Amber Archive Oct 2020: by date

Wednesday, 30 September 2020
- Re: [AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am
- Re: [AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am
Thursday, 1 October 2020
- Re: [AMBER] Modification of dihedral torsion potential David A Case
- Re: [AMBER] Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT Matias Machado
- [AMBER] pmemd aishen
- Re: [AMBER] pmemd Elvis Martis
- [AMBER] Error: Failed to generate parameters Jatin Kashyap
- Re: [AMBER] Problem in AMBER18 Installation Mariangela Dametto
- Re: [AMBER] Query regarding Dialanine peptide 2d ABMD tutorial in the NFE category SHAUNAK BADANI
- Re: [AMBER] pmemd David A Case
- Re: [AMBER] Error: Failed to generate parameters David A Case
- [AMBER] pmemd aishen
- [AMBER] MMPBSA.py TypeError: a bytes-like object is required, not 'str' سید حامد سادات حیاتشاهی
- Re: [AMBER] Error: Failed to generate parameters Jatin Kashyap
- Re: [AMBER] [External] Re: Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT Nick Palmer
- [AMBER] partial charges for modified nucleotide Farkhad Maksudov
- [AMBER] Additional restraints in Umbrella sampling? Qing Lv
- Re: [AMBER] MMPBSA.py TypeError: a bytes-like object is required, not 'str' Ray Luo
Friday, 2 October 2020
- Re: [AMBER] pmemd Dr. Anselm Horn
- [AMBER] Compiling CPPTRAJ from GitHub Gustaf Olsson
- Re: [AMBER] Compiling CPPTRAJ from GitHub Gustaf Olsson
- [AMBER] image protein complex iwrap=1 Ari Zeida
- [AMBER] how to use one prmtop for two trajectories with just one ion difference Vaibhav Dixit
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Carlos Simmerling
- Re: [AMBER] Query regarding Dialanine peptide 2d ABMD tutorial in the NFE category David A Case
- Re: [AMBER] Error: Failed to generate parameters David A Case
- Re: [AMBER] partial charges for modified nucleotide David A Case
- Re: [AMBER] Compiling CPPTRAJ from GitHub David A Case
- Re: [AMBER] Compiling CPPTRAJ from GitHub Daniel Roe
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Vaibhav Dixit
- Re: [AMBER] image protein complex iwrap=1 David A Case
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Carlos Simmerling
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Vaibhav Dixit
- Re: [AMBER] partial charges for modified nucleotide Kenneth Huang
Saturday, 3 October 2020
- [AMBER] about translation aishen
- [AMBER] MMGBSA/MMPBSA Help Abdul-Rashid III Sampaco
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Carlos Simmerling
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Vaibhav Dixit
- [AMBER] RMSD of ligand in pocket Debarati DasGupta
- Re: [AMBER] [External] Re: Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT Matias Machado
- [AMBER] Query regarding ion constraint in MD simulations Nisha Amarnath Jonniya
- [AMBER] cpptraj unable to write pdb files using Vaibhav Dixit
Sunday, 4 October 2020
- Re: [AMBER] cpptraj unable to write pdb files using Daniel Roe
- Re: [AMBER] RMSD of ligand in pocket Daniel Roe
- Re: [AMBER] image protein complex iwrap=1 Daniel Roe
- [AMBER] usage of nmr (between COMs) restraints with pmem.cuda Dmitry Karlov
- Re: [AMBER] cpptraj unable to write pdb files using Vaibhav Dixit
- Re: [AMBER] cpptraj unable to write pdb files using Elvis Martis
- Re: [AMBER] RMSD of ligand in pocket Debarati DasGupta
- Re: [AMBER] RMSD of ligand in pocket David A Case
- [AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am
Monday, 5 October 2020
- Re: [AMBER] Compiling CPPTRAJ from GitHub Gustaf Olsson
- Re: [AMBER] RMSD of ligand in pocket Debarati DasGupta
- Re: [AMBER] RMSD of ligand in pocket Juraj Dobias
- Re: [AMBER] Compiling CPPTRAJ from GitHub David A Case
- Re: [AMBER] Compiling CPPTRAJ from GitHub Daniel Roe
- Re: [AMBER] controversy in PBSA and GBSA results Ray Luo
- [AMBER] Different atomic partial charges on OD1/OD2 Margareta Hellmann
- [AMBER] Hitting the supercomputer wall limit before completion of minimization step Jatin Kashyap
- [AMBER] REST2 in Amber Qinghua Liao
- [AMBER] Question about force field for proteins Asaf Farhi
- Re: [AMBER] Question about force field for proteins Carlos Simmerling
- Re: [AMBER] Hitting the supercomputer wall limit before completion of minimization step Carlos Simmerling
- Re: [AMBER] Question about force field for proteins Asaf Farhi
- [AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am
- Re: [AMBER] Hitting the supercomputer wall limit before completion of minimization step Jatin Kashyap
- Re: [AMBER] MMPBSA.py TypeError: a bytes-like object is required, not 'str' Hamed S. Hayatshahi
- Re: [AMBER] Hitting the supercomputer wall limit before completion of minimization step Carlos Simmerling
- [AMBER] How does one build MMPBSA.py.MPI on a Centos 7 system? Hamed S. Hayatshahi
- Re: [AMBER] How does one build MMPBSA.py.MPI on a Centos 7 system? David A Case
- [AMBER] Which OS/Amber combinations are supported? Kevin Keane
- Re: [AMBER] cpptraj unable to write pdb files using Vaibhav Dixit
- Re: [AMBER] cpptraj unable to write pdb files using Elvis Martis
- Re: [AMBER] cpptraj unable to write pdb files using Vaibhav Dixit
- Re: [AMBER] Which OS/Amber combinations are supported? Gerald Monard
Tuesday, 6 October 2020
- [AMBER] Imaging issues with cpptraj Suchetana Gupta
- Re: [AMBER] A100 and RTX3090 Benchmarks Filip Fratev
- Re: [AMBER] Compiling CPPTRAJ from GitHub Gustaf Olsson
- Re: [AMBER] Compiling CPPTRAJ from GitHub Gustaf Olsson
- Re: [AMBER] Compiling CPPTRAJ from GitHub Gustaf Olsson
- Re: [AMBER] A100 and RTX3090 Benchmarks David A Case
- Re: [AMBER] A100 and RTX3090 Benchmarks Ross Walker
- Re: [AMBER] A100 and RTX3090 Benchmarks Ross Walker
- [AMBER] Amber performance Jonathan Gabriel Canan Gomez
- Re: [AMBER] Amber performance Bill Ross
- Re: [AMBER] Amber performance Ross Walker
- [AMBER] Fwd: Imaging issues with cpptraj Suchetana Gupta
- Re: [AMBER] Fwd: Imaging issues with cpptraj Suchetana Gupta
Wednesday, 7 October 2020
- Re: [AMBER] Fwd: Imaging issues with cpptraj Suchetana Gupta
- Re: [AMBER] cpptraj unable to write pdb files using Vaibhav Dixit
- Re: [AMBER] cpptraj unable to write pdb files using Elvis Martis
- [AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am
- Re: [AMBER] cpptraj unable to write pdb files using Vaibhav Dixit
- [AMBER] Problems with using pdb4amber (and possibly other programs) on Ubuntu 20.04 bgostyns.cbmm.lodz.pl
- [AMBER] Cannot run NPT mohamed marzouk
- Re: [AMBER] Compiling CPPTRAJ from GitHub Daniel Roe
- Re: [AMBER] cpptraj unable to write pdb files using Daniel Roe
- Re: [AMBER] cpptraj unable to write pdb files using Daniel Roe
- Re: [AMBER] cpptraj unable to write pdb files using Elvis Martis
- Re: [AMBER] Fwd: Imaging issues with cpptraj Daniel Roe
- Re: [AMBER] RMSD of ligand in pocket Daniel Roe
- Re: [AMBER] cpptraj unable to write pdb files using David A Case
- Re: [AMBER] Problems with using pdb4amber (and possibly other programs) on Ubuntu 20.04 David A Case
- Re: [AMBER] Cannot run NPT David A Case
- Re: [AMBER] cpptraj unable to write pdb files using Daniel Roe
- Re: [AMBER] controversy in PBSA and GBSA results Ray Luo
- Re: [AMBER] controversy in PBSA and GBSA results Ray Luo
- [AMBER] QMMM SCC-DFTB: Convergence could not be achieved Sarah Jane
- Re: [AMBER] controversy in PBSA and GBSA results Ray Luo
- [AMBER] Verbose - Output File Information Not Changing An Ta
- Re: [AMBER] Problems with using pdb4amber (and possibly other programs) on Ubuntu 20.04 Hai Nguyen
- Re: [AMBER] RMSD of ligand in pocket Debarati DasGupta
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Thomas Cheatham
- Re: [AMBER] Verbose - Output File Information Not Changing An Ta
- Re: [AMBER] Verbose - Output File Information Not Changing An Ta
- Re: [AMBER] Cannot run NPT mohamed marzouk
- Re: [AMBER] cpptraj unable to write pdb files using Vaibhav Dixit
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Vaibhav Dixit
- [AMBER] Amber20 compilation issue (related to boost?) Suman Chakrabarty
Thursday, 8 October 2020
- Re: [AMBER] Problems with using pdb4amber (and possibly other programs) on Ubuntu 20.04 bgostyns.cbmm.lodz.pl
- Re: [AMBER] Cannot run NPT Juraj Dobias
- Re: [AMBER] Cannot run NPT David A Case
- Re: [AMBER] Compiling CPPTRAJ from GitHub Gustaf Olsson
- [AMBER] not writing restart file Erik Zuiderweg
- Re: [AMBER] not writing restart file Qinghua Liao
- [AMBER] ERROR: The file contained 14 atoms not in residue templates Jatin Kashyap
- Re: [AMBER] ERROR: The file contained 14 atoms not in residue templates Carlos Simmerling
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Thomas Cheatham
- Re: [AMBER] Amber20 compilation issue (related to boost?) George M. Giambasu
Friday, 9 October 2020
- Re: [AMBER] Amber20 compilation issue (related to boost?) Suman Chakrabarty
- Re: [AMBER] not writing restart file Erik Zuiderweg
- [AMBER] Permute dihedrals David Poole
- Re: [AMBER] Verbose - Output File Information Not Changing David A Case
- Re: [AMBER] Permute dihedrals Daniel Roe
- [AMBER] NVIDIA GeForce RTX 3080 GPUs Mike Mazanetz
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs David Cerutti
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs Adrian Roitberg
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs Mike Mazanetz
- [AMBER] CPPTRAJ: Cluster structures keeping only one water, by position? Gustavo Seabra
- Re: [AMBER] CPPTRAJ: Cluster structures keeping only one water, by position? Niel Henriksen
- Re: [AMBER] CPPTRAJ: Cluster structures keeping only one water, by position? Gustavo Seabra
- Re: [AMBER] AmberMdPrep github cpptraj not sourced Vaibhav Dixit
Saturday, 10 October 2020
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs Ross Walker
- Re: [AMBER] Question about force field for proteins Asaf Farhi
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs (Ross Walker) German P. Barletta
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs Mike Mazanetz
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs (Ross Walker) Ross Walker
- [AMBER] Conda installation of AmberTools mukesh raval
Sunday, 11 October 2020
- Re: [AMBER] Question about force field for proteins Carlos Simmerling
- [AMBER] NVIDIA GeForce RTX 3080 GPUs German P. Barletta
Monday, 12 October 2020
- Re: [AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule BLUNTZER Marie
- [AMBER] Fw: partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule BLUNTZER Marie
- Re: [AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule David A Case
- Re: [AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule BLUNTZER Marie
- Re: [AMBER] Conda installation of AmberTools Hai Nguyen
- Re: [AMBER] Cannot run NPT mohamed marzouk
- [AMBER] RMSD, Rg density map mohamed marzouk
- Re: [AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule James Kress
Tuesday, 13 October 2020
- [AMBER] MMGBSA Ligand Mask issues Suchetana Gupta
- [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros Állan Ferrari
- Re: [AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule BLUNTZER Marie
- Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros David A Case
- [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? Liao
- [AMBER] Using parmchk2 with GLYCAM_06j.dat Delwakkada Liyanage, Senal Dinuka
Wednesday, 14 October 2020
- [AMBER] Fwd: MMGBSA Ligand Mask issues Suchetana Gupta
- [AMBER] Installation of AMBER20 on CentOS 7 Pandey Anwesh
- Re: [AMBER] RMSD, Rg density map Daniel Roe
- Re: [AMBER] Installation of AMBER20 on CentOS 7 David A Case
- Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros Állan Ferrari
- [AMBER] assess which structures are similar between two MD-trajectories Vaibhav Dixit
Thursday, 15 October 2020
- Re: [AMBER] PMF calculation somdev pahari
- Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros David A Case
- Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? David A Case
- Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros Állan Ferrari
- Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros David A Case
- [AMBER] mdout issue Alejandro Cagnoni
- Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros Állan Ferrari
- Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? Liao
- [AMBER] Query about using MMPBSA.py to calculate the binding free energy for a ligand bound enzyme SATYAJIT KHATUA
- Re: [AMBER] Query about using MMPBSA.py to calculate the binding free energy for a ligand bound enzyme David A Case
- Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? David A Case
- [AMBER] cpptraj's hbond shows hbonds with carbon hydrogens German P. Barletta
- [AMBER] Adding catalytic Magnesium ion Jisha B
- Re: [AMBER] cpptraj's hbond shows hbonds with carbon hydrogens Daniel Roe
- [AMBER] KeyError: 'H262' Wu Xu
- [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Wu Xu
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Bill Ross
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Elvis Martis
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Vaibhav Dixit
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd aishen
Friday, 16 October 2020
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Mariano Curti
- [AMBER] Loading R.E.D server parameters into xleap Sruthi Sudhakar
Thursday, 15 October 2020
- [AMBER] Fwd: AMBER Digest, Vol 3153, Issue 1 SATYAJIT KHATUA
Friday, 16 October 2020
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd viktor
- Re: [AMBER] Fwd: AMBER Digest, Vol 3153, Issue 1 David A Case
- Re: [AMBER] Loading R.E.D server parameters into xleap Emmett Leddin
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Wu Xu
- Re: [AMBER] Loading R.E.D server parameters into xleap Sruthi Sudhakar
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd aishen.free.fr
- [AMBER] mm-pbsa calculation Serena Vittorio
- [AMBER] rms(d) or (f) per residue Seibold, Steve Allan
- Re: [AMBER] RMSD, Rg density map mohamed marzouk
- Re: [AMBER] rms(d) or (f) per residue Daniel Roe
- Re: [AMBER] Loading R.E.D server parameters into xleap Emmett Leddin
- Re: [AMBER] rms(d) or (f) per residue Seibold, Steve Allan
- Re: [AMBER] rms(d) or (f) per residue Daniel Roe
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Grant Keller
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Daniel Roe
- [AMBER] NAMD trajectory analysis with cpptraj sangita kachhap
- [AMBER] cpptraj's hbond shows hbonds with carbon hydrogens German P. Barletta
- Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? Liao
- Re: [AMBER] Question about force field for proteins Asaf Farhi
- Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? Elvis Martis
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Wu Xu
- [AMBER] Creating a coordinate bond in Leap Jenny 148
- Re: [AMBER] Creating a coordinate bond in Leap Elvis Martis
- Re: [AMBER] Creating a coordinate bond in Leap Bill Ross
Saturday, 17 October 2020
- Re: [AMBER] NAMD trajectory analysis with cpptraj Daniel Roe
- Re: [AMBER] NAMD trajectory analysis with cpptraj sangita kachhap
- Re: [AMBER] Adding catalytic Magnesium ion Jisha B
- Re: [AMBER] rms(d) or (f) per residue Seibold, Steve Allan
- Re: [AMBER] Creating a coordinate bond in Leap Bill Ross
- [AMBER] process_mdout.perl for pmemd Jorge Iulek
- Re: [AMBER] Adding catalytic Magnesium ion Abhilash J
- Re: [AMBER] process_mdout.perl for pmemd Rodrigo Galindo-Murillo
Sunday, 18 October 2020
- Re: [AMBER] mm-pbsa calculation Suchetana Gupta
- Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros David A Case
- [AMBER] Amber20 compiling warning Tom Wang
- Re: [AMBER] RMSD of ligand in pocket Debarati DasGupta
- Re: [AMBER] process_mdout.perl for pmemd Jorge Iulek
- [AMBER] Bond: Maximum coordination exceeded Sarah Jane
- [AMBER] Adding missing residues in a pdb file using tleap SUNITA MUDULI
- [AMBER] RMSD (non mass-weighted) as collective variable in Amber-18 Madhur Aggarwal
- [AMBER] MD error Kehinde Idowu
Monday, 19 October 2020
- Re: [AMBER] Adding catalytic Magnesium ion Juraj Dobias
- [AMBER] Metalloprotein-ligand complex modelling for MMPBSA.py SATYAJIT KHATUA
- [AMBER] mm-pbsa calculation: SA Bomb in circle(): Stored surface arcs over limit Serena Vittorio
- [AMBER] R: mm-pbsa calculation Serena Vittorio
- Re: [AMBER] Amber20 compiling warning David A Case
- Re: [AMBER] Bond: Maximum coordination exceeded David A Case
- Re: [AMBER] Adding missing residues in a pdb file using tleap David A Case
- Re: [AMBER] MD error David A Case
- Re: [AMBER] mm-pbsa calculation: SA Bomb in circle(): Stored surface arcs over limit David A Case
- [AMBER] Steered MD at constant force Vishal Singh
- [AMBER] NOE analysis with cpptraj Pavlína Pokorná
- Re: [AMBER] MD error Kehinde Idowu
- [AMBER] Changing lj_radius without changing lj_14_radius Batuhan Kav
- [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Vlad Cojocaru
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Scott Brozell
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Scott Brozell
- [AMBER] Bacteria cell membrane PDB Loo Kang
Tuesday, 20 October 2020
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Vlad Cojocaru
- [AMBER] mdout error Alejandro Cagnoni
- [AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am
- Re: [AMBER] controversy in PBSA and GBSA results Carlos Simmerling
- [AMBER] calculating differences in binding energy for enantiomers to amino acid based surfactants Billiot, Eugene
- [AMBER] Adding Ions Gustaf Olsson
- [AMBER] TI not compatible with GB on GPU Vaibhav Dixit
- Re: [AMBER] Adding Ions Bill Ross
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Vlad Cojocaru
- [AMBER] AMBER16 problem Seibold, Steve Allan
- Re: [AMBER] controversy in PBSA and GBSA results Ray Luo
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler David A Case
- Re: [AMBER] AMBER16 problem David A Case
- Re: [AMBER] RMSD, Rg density map mohamed marzouk
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Scott Brozell
- Re: [AMBER] Error building Amber Kazuo Ohta
- Re: [AMBER] RMSD, Rg density map mohamed marzouk
Wednesday, 21 October 2020
- Re: [AMBER] Adding Ions Gustaf Olsson
- [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson
- [AMBER] MMPBS decomposition error MYRIAN TORRES RICO
- Re: [AMBER] AmberMdPrep github cpptraj not sourced Daniel Roe
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Vlad Cojocaru
- Re: [AMBER] AmberMdPrep github cpptraj not sourced Vaibhav Dixit
- Re: [AMBER] TI not compatible with GB on GPU Debarati DasGupta
- Re: [AMBER] Adding Ions Gustaf Olsson
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson
- Re: [AMBER] Adding Ions David A Case
- Re: [AMBER] TI not compatible with GB on GPU Vaibhav Dixit
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling
- Re: [AMBER] TI not compatible with GB on GPU Debarati DasGupta
- Re: [AMBER] TI not compatible with GB on GPU Debarati DasGupta
- Re: [AMBER] AMBER16 problem Seibold, Steve Allan
- Re: [AMBER] Adding Ions Matias Machado
- [AMBER] installing Amber18 and AmberTools20 Seibold, Steve Allan
- Re: [AMBER] Changing lj_radius without changing lj_14_radius Matias Machado
- [AMBER] drms comparison in sander during minimization? Kenneth Huang
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Scott Brozell
Thursday, 22 October 2020
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson
- Re: [AMBER] Adding Ions Gustaf Olsson
- Re: [AMBER] Changing lj_radius without changing lj_14_radius Batuhan Kav
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson
Wednesday, 21 October 2020
- Re: [AMBER] TI not compatible with GB on GPU Vaibhav Dixit
Thursday, 22 October 2020
- Re: [AMBER] TI not compatible with GB on GPU David A Case
- Re: [AMBER] NVIDIA GeForce RTX 3090 GPUs Mike Mazanetz
- Re: [AMBER] Adding Ions David A Case
- Re: [AMBER] Adding Ions Gustaf Olsson
- Re: [AMBER] installing Amber18 and AmberTools20 David A Case
- Re: [AMBER] drms comparison in sander during minimization? David A Case
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP David A Case
- [AMBER] correct md-input & prmtop for TI calculations Vaibhav Dixit
- Re: [AMBER] TI not compatible with GB on GPU Vaibhav Dixit
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling
- [AMBER] Is the amber website down? 9am EST Debarati DasGupta
- [AMBER] server issues 403 on ambermd.org Mike Mazanetz
- Re: [AMBER] Changing lj_radius without changing lj_14_radius Matias Machado
- [AMBER] Cannot access amber website Lang,Lijun
- Re: [AMBER] Cannot access amber website Elvis Martis
- [AMBER] error 403 Ayesha Fatima
- [AMBER] Fwd: MMPBSA calculations with 1 explicit water molecule divyabharathi korlepara
- [AMBER] Trouble installing pbsa cuda code Wesley Michael Botello-Smith
- Re: [AMBER] Is the amber website down? 9am EST David A Case
- Re: [AMBER] Trouble installing pbsa cuda code David A Case
- Re: [AMBER] MCPB with OPC water? Pengfei Li
- Re: [AMBER] Trouble installing pbsa cuda code Tru Huynh
- Re: [AMBER] ddikick.x error during Fe3+ ion parameter derivation using Gamess Pengfei Li
- Re: [AMBER] Prmtop for protein + 2 identical ligands has wrong dihedral parameters for the second ligand. LEaP bug? Pengfei Li
- Re: [AMBER] Tri-coordination environment in zinc Pengfei Li
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Pengfei Li
- [AMBER] GaMD Neha Gandhi
- Re: [AMBER] KeyError: 'H262' Pengfei Li
- Re: [AMBER] MCPB with OPC water? Gustavo Seabra
- Re: [AMBER] KeyError: 'H262' Wu Xu
- Re: [AMBER] drms comparison in sander during minimization? Kenneth Huang
- Re: [AMBER] server issues 403 on ambermd.org Gustaf Olsson
Friday, 23 October 2020
- [AMBER] doubt charges MYRIAN TORRES RICO
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Vlad Cojocaru
- Re: [AMBER] doubt charges Dr. Anselm Horn
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Daniel Roe
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Daniel Roe
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling
- Re: [AMBER] doubt charges MYRIAN TORRES RICO
- Re: [AMBER] drms comparison in sander during minimization? David A Case
- Re: [AMBER] doubt charges David A Case
- Re: [AMBER] doubt charges MYRIAN TORRES RICO
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Daniel Roe
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling
- Re: [AMBER] doubt charges Dr. Anselm Horn
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Daniel Roe
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling
- [AMBER] Is there a way to analyze contact maps of mixtures of more than 2 components? Naxhije Berisha
- Re: [AMBER] doubt charges gagandeep singh
- Re: [AMBER] KeyError: 'H262' Wu Xu
- [AMBER] amber14 and amber16 are not working in new installation Marcelo Andrade Chagas
- Re: [AMBER] Trouble installing pbsa cuda code Wesley Michael Botello-Smith
Saturday, 24 October 2020
- Re: [AMBER] Trouble installing pbsa cuda code David A Case
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling
Sunday, 25 October 2020
- Re: [AMBER] [GaMD-discuss] GaMD Neha Gandhi
Monday, 26 October 2020
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson
- Re: [AMBER] doubt charges MYRIAN TORRES RICO
- Re: [AMBER] doubt charges MYRIAN TORRES RICO
- Re: [AMBER] Prmtop for protein + 2 identical ligands has wrong dihedral parameters for the second ligand. LEaP bug? Mariano Curti
- Re: [AMBER] correct md-input & prmtop for TI calculations Vaibhav Dixit
- [AMBER] Steered MD at constant force Vishal Singh
- [AMBER] mmpbsa error MYRIAN TORRES RICO
- Re: [AMBER] amber14 and amber16 are not working in new installation David A Case
- Re: [AMBER] mmpbsa error David A Case
- Re: [AMBER] Changing lj_radius without changing lj_14_radius Batuhan Kav
- Re: [AMBER] mmpbsa error MYRIAN TORRES RICO
- [AMBER] Amber20: Ampere microarchitecture support and next Amber release Kraus, Sebastian
- Re: [AMBER] Changing lj_radius without changing lj_14_radius Matias Machado
- [AMBER] AMBER 20 Benchmarks on NVIDIA RTX 3080/3090 and more Jason Hogrefe
- Re: [AMBER] mmpbsa error David A Case
- Re: [AMBER] Amber20: Ampere microarchitecture support and next Amber release David A Case
- [AMBER] System preparation for MMPBSA.py SATYAJIT KHATUA
Tuesday, 27 October 2020
- [AMBER] Amber20: Ampere microarchitecture support and Amber release in 2021 Kraus, Sebastian
- Re: [AMBER] mmpbsa error MYRIAN TORRES RICO
- Re: [AMBER] AMBER 20 Benchmarks on NVIDIA RTX 3080/3090 and more Mike Mazanetz
- [AMBER] TI calculation input clarification Delwakkada Liyanage, Senal Dinuka
- [AMBER] pmemd with hybrid mpi/mp Bill Abbott
- Re: [AMBER] pmemd with hybrid mpi/mp David A Case
- Re: [AMBER] pmemd with hybrid mpi/mp Bill Abbott
- [AMBER] pmemd.cuda and CPU cores Abdul Basit
- Re: [AMBER] R: mm-pbsa calculation Suchetana Gupta
Wednesday, 28 October 2020
- Re: [AMBER] R: mm-pbsa calculation Giulio Poli
- [AMBER] Amber20 and RNA simulations Piia Kokkonen
- Re: [AMBER] pmemd.cuda and CPU cores David A Case
- Re: [AMBER] Amber20 and RNA simulations David A Case
- Re: [AMBER] Amber20 and RNA simulations Piia Kokkonen
- [AMBER] Help with parameterization of non-standard amino acid Amit Sharma (Asstt. Prof., MCARS)
- Re: [AMBER] Help with parameterization of non-standard amino acid Dr. Anselm Horn
- [AMBER] Amber TI - crgmask Delwakkada Liyanage, Senal Dinuka
- [AMBER] CO2 Michele Vanini
- Re: [AMBER] CO2 Raman Preet Singh
- Re: [AMBER] CO2 Michele Vanini
- [AMBER] a metal bound Met Wu Xu
- Re: [AMBER] CO2 Carlos Simmerling
- Re: [AMBER] a metal bound Met Vaibhav Dixit
- Re: [AMBER] a metal bound Met Wu Xu
- [AMBER] How to import (.pdb) files into xleap of AMBER generated by Cellulose builder Pinky Mazumder
- Re: [AMBER] CO2 Raman Preet Singh
Thursday, 29 October 2020
- [AMBER] cellulose crystal structure ( cellulose bundles) Pinky Mazumder
- Re: [AMBER] Amber TI - crgmask Juraj Dobias
- [AMBER] Xleap error Jisha B
- Re: [AMBER] How to import (.pdb) files into xleap of AMBER generated by Cellulose builder Dr. Anselm Horn
- Re: [AMBER] Xleap error Elvis Martis
- Re: [AMBER] cellulose crystal structure ( cellulose bundles) David A Case
- Re: [AMBER] Amber TI - crgmask Delwakkada Liyanage, Senal Dinuka
- [AMBER] Force field for IDP mohamed marzouk
- [AMBER] Normalized eigen values DHEERAJ CHITARA
- Re: [AMBER] cellulose crystal structure ( cellulose bundles) Pinky Mazumder
- Re: [AMBER] How to import (.pdb) files into xleap of AMBER generated by Cellulose builder Pinky Mazumder
- Re: [AMBER] How to import (.pdb) files into xleap of AMBER generated by Cellulose builder Bill Ross
- Re: [AMBER] cellulose crystal structure ( cellulose bundles) Bill Ross
- [AMBER] Amber20 installation for MPI, CUDA issues. Luka Bilić
- [AMBER] MM/PBSA after minimization h_sahakyan.mb.sci.am
- [AMBER] Constant Force SMD simulation Vishal Singh
- Re: [AMBER] Constant Force SMD simulation MR. RABINDRANATH PAUL
- Re: [AMBER] Constant Force SMD simulation Vishal Singh
- Re: [AMBER] Tri-coordination environment in zinc SATYAJIT KHATUA
- Re: [AMBER] Tri-coordination environment in zinc Bill Ross
Friday, 30 October 2020
- Re: [AMBER] Amber20 installation for MPI, CUDA issues. Luka Bilić
- Re: [AMBER] Amber TI - crgmask Juraj Dobias
- Re: [AMBER] Force field for IDP David A Case
- Re: [AMBER] MM/PBSA after minimization David A Case
- Re: [AMBER] MMGBSA/MMPBSA Help Ray Luo
- Re: [AMBER] Fwd: MMPBSA calculations with 1 explicit water molecule Ray Luo
- Re: [AMBER] System preparation for MMPBSA.py Ray Luo
- [AMBER] how find Es from mdout to estimate vertical energy gap Vaibhav Dixit
- Re: [AMBER] how find Es from mdout to estimate vertical energy gap Adrian Roitberg
- [AMBER] NMR restraints Debarati DasGupta
- Re: [AMBER] how find Es from mdout to estimate vertical energy gap Vaibhav Dixit
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Scott Brozell
- Re: [AMBER] how find Es from mdout to estimate vertical energy gap Vaibhav Dixit
- Re: [AMBER] NMR restraints Carlos Simmerling
- Re: [AMBER] NMR restraints David A Case
Saturday, 31 October 2020
- [AMBER] Problem with acpype Michele Vanini
- Re: [AMBER] NMR restraints Debarati DasGupta
- Re: [AMBER] NMR restraints Carlos Simmerling
- Re: [AMBER] NMR restraints Debarati DasGupta
- Re: [AMBER] NMR restraints Debarati DasGupta
- Re: [AMBER] how find Es from mdout to estimate vertical energy gap Adrian Roitberg

Last message date: Sat Oct 31 2020 - 09:30:02 PDT
Archived on: Wed Nov 13 2024 - 05:55:59 PST

Amber Archive Oct 2020 by date