Amber Archive Jan 2021: by date

Friday, 1 January 2021
- [AMBER] Problem with cudaMalloc GpuBuffer Allocate failed out of memory assawin daducale
- Re: [AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card Mohd Farid Ismail
- Re: [AMBER] Problem with cudaMalloc GpuBuffer Allocate failed out of memory Elvis A F Martis
Saturday, 2 January 2021
- [AMBER] doubt frames simulation MYRIAN TORRES RICO
- Re: [AMBER] doubt frames simulation Carlos Simmerling
- Re: [AMBER] doubt frames simulation David A Case
- Re: [AMBER] doubt frames simulation MYRIAN TORRES RICO
- [AMBER] Problem with PB calculation CAVALLARO MATTIA
- [AMBER] Generating LJ paramters of divalent copper ions angad sharma
- Re: [AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card liu kai
Sunday, 3 January 2021
- [AMBER] do you know Gordon Richard Chalmers
- Re: [AMBER] Generating LJ paramters of divalent copper ions David A Case
- Re: [AMBER] do you know David A Case
- [AMBER] error... MYRIAN TORRES RICO
- [AMBER] SMD & MULTI_RMSD Fabian Glaser
- Re: [AMBER] error... Bill Ross
- Re: [AMBER] error... MYRIAN TORRES RICO
- [AMBER] Setting PME cutoff in Crystal Simulations Matthew Guberman-Pfeffer
- [AMBER] How to apply GLYCAM Parameters Matthew Guberman-Pfeffer
- Re: [AMBER] SMD & MULTI_RMSD Feng Pan
- Re: [AMBER] SMD & MULTI_RMSD Fabian Glaser
- Re: [AMBER] error... Bill Ross
- Re: [AMBER] error... Carlos Simmerling
- Re: [AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card Setyanto Md
Monday, 4 January 2021
- Re: [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi
- Re: [AMBER] error... MYRIAN TORRES RICO
- Re: [AMBER] Setting PME cutoff in Crystal Simulations David A Case
- Re: [AMBER] PROTEIN-DNA rmsd plot David A Case
- Re: [AMBER] error... Carlos Simmerling
- Re: [AMBER] PROTEIN-DNA rmsd plot Daniel Roe
- Re: [AMBER] MMPBSA.py.MPI not build in Amber20 Li,Haoxi
- Re: [AMBER] MMPBSA.py.MPI not build in Amber20 Elvis A F Martis
- [AMBER] Amber 20 installation, problems with the testing phase Beatriz Gomes Guimaraes
- [AMBER] Error in the apr.py code - steered MD simulation Eduardo R. Almeida
- [AMBER] cif to pdb Pinky Mazumder
- [AMBER] Energy Evaluations Matthew Guberman-Pfeffer
- Re: [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi
Tuesday, 5 January 2021
- Re: [AMBER] Setting PME cutoff in Crystal Simulations Matthew Guberman-Pfeffer
- Re: [AMBER] Energy Evaluations Carlos Simmerling
- Re: [AMBER] Amber 20 installation, problems with the testing phase David A Case
- Re: [AMBER] cif to pdb David A Case
- Re: [AMBER] Setting PME cutoff in Crystal Simulations David A Case
- Re: [AMBER] Amber 20 installation, problems with the testing phase Beatriz Gomes Guimaraes
- Re: [AMBER] SMD & MULTI_RMSD Feng Pan
- Re: [AMBER] Energy Evaluations Daniel Roe
- [AMBER] tinker_to_amber Юлия Беляева
- [AMBER] NaN VDWAALS Error During Minimization Jatin Kashyap
- Re: [AMBER] NaN VDWAALS Error During Minimization David Cerutti
- Re: [AMBER] Setting PME cutoff in Crystal Simulations Matthew Guberman-Pfeffer
- Re: [AMBER] NaN VDWAALS Error During Minimization Bill Ross
- Re: [AMBER] NaN VDWAALS Error During Minimization Jatin Kashyap
- Re: [AMBER] Amber 20 installation, problems with the testing phase David A Case
- Re: [AMBER] NaN VDWAALS Error During Minimization David A Case
- Re: [AMBER] NaN VDWAALS Error During Minimization Bill Ross
- Re: [AMBER] NaN VDWAALS Error During Minimization Jatin Kashyap
- Re: [AMBER] NaN VDWAALS Error During Minimization Bill Ross
- Re: [AMBER] NaN VDWAALS Error During Minimization Bill Ross
- Re: [AMBER] NaN VDWAALS Error During Minimization Thomas Cheatham
- Re: [AMBER] NaN VDWAALS Error During Minimization Thomas Cheatham
- [AMBER] pytraj in python 3.9 Abdul-Rashid III Sampaco
- Re: [AMBER] NaN VDWAALS Error During Minimization Jatin Kashyap
- Re: [AMBER] NaN VDWAALS Error During Minimization Bill Ross
- Re: [AMBER] NaN VDWAALS Error During Minimization Jatin Kashyap
- Re: [AMBER] NaN VDWAALS Error During Minimization David Cerutti
- Re: [AMBER] cif to pdb Pinky Mazumder
Wednesday, 6 January 2021
- Re: [AMBER] Setting PME cutoff in Crystal Simulations Matthew Guberman-Pfeffer
- Re: [AMBER] NaN VDWAALS Error During Minimization Bill Ross
- Re: [AMBER] cif to pdb Daniel Roe
- [AMBER] Sander code doesn’t output trajectory files K Jan
- [AMBER] Fwd: copper RISM angad sharma
- Re: [AMBER] Setting PME cutoff in Crystal Simulations David A Case
- Re: [AMBER] Sander code doesn’t output trajectory files Carlos Simmerling
- [AMBER] GB pairwise decomposition - Salt Bridge Tarsis
- Re: [AMBER] pytraj in python 3.9 David A Case
- Re: [AMBER] Sander code doesn’t output trajectory files David A Case
- [AMBER] Bug in the Mol2 format: space converted into a new oxygen atom Mateusz Bieniek
- Re: [AMBER] GB pairwise decomposition - Salt Bridge Carlos Simmerling
- Re: [AMBER] Sander code doesn’t output trajectory files K Jan
- Re: [AMBER] Sander code doesn’t output trajectory files Roitberg,Adrian E
- Re: [AMBER] Sander code doesn’t output trajectory files K Jan
- Re: [AMBER] Amber 20 installation, problems with the testing phase Beatriz Gomes Guimaraes
- [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Eduardo R. Almeida
- Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Bill Ross
- Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Bill Ross
- Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Eduardo R. Almeida
- Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Eduardo R. Almeida
- Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Bill Ross
- Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Eduardo R. Almeida
- Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Bill Ross
- Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Eduardo R. Almeida
- Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Bill Ross
- Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Bill Ross
- Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Eduardo R. Almeida
- Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Hector A. Baldoni
- Re: [AMBER] pytraj in python 3.9 Abdul-Rashid III Sampaco
Thursday, 7 January 2021
- Re: [AMBER] Amber 20 installation, problems with the testing phase Beatriz Gomes Guimaraes
- Re: [AMBER] NaN VDWAALS Error During Minimization Jatin Kashyap
- Re: [AMBER] Amber 20 installation, problems with the testing phase David A Case
- Re: [AMBER] Amber 20 installation, problems with the testing phase Beatriz Gomes Guimaraes
- [AMBER] RMSD analysis K Jan
- [AMBER] MD GPU Scaling Performance Jatin Kashyap
- Re: [AMBER] RMSD analysis Kenneth Huang
- Re: [AMBER] RMSD analysis K Jan
- Re: [AMBER] RMSD analysis Carlos Simmerling
Friday, 8 January 2021
- Re: [AMBER] MD GPU Scaling Performance David A Case
- Re: [AMBER] tinker_to_amber David A Case
- Re: [AMBER] Bug in the Mol2 format: space converted into a new oxygen atom David A Case
- Re: [AMBER] MMPBSA.py.MPI not build in Amber20 David A Case
- Re: [AMBER] MMPBSA.py.MPI not build in Amber20 Elvis A F Martis
- [AMBER] CPPTRAJ error while Clustering Maghsoud, Yazdan
- Re: [AMBER] CPPTRAJ error while Clustering Daniel Roe
- Re: [AMBER] RMSD analysis Daniel Roe
- Re: [AMBER] MMPBSA.py.MPI not build in Amber20 Li,Haoxi
- [AMBER] Error in xleap: water molecules Eduardo R. Almeida
- [AMBER] how to pull group of atoms towards a fixed molecule using Steered molecular dynamics simulation Pinky Mazumder
- Re: [AMBER] Error in xleap: water molecules Bill Ross
- [AMBER] How to apply shear loading on carbohydrates Pinky Mazumder
- [AMBER] Domain distances using cpptraj Athena N
Saturday, 9 January 2021
- Re: [AMBER] Error in xleap: water molecules David A Case
- Re: [AMBER] Error in xleap: water molecules Eduardo R. Almeida
- Re: [AMBER] Error in xleap: water molecules Bill Ross
- Re: [AMBER] Error in xleap: water molecules David A Case
- Re: [AMBER] Error in xleap: water molecules Bill Ross
- Re: [AMBER] Error in xleap: water molecules Eduardo R. Almeida
- Re: [AMBER] Error in xleap: water molecules Bill Ross
- Re: [AMBER] Error in xleap: water molecules Eduardo R. Almeida
- Re: [AMBER] Error in xleap: water molecules Bill Ross
- Re: [AMBER] Error in xleap: water molecules David A Case
- Re: [AMBER] Error in xleap: water molecules Bill Ross
- Re: [AMBER] Error in xleap: water molecules Eduardo R. Almeida
- [AMBER] Fwd: Domain distances using cpptraj Athena N
- [AMBER] How to pull/push group of atoms Pinky Mazumder
Sunday, 10 January 2021
- [AMBER] Probmlems compiling under macOS Gustaf Olsson
- [AMBER] Error searching for compatible GPU Hongwei Tan
- Re: [AMBER] Fwd: Domain distances using cpptraj David A Case
- Re: [AMBER] Probmlems compiling under macOS David A Case
- [AMBER] Issue about the generaton of rst files 辛志宏
- Re: [AMBER] Error searching for compatible GPU David A Case
- Re: [AMBER] Error in xleap: water molecules David A Case
- Re: [AMBER] Probmlems compiling under macOS Gustaf Olsson
- [AMBER] TI simulation blowing up with pmemd.CUDA Delwakkada Liyanage, Senal Dinuka
- Re: [AMBER] Error in xleap: water molecules Eduardo R. Almeida
- Re: [AMBER] TI simulation blowing up with pmemd.CUDA David A Case
- [AMBER] Amber GPU performance history David A Case
- Re: [AMBER] TI simulation blowing up with pmemd.CUDA Delwakkada Liyanage, Senal Dinuka
- Re: [AMBER] Probmlems compiling under macOS Gustaf Olsson
- Re: [AMBER] Error searching for compatible GPU Hongwei Tan
- [AMBER] Preparation of input file for RAMD (Geng Dong) 东庚
- [AMBER] Lateral movement of membrane bound protein during MD simulation in Amber Biplab Ghosh
- [AMBER] How to use AM1 for Ti atom in Amber? 孙天宇
- [AMBER] backbone rmsd between mutant trajectories, comparing conformational space sampled Vaibhav Dixit
- [AMBER] Cpptraj v13 command is not working fixatomorder Ana Ziad
- [AMBER] Problem in running cmake Airy Sanjeev
Monday, 11 January 2021
- [AMBER] error job MYRIAN TORRES RICO
- Re: [AMBER] Lateral movement of membrane bound protein during MD simulation in Amber Stephan Schott
- [AMBER] LEaP Error/questions. Sam Walsworth (Researcher)
- Re: [AMBER] TI simulation blowing up with pmemd.CUDA David A Case
- Re: [AMBER] Probmlems compiling under macOS David A Case
- Re: [AMBER] backbone rmsd between mutant trajectories, comparing conformational space sampled David A Case
- Re: [AMBER] Problem in running cmake David A Case
- Re: [AMBER] error job David A Case
- Re: [AMBER] LEaP Error/questions. David A Case
- Re: [AMBER] How to use AM1 for Ti atom in Amber? David A Case
- Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher)
- Re: [AMBER] TI simulation blowing up with pmemd.CUDA Debarati DasGupta
- Re: [AMBER] SMD & MULTI_RMSD Fabian Glaser
- [AMBER] US or SMD for torsion angle steering? Fabian Glaser
- Re: [AMBER] TI simulation blowing up with pmemd.CUDA Debarati DasGupta
- Re: [AMBER] LEaP Error/questions. David A Case
- Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher)
- Re: [AMBER] LEaP Error/questions. Carlos Simmerling
- Re: [AMBER] LEaP Error/questions. Maria Nagan
- Re: [AMBER] TI simulation blowing up with pmemd.CUDA Debarati DasGupta
- Re: [AMBER] Issue about the generaton of rst files Daniel Roe
- Re: [AMBER] Cpptraj v13 command is not working fixatomorder Daniel Roe
- [AMBER] Pull group of atoms together Pinky Mazumder
- Re: [AMBER] Pull group of atoms together Carlos Simmerling
- Re: [AMBER] SMD & MULTI_RMSD Feng Pan
- [AMBER] Spam purewater keyword Debarati DasGupta
- Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher)
- [AMBER] Fwd: Creating a bond in leap Victoria E Hill
- Re: [AMBER] Fwd: Creating a bond in leap Kenneth Huang
- Re: [AMBER] LEaP Error/questions. Carlos Simmerling
- Re: [AMBER] Problem in running cmake Airy Sanjeev
- [AMBER] Amber20 with PLUMED running slow, with GPU utilisation ~40% Amanda Buyan
- Re: [AMBER] backbone rmsd between mutant trajectories, comparing conformational space sampled Vaibhav Dixit
Tuesday, 12 January 2021
- Re: [AMBER] error job MYRIAN TORRES RICO
- Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher)
- [AMBER] Issue about the generaton of rst files 辛志宏
- Re: [AMBER] LEaP Error/questions. Carlos Simmerling
- Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher)
- Re: [AMBER] LEaP Error/questions. David A Case
- Re: [AMBER] LEaP Error/questions. David A Case
- Re: [AMBER] error job David A Case
- [AMBER] ff15ipq-m force field for protein mimetics Lillian Chong
- Re: [AMBER] Issue about the generaton of rst files Daniel Roe
- [AMBER] Problems when running make test.parallel Beatriz Gomes Guimaraes
- Re: [AMBER] US or SMD for torsion angle steering? Feng Pan
- Re: [AMBER] error job MYRIAN TORRES RICO
- Re: [AMBER] error job Carlos Simmerling
- Re: [AMBER] error job MYRIAN TORRES RICO
- Re: [AMBER] error job Carlos Simmerling
- Re: [AMBER] Pull group of atoms together Pinky Mazumder
- Re: [AMBER] backbone rmsd between mutant trajectories, comparing conformational space sampled Hector A. Baldoni
- Re: [AMBER] Problems when running make test.parallel Daniel Roe
- Re: [AMBER] error job MYRIAN TORRES RICO
- Re: [AMBER] Amber20 with PLUMED running slow, with GPU utilisation ~40% David A Case
- Re: [AMBER] Amber20 with PLUMED running slow, with GPU utilisation ~40% Adrian Roitberg
- [AMBER] abfQMMM with Terachem Eugen Hruska
- [AMBER] Non-integer/zero charges from RESP fitting? Kenneth Huang
- Re: [AMBER] Pull group of atoms together Carlos Simmerling
- Re: [AMBER] Pull group of atoms together Pinky Mazumder
- Re: [AMBER] Pull group of atoms together Carlos Simmerling
- Re: [AMBER] Pull group of atoms together Pinky Mazumder
- Re: [AMBER] Amber20 with PLUMED running slow, with GPU utilisation ~40% Amanda Buyan
- Re: [AMBER] Missing Iron (Fe) DFTB3 parameters for QM/MM simulation of Enzyme Goetz, Andreas
Wednesday, 13 January 2021
- [AMBER] Python Error in MMPBSA.py, only for PBSA on final output Lennart Gundelach
- [AMBER] Errors whilst installing GPU Amber20 Victoria E Hill
- Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher)
- Re: [AMBER] LEaP Error/questions. Carlos Simmerling
- Re: [AMBER] error job Carlos Simmerling
- Re: [AMBER] Non-integer/zero charges from RESP fitting? David A Case
- Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher)
- Re: [AMBER] Errors whilst installing GPU Amber20 David A Case
- Re: [AMBER] LEaP Error/questions. Daniel Roe
- Re: [AMBER] LEaP Error/questions. Carlos Simmerling
- Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher)
- Re: [AMBER] LEaP Error/questions. Carlos Simmerling
- Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher)
- Re: [AMBER] LEaP Error/questions. David A Case
- Re: [AMBER] Errors whilst installing GPU Amber20 Victoria E Hill
- Re: [AMBER] Errors whilst installing GPU Amber20 tluchko
- Re: [AMBER] Python Error in MMPBSA.py, only for PBSA on final output Ray Luo
- Re: [AMBER] Errors whilst installing GPU Amber20 Victoria E Hill
- Re: [AMBER] Non-integer/zero charges from RESP fitting? Kenneth Huang
- Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher)
- Re: [AMBER] Probmlems compiling under macOS Gustaf Olsson
Thursday, 14 January 2021
- Re: [AMBER] error job MYRIAN TORRES RICO
- [AMBER] gaff/parm MYRIAN TORRES RICO
- [AMBER] PROTEIN-DNA RMSD plots Syeda Amna Arshi
- Re: [AMBER] PROTEIN-DNA RMSD plots Carlos Simmerling
- Re: [AMBER] PROTEIN-DNA RMSD plots Dr. Anselm Horn
- [AMBER] Error while clustering on CPPTRAJ dnlfr1994.gmail.com
- Re: [AMBER] gaff/parm David A Case
- Re: [AMBER] gaff/parm MYRIAN TORRES RICO
- Re: [AMBER] Error while clustering on CPPTRAJ Daniel Roe
- [AMBER] Number of na, cl ions Женя Елизарова
- Re: [AMBER] Error while clustering on CPPTRAJ dnlfr1994.gmail.com
- Re: [AMBER] Number of na, cl ions David A Case
- Re: [AMBER] LEaP Error/questions. David A Case
- Re: [AMBER] Error while clustering on CPPTRAJ Daniel Roe
- [AMBER] DNA-ligand simulation Kehinde Idowu
- Re: [AMBER] DNA-ligand simulation Thomas Cheatham
- [AMBER] Question of targeted molecular dynamics simulation 吴晓东
Friday, 15 January 2021
- Re: [AMBER] Question of targeted molecular dynamics simulation Dr. Anselm Horn
- Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher)
- [AMBER] Typo in update.13 for AmberTools20 Hashemi, Mohtadin
- Re: [AMBER] LEaP Error/questions. David A Case
- Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher)
- [AMBER] How to use GLYCAM_06j-1 in LAMMPS Pinky Mazumder
- Re: [AMBER] Steered molecular dynamics Simulation Pinky Mazumder
Saturday, 16 January 2021
- Re: [AMBER] Python Error in MMPBSA.py, only for PBSA on final output Lennart Gundelach
- [AMBER] NonUniversalWarning: Modified off-diagonal LJ parameters detected Loki
- Re: [AMBER] How to use GLYCAM_06j-1 in LAMMPS David A Case
- Re: [AMBER] NonUniversalWarning: Modified off-diagonal LJ parameters detected David A Case
- Re: [AMBER] Steered molecular dynamics Simulation Fabian Glaser
- Re: [AMBER] NonUniversalWarning: Modified off-diagonal LJ parameters detected Loki
- Re: [AMBER] Steered molecular dynamics Simulation Pinky Mazumder
- Re: [AMBER] NonUniversalWarning: Modified off-diagonal LJ parameters detected David A Case
- Re: [AMBER] How to use GLYCAM_06j-1 in LAMMPS Pinky Mazumder
- Re: [AMBER] Steered molecular dynamics Simulation Pinky Mazumder
- [AMBER] Langevin thermostat different gamma_ln giving systematically different energies? Liao
- Re: [AMBER] Python Error in MMPBSA.py, only for PBSA on final output Ray Luo
- Re: [AMBER] Langevin thermostat different gamma_ln giving systematically different energies? Thomas Cheatham
- [AMBER] How to apply Compressive loading on wood Pinky Mazumder
- Re: [AMBER] lj1264 in vacuum Pengfei Li
- Re: [AMBER] Tri-coordination environment in zinc Pengfei Li
- [AMBER] antechamber assigns DU as atom type for nitrogen nguerin
Sunday, 17 January 2021
- [AMBER] working with mmpbsa with protein and three ligands in same complex Sadaf Rani
- Re: [AMBER] working with mmpbsa with protein and three ligands in same complex David A Case
- [AMBER] Distance of every c alpha in a protein to every other c alpha Jenny 148
Monday, 18 January 2021
- Re: [AMBER] Problems when running make test.parallel Beatriz Gomes Guimaraes
- [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Jatin Kashyap
- Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Carlos Simmerling
- Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Jatin Kashyap
- Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Carlos Simmerling
- Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Jatin Kashyap
- Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Carlos Simmerling
- Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Jatin Kashyap
- Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Roitberg,Adrian E
- Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Jatin Kashyap
- Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Carlos Simmerling
- Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Jatin Kashyap
- Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Carlos Simmerling
- [AMBER] Extending DNA structure Airy Sanjeev
Tuesday, 19 January 2021
- Re: [AMBER] Extending DNA structure Vlad Cojocaru
- Re: [AMBER] Extending DNA structure Airy Sanjeev
- Re: [AMBER] Distance of every c alpha in a protein to every other c alpha Daniel Roe
- Re: [AMBER] Error while clustering on CPPTRAJ dnlfr1994.gmail.com
- Re: [AMBER] Error while clustering on CPPTRAJ Daniel Roe
- Re: [AMBER] Error while clustering on CPPTRAJ Daniel Fernández Remacha
- Re: [AMBER] Error while clustering on CPPTRAJ Daniel Roe
- [AMBER] vlimit exceeded for step 0; vmax = 50.6241 Pinky Mazumder
- [AMBER] Creating input files using tleap Nicy yadav
- Re: [AMBER] working with mmpbsa with protein and three ligands in same complex Sadaf Rani
Wednesday, 20 January 2021
- [AMBER] makedepend for sander Antoine MARION
- Re: [AMBER] makedepend for sander David A Case
- Re: [AMBER] Creating input files using tleap David A Case
- [AMBER] combining crashed trajectories Ayesha Fatima
- Re: [AMBER] makedepend for sander Antoine MARION
- Re: [AMBER] Creating input files using tleap Nicy yadav
- [AMBER] The long and winding STSM Luis Simon
- Re: [AMBER] combining crashed trajectories Dr. Anselm Horn
- [AMBER] Major Cpptraj Update (GitHub) Daniel Roe
- [AMBER] ZAFF force field Tabassum Khair Barbhuiya
- [AMBER] MMPBSA calculation cpptraj failed with ligand prmtop Sadaf Rani
- Re: [AMBER] MMPBSA calculation cpptraj failed with ligand prmtop Elvis A F Martis
Thursday, 21 January 2021
- [AMBER] Fwd: Error during amber16 installation spss4.iacs.res.in
- [AMBER] question MYRIAN TORRES RICO
- Re: [AMBER] Fwd: Error during amber16 installation David A Case
- Re: [AMBER] question David A Case
- [AMBER] Cpptraj Stejskal, Lenka
- Re: [AMBER] Cpptraj Daniel Roe
- [AMBER] Nvidia RTX 3080/3090 Servers mish
- Re: [AMBER] Fwd: Error during amber16 installation spss4.iacs.res.in
Friday, 22 January 2021
- Re: [AMBER] Python Error in MMPBSA.py, only for PBSA on final output Lennart Gundelach
- [AMBER] Energy minimization script raissa.conceicao.bol.com.br
- Re: [AMBER] Nvidia RTX 3080/3090 Servers Ross Walker
- Re: [AMBER] Nvidia RTX 3080/3090 Servers mish
- [AMBER] How to extract restart file with velocity from a trajectory file? 辛志宏
- Re: [AMBER] Fwd: Error during amber16 installation David A Case
- Re: [AMBER] Energy minimization script David A Case
- Re: [AMBER] Cpptraj Daniel Roe
- Re: [AMBER] How to extract restart file with velocity from a trajectory file? Carlos Simmerling
- Re: [AMBER] combining crashed trajectories Daniel Roe
- Re: [AMBER] Energy minimization script raissa.conceicao.bol.com.br
- [AMBER] Understanding File Format Specifications nguerin
- Re: [AMBER] Understanding File Format Specifications Thomas Cheatham
Saturday, 23 January 2021
- Re: [AMBER] antechamber assigns DU as atom type for nitrogen David A Case
Sunday, 24 January 2021
- [AMBER] How to pull two group of atoms in two different direction? Pinky Mazumder
- Re: [AMBER] MMPBSA calculation cpptraj failed with ligand prmtop Sadaf Rani
- Re: [AMBER] MMPBSA calculation cpptraj failed with ligand prmtop Sadaf Rani
- [AMBER] Running simulations richa anand
Monday, 25 January 2021
- [AMBER] Amber 16/cpptraj diffusion command Pau Mayorga Delgado
- [AMBER] DNA protein simulation protocol Airy Sanjeev
- [AMBER] Fwd: Distance of every c alpha in a protein to every other c alpha Jenny 148
- Re: [AMBER] Amber 16/cpptraj diffusion command Daniel Roe
- Re: [AMBER] Fwd: Distance of every c alpha in a protein to every other c alpha Daniel Roe
- [AMBER] pdb4amber error Nicy yadav
- [AMBER] overall and internal correlation function Mani Radh
- [AMBER] OPC monovalent ion parameters Sebastian Oleksy
- Re: [AMBER] OPC monovalent ion parameters Carlos Simmerling
- [AMBER] abmd ignores cv_min cv_max and resolution for colvar="TORSION" Luis Simon
- [AMBER] Help to generate prmtop and .crd files from a PDB trajectory Devlina Chakravarty
- [AMBER] PrmtopError: Complex natom != receptor natom + ligand natom Renato Araujo
- Re: [AMBER] DNA protein simulation protocol David A Case
- Re: [AMBER] PrmtopError: Complex natom != receptor natom + ligand natom David A Case
Tuesday, 26 January 2021
- Re: [AMBER] PrmtopError: Complex natom != receptor natom + ligand natom Renato Araujo
- Re: [AMBER] PrmtopError: Complex natom != receptor natom + ligand natom David A Case
- Re: [AMBER] Running simulations David A Case
- Re: [AMBER] Help to generate prmtop and .crd files from a PDB trajectory Kenneth Huang
- Re: [AMBER] pdb4amber error Scott Brozell
Wednesday, 27 January 2021
- [AMBER] how to get amber 18 tools Sadaf Rani
- [AMBER] technical problems with installing amber20 Игорь Злотников
- Re: [AMBER] pdb4amber error David A Case
- Re: [AMBER] how to get amber 18 tools Carlos Simmerling
- [AMBER] rotdif analysis in cpptraj Adeleh Mokhles Gerami
- Re: [AMBER] how to get amber 18 tools Sadaf Rani
- Re: [AMBER] how to get amber 18 tools David A Case
- Re: [AMBER] technical problems with installing amber20 David A Case
- Re: [AMBER] technical problems with installing amber20 Игорь Злотников
- [AMBER] max pairlist cutoff must be less than unit cell max sphere radius! Pinky Mazumder
- [AMBER] How to fix the issue of generating restart file from a trajectory? 辛志宏
Thursday, 28 January 2021
- Re: [AMBER] Help to generate prmtop and .crd files from a PDB trajectory Daniel Roe
- Re: [AMBER] technical problems with installing amber20 David A Case
- Re: [AMBER] max pairlist cutoff must be less than unit cell max sphere radius! David A Case
- Re: [AMBER] How to fix the issue of generating restart file from a trajectory? Daniel Roe
- Re: [AMBER] max pairlist cutoff must be less than unit cell max sphere radius! Pinky Mazumder
- [AMBER] Error in minimization Kehinde Idowu
- Re: [AMBER] Error in minimization Carlos Simmerling
Friday, 29 January 2021
- [AMBER] Can we perform combined clustering with multiple prmtop files and mdcrd files? Debarati DasGupta
- [AMBER] in chimera, which one should I use for carbohydrates Pinky Mazumder
- [AMBER] Potential energy discrepancy in RXSGLD Charo del Genio
- Re: [AMBER] in chimera, which one should I use for carbohydrates David A Case
- Re: [AMBER] Can we perform combined clustering with multiple prmtop files and mdcrd files? Kenneth Huang
- Re: [AMBER] The long and winding STSM Feng Pan
- Re: [AMBER] abmd ignores cv_min cv_max and resolution for colvar="TORSION" Feng Pan
- [AMBER] Suggestions on crossing energy barrier to break strong HBs Amit Sharma (Asstt. Prof., MCARS)
- Re: [AMBER] Suggestions on crossing energy barrier to break strong HBs David A Case
- Re: [AMBER] Suggestions on crossing energy barrier to break strong HBs Amit Sharma (Asstt. Prof., MCARS)
Saturday, 30 January 2021
- [AMBER] Bug when using RESPA in REMD runs Charo del Genio
- Re: [AMBER] Bug when using RESPA in REMD runs David A Case
- Re: [AMBER] Bug when using RESPA in REMD runs Brian Radak
- Re: [AMBER] Bug when using RESPA in REMD runs Carlos Simmerling
- Re: [AMBER] Bug when using RESPA in REMD runs Charo del Genio
- Re: [AMBER] Suggestions on crossing energy barrier to break strong HBs Kenneth Huang
Sunday, 31 January 2021
- [AMBER] Can't restart a RXSGLD run (possible bug) Charo del Genio
- [AMBER] Found bug in sander in restarting SGLD replica exchange runs Charo del Genio
- [AMBER] Non zero ligand warning Ayesha Fatima
- Re: [AMBER] Non zero ligand warning David A Case
- Re: [AMBER] Non zero ligand warning Kenneth Huang
- [AMBER] Patches to fix the replica exchange restart bug Charo del Genio

Last message date: Sun Jan 31 2021 - 12:30:02 PST
Archived on: Mon Dec 30 2024 - 05:55:58 PST

Amber Archive Jan 2021 by date