill Ross
- Re: [AMBER] Thermodynamic integration Charles Lin
- Re: [AMBER] CPPTRAJ parameter file error Rui Chen
- Re: [AMBER] Error during the test of amber 18 installation Sunita Patel
Friday, 11 October 2019
- [AMBER] Is it necessary to set "baroscalingdir" in the membrane system? xmgign.126.com
- Re: [AMBER] "Could not import Amber Python modules!" error sunyeping
- Re: [AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber David A Case
- Re: [AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber Suruzhon M.
- Re: [AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber Hai Nguyen
- [AMBER] Query regarding DNA Saikat Pal
- [AMBER] What is the correction in amber99SB-*-ILDN? Dawid das
- Re: [AMBER] What is the correction in amber99SB-*-ILDN? Carlos Simmerling
- [AMBER] Adding OH⁻ in a water box Lucas Bandeira
- Re: [AMBER] Query regarding DNA David A Case
- [AMBER] Problems in compilation: fftw3.a ?? Margarita I. Bernal-Uruchurtu
- Re: [AMBER] Problems in compilation: fftw3.a ?? David Cerutti
- Re: [AMBER] Adding OH⁻ in a water box Matias Machado
- Re: [AMBER] Query regarding DNA Matias Machado
- Re: [AMBER] Adding OH⁻ in a water box David Case
- [AMBER] Trouble Installing Amber on Mac Faisal Malik
- Re: [AMBER] Trouble Installing Amber on Mac Bill Ross
- Re: [AMBER] Trouble Installing Amber on Mac Faisal Malik
Saturday, 12 October 2019
- Re: [AMBER] Trouble Installing Amber on Mac Bill Ross
- Re: [AMBER] Problems in compilation: fftw3.a ?? David Case
- Re: [AMBER] What is the correction in amber99SB-*-ILDN? Dawid das
- Re: [AMBER] Adding OH⁻ in a water box Lucas Bandeira
- Re: [AMBER] H - bond tools shivangi agarwal
Sunday, 13 October 2019
- [AMBER] Adding OH- to a water box David Case
- Re: [AMBER] Adding OH- to a water box Lucas Bandeira
- [AMBER] Cataline Gustaf Olsson
- Re: [AMBER] Cataline Bill Ross
- [AMBER] MMPBSA.py resulted in DELTA TOTAL= 1414 kcal/mole Seketoulie Keretsu
- Re: [AMBER] Cataline Gustaf Olsson
Monday, 14 October 2019
- Re: [AMBER] Cataline Bill Ross
- [AMBER] Problem in extracting pdb file from mdcrd file Airy Sanjeev
- Re: [AMBER] Problem in extracting pdb file from mdcrd file Elvis Martis
- Re: [AMBER] Thermodynamic integration Sadaf Rani
- Re: [AMBER] Trouble Installing Amber on Mac David A Case
- Re: [AMBER] What is the correction in amber99SB-*-ILDN? David A Case
- Re: [AMBER] Cataline David A Case
- [AMBER] symmetry corrected rms fitting Venkata Krishnan Ramaswamy
- Re: [AMBER] Thermodynamic integration Charles Lin
- Re: [AMBER] Thermodynamic integration Sadaf Rani
- Re: [AMBER] Thermodynamic integration Charles Lin
- [AMBER] More ... problems in compilation: fftw3a | Case1 - Using GNU Margarita I. Bernal-Uruchurtu
- [AMBER] More ... problems in compilation: fftw3a | Case2 - Using intel Margarita I. Bernal-Uruchurtu
- Re: [AMBER] Thermodynamic integration Sadaf Rani
- Re: [AMBER] Thermodynamic integration Charles Lin
- Re: [AMBER] Cataline Gustaf Olsson
- [AMBER] make install errors Alen Ahmetovic
- Re: [AMBER] make install errors Hai Nguyen
Tuesday, 15 October 2019
- [AMBER] (long) OSX/catalina Ambertools19 building success with brew Tru Huynh
- [AMBER] Paste command for xleap Gert Kruger
- Re: [AMBER] More ... problems in compilation: fftw3a | Case2 - Using intel David A Case
- Re: [AMBER] Paste command for xleap Bill Ross
- Re: [AMBER] (long) OSX/catalina Ambertools19 building success with brew Hai Nguyen
- [AMBER] PTRAJ (clustering)-Segmentation fault Rui Chen
- Re: [AMBER] PTRAJ (clustering)-Segmentation fault Thomas Cheatham
- [AMBER] minimize protein with a small molecule tethered at a fixed location Debarati DasGupta
Wednesday, 16 October 2019
- [AMBER] Problem in running MMPBSA Airy Sanjeev
- Re: [AMBER] Problem in running MMPBSA Bill Ross
- Re: [AMBER] Problem in running MMPBSA Airy Sanjeev
- Re: [AMBER] minimize protein with a small molecule tethered at a fixed location David A Case
- Re: [AMBER] Problem in running MMPBSA David A Case
- [AMBER] ff19SB update Åsmund Røhr Kjendseth
- Re: [AMBER] minimize protein with a small molecule tethered at a fixed location Debarati DasGupta
- Re: [AMBER] minimize protein with a small molecule tethered at a fixed location Bill Ross
- Re: [AMBER] minimize protein with a small molecule tethered at a fixed location Debarati DasGupta
- Re: [AMBER] minimize protein with a small molecule tethered at a fixed location Bill Ross
- [AMBER] minimization using restrain weight Debarati DasGupta
- Re: [AMBER] ff19SB update Chuan Tian
- Re: [AMBER] Problem in extracting pdb file from mdcrd file Daniel Roe
- Re: [AMBER] ff19SB update David A Case
- Re: [AMBER] minimization using restrain weight David A Case
- Re: [AMBER] Cataline Gustaf Olsson
- Re: [AMBER] Cataline Hai Nguyen
- [AMBER] Check for updates failed Gustaf Olsson
- Re: [AMBER] Cataline Gustaf Olsson
- Re: [AMBER] (long) OSX/catalina Ambertools19 building success with brew Gustaf Olsson
- Re: [AMBER] make install errors Alen Ahmetovic
- Re: [AMBER] make install errors Alen Ahmetovic
- [AMBER] Incorrect instructions in tutorial B1 Cavender, Chapin
- Re: [AMBER] Cataline David Case
- Re: [AMBER] Check for updates failed David Case
- [AMBER] more efficient TI rerun over existing trajectory 杨明俊
- Re: [AMBER] Check for updates failed Gustaf Olsson
Thursday, 17 October 2019
- Re: [AMBER] more efficient TI rerun over existing trajectory Carlos Simmerling
- Re: [AMBER] Thermodynamic integration Sadaf Rani
- Re: [AMBER] Check for updates failed David A Case
- Re: [AMBER] Adding OH- to a water box Matias Machado
- Re: [AMBER] Check for updates failed Gustaf Olsson
- Re: [AMBER] more efficient TI rerun over existing trajectory 杨明俊
- [AMBER] Convergence value for GMAX Anuja Ware
- Re: [AMBER] Thermodynamic integration Charles Lin
- Re: [AMBER] more efficient TI rerun over existing trajectory Charles Lin
- Re: [AMBER] (long) OSX/catalina Ambertools19 building success with brew Tru Huynh
- Re: [AMBER] Convergence value for GMAX David A Case
- Re: [AMBER] more efficient TI rerun over existing trajectory Carlos Simmerling
- [AMBER] Some short Catalina experience David A Case
- Re: [AMBER] Some short Catalina experience Scott Brozell
- Re: [AMBER] Some short Catalina experience Hai Nguyen
- Re: [AMBER] (long) OSX/catalina Ambertools19 building success with brew Gustaf Olsson
- Re: [AMBER] Some short Catalina experience David Case
- Re: [AMBER] Paste command for xleap Gert Kruger
- Re: [AMBER] ff19SB update Åsmund Røhr Kjendseth
- Re: [AMBER] Some short Catalina experience Gustaf Olsson
Friday, 18 October 2019
- Re: [AMBER] ff19SB update David A Case
- Re: [AMBER] (long) OSX/catalina Ambertools19 building success with brew David A Case
- Re: [AMBER] Adding OH- to a water box Lucas Bandeira
Saturday, 19 October 2019
- [AMBER] Problem with Installation of AMBER 조준범
- Re: [AMBER] Problem with Installation of AMBER David Case
- [AMBER] clustering using distance matrix file only Tim Davis
Sunday, 20 October 2019
- [AMBER] TI tutorial for preparation of ligand Debarati DasGupta
Monday, 21 October 2019
- [AMBER] Post-doc position in molecular simulations and structural bioinformatics Jan Brezovsky
- [AMBER] Problem with installation of AMBER 조준범
- Re: [AMBER] Calculate MMGBSA keeping water in binding site Rosellen, Martin
- Re: [AMBER] Problem with installation of AMBER David A Case
- Re: [AMBER] Problem with installation of AMBER Bill Ross
- Re: [AMBER] Calculate MMGBSA keeping water in binding site Carlos Simmerling
- [AMBER] NAN error Hira Jabeen
- Re: [AMBER] NAN error Bill Ross
- Re: [AMBER] NAN error Hira Jabeen
- Re: [AMBER] NAN error Bill Ross
- [AMBER] sander/lmod parallel execution Charles-Alexandre Mattelaer
- Re: [AMBER] NAN error Hira Jabeen
- Re: [AMBER] NAN error Bill Ross
- Re: [AMBER] NAN error Hira Jabeen
- Re: [AMBER] sander/lmod parallel execution Scott Brozell
- [AMBER] Error adding OH⁻ ions in a simulation box Lucas Bandeira
- Re: [AMBER] NAN error Bill Ross
- Re: [AMBER] Error adding OH⁻ ions in a simulation box Matias Machado
- Re: [AMBER] clustering using distance matrix file only Matias Machado
- [AMBER] How to obtain the pressure in NVT ensemble jinfeng liu
Tuesday, 22 October 2019
- [AMBER] Regarding GIST analysis MR. RABINDRANATH PAUL
- Re: [AMBER] sander/lmod parallel execution Charles-Alexandre Mattelaer
- Re: [AMBER] How to obtain the pressure in NVT ensemble Bill Ross
- [AMBER] error while running pmemd.cuda after reinstallation of amber 16 Schröder, David Christopher
- [AMBER] iwrap Andrea H. Kasun
- Re: [AMBER] iwrap Carlos Simmerling
- Re: [AMBER] iwrap Andrea H. Kasun
- Re: [AMBER] How to obtain the pressure in NVT ensemble David A Case
- Re: [AMBER] error while running pmemd.cuda after reinstallation of amber 16 David A Case
- Re: [AMBER] iwrap David A Case
- Re: [AMBER] Error adding OH⁻ ions in a simulation box David A Case
- Re: [AMBER] clustering using distance matrix file only Daniel Roe
- Re: [AMBER] Regarding GIST analysis Steven Ramsey
- [AMBER] thermodynamic integration parameters in input file Debarati DasGupta
- [AMBER] free energy calculation and leap error Sadaf Rani
- [AMBER] Prmtop file creation for thermodynamic integration Debarati DasGupta
- Re: [AMBER] Prmtop file creation for thermodynamic integration Sadaf Rani
- Re: [AMBER] thermodynamic integration parameters in input file David A Case
- Re: [AMBER] free energy calculation and leap error David A Case
- [AMBER] compiling with -noX11 option Swantje Mohr
- [AMBER] constraining ligands to some distance from a target molecule on pmemd.cuda Homeo Morphism
- Re: [AMBER] Prmtop file creation for thermodynamic integration Debarati DasGupta
- Re: [AMBER] constraining ligands to some distance from a target molecule on pmemd.cuda Carlos Simmerling
- Re: [AMBER] clustering using distance matrix file only Tim Davis
- Re: [AMBER] Error adding OH⁻ ions in a simulation box Lucas Bandeira
Wednesday, 23 October 2019
- [AMBER] Extract the last 90ns trajectory Airy Sanjeev
- Re: [AMBER] Extract the last 90ns trajectory Carlos Simmerling
- Re: [AMBER] NAN error David A Case
- [AMBER] Thermodynamic integration more questions! Debarati DasGupta
- Re: [AMBER] error while running pmemd.cuda after reinstallation of amber 16 Schröder, David Christopher
- Re: [AMBER] Extract the last 90ns trajectory Daniel Roe
- [AMBER] Combining FF14Sb and ForceField_PTM (FF03)... What could possibly go wrong? Gustavo Seabra
- Re: [AMBER] Combining FF14Sb and ForceField_PTM (FF03)... What could possibly go wrong? Carlos Simmerling
- Re: [AMBER] Combining FF14Sb and ForceField_PTM (FF03)... What could possibly go wrong? Gustavo Seabra
- [AMBER] Problem in Leap PDB Reading Robert Molt
- Re: [AMBER] Problem in Leap PDB Reading Bill Ross
Thursday, 24 October 2019
- Re: [AMBER] NAN error Hira Jabeen
- [AMBER] Lennard-Jones parameters in amber and gromacs Hadi Rahmaninejad
- Re: [AMBER] Lennard-Jones parameters in amber and gromacs Carlos Simmerling
- [AMBER] TI on gpus Debarati DasGupta
- [AMBER] PARMFIT and CHARMM David Ricardo Figueroa Blanco
- Re: [AMBER] TI on gpus Ross Walker
- [AMBER] REMD Error Rinsha Chk
- Re: [AMBER] REMD Error Elvis Martis
- Re: [AMBER] REMD Error Rinsha Chk
Friday, 25 October 2019
- Re: [AMBER] TI on gpus Debarati DasGupta
- Re: [AMBER] TI on gpus David A Case
- Re: [AMBER] Problem in Leap PDB Reading David A Case
- [AMBER] strip problem in cpptraj Sadaf Rani
- Re: [AMBER] REMD Error Carlos Simmerling
- Re: [AMBER] TI on gpus Debarati DasGupta
- [AMBER] atomicfluct/rmsf time Shayna Hilburg
- [AMBER] How to check the convergence of NEB calculation? Yang JIANG
- Re: [AMBER] REMD Error Rinsha Chk
Saturday, 26 October 2019
- Re: [AMBER] REMD Error Carlos Simmerling
- Re: [AMBER] REMD Error Rinsha Chk
- Re: [AMBER] REMD Error Carlos Simmerling
- Re: [AMBER] atomicfluct/rmsf time David Case
- [AMBER] Assigning am1-bcc charges to a whole library of ligands Liao
- Re: [AMBER] Assigning am1-bcc charges to a whole library of ligands Elvis Martis
- [AMBER] MD simulation system Sudad Dayl
- Re: [AMBER] atomicfluct/rmsf time Shayna Hilburg
Sunday, 27 October 2019
- Re: [AMBER] Assigning am1-bcc charges to a whole library of ligands David Case
- Re: [AMBER] REMD Error Rinsha Chk
- Re: [AMBER] REMD Error Rinsha Chk
- Re: [AMBER] Assigning am1-bcc charges to a whole library of ligands Liao
Monday, 28 October 2019
- [AMBER] About the unit of the pressure in the md.out file? 邸春艳
- Re: [AMBER] more efficient TI rerun over existing trajectory 杨明俊
- Re: [AMBER] REMD Error Carlos Simmerling
- [AMBER] compiling Amber with gcc 9.2 and intel mpi 2019 Vlad Cojocaru
- Re: [AMBER] compiling Amber with gcc 9.2 and intel mpi 2019 David A Case
- Re: [AMBER] REMD Error Rinsha Chk
- [AMBER] Problem in the x-axis of SASA analysis Airy Sanjeev
Tuesday, 29 October 2019
- Re: [AMBER] Problem in the x-axis of SASA analysis David A Case
- Re: [AMBER] more efficient TI rerun over existing trajectory David A Case
- Re: [AMBER] Some short Catalina experience David A Case
- Re: [AMBER] Some short Catalina experience Gustaf Olsson
- [AMBER] if the ligand doesn't bind when it should, what does it say about quality of my simulations and what can I do? Homeo Morphism
- [AMBER] Multiple simulations on one GPU Aiden Aceves
- [AMBER] Thermodynamic integration questions questions and questions Debarati DasGupta
- Re: [AMBER] Multiple simulations on one GPU Piotr Fajer
- Re: [AMBER] if the ligand doesn't bind when it should, what does it say about quality of my simulations and what can I do? Carlos Simmerling
- Re: [AMBER] REMD Error Carlos Simmerling
- Re: [AMBER] Multiple simulations on one GPU David Cerutti
- Re: [AMBER] if the ligand doesn't bind when it should, what does it say about quality of my simulations and what can I do? Wesley Michael Botello-Smith
- Re: [AMBER] make install errors Alen Ahmetovic
- Re: [AMBER] make install errors David Case
- Re: [AMBER] make install errors Hai Nguyen
- Re: [AMBER] REMD Error Rinsha Chk
- [AMBER] umbrella sampling question 钟海洋
Wednesday, 30 October 2019
- [AMBER] Error in Step two of MCPB Sodiq Waheed
- Re: [AMBER] Error in Step two of MCPB Akinpelu Olayinka
- Re: [AMBER] Problem in the x-axis of SASA analysis Daniel Roe
- Re: [AMBER] compiling Amber with gcc 9.2 and intel mpi 2019 Daniel Roe
- Re: [AMBER] umbrella sampling question diego.soler.uam.es
- Re: [AMBER] atomicfluct/rmsf time Daniel Roe
- Re: [AMBER] Multiple simulations on one GPU Aiden Aceves
- Re: [AMBER] umbrella sampling question 钟海洋
Thursday, 31 October 2019
- [AMBER] tip4pew water module in different version performs different 钟海洋
- [AMBER] Any ideas what may be wrong Debarati DasGupta

Last message date: Thu Oct 31 2019 - 06:00:02 PDT
Archived on: Mon Nov 25 2024 - 05:55:46 PST

Amber Archive Oct 2019 by date