Amber Archive Jan 2022: by date

Saturday, 1 January 2022
- Re: [AMBER] sqm performance: does it run in parallel? Alan
- Re: [AMBER] Non-standard residue parameterization questions Matthew Guberman-Pfeffer
- [AMBER] Why SANDER can't rotate the dihedral for some angles? [Metal Center] Erdem Yeler
Sunday, 2 January 2022
- Re: [AMBER] DE Shaw RNA parameters error David A Case
- Re: [AMBER] TIP4PD water box error David A Case
Monday, 3 January 2022
- Re: [AMBER] Why SANDER can't rotate the dihedral for some angles? [Metal Center] David A Case
- Re: [AMBER] Extending constant pH to additional titratable groups Jason Swails
- Re: [AMBER] Li salt parameterisation issue Damiano Spadoni
- Re: [AMBER] amber20 - test suite picks up the wrong libgfortran David A Case
Tuesday, 4 January 2022
- [AMBER] Fw: regarding no tortion terms MIRA JHAWAR
- [AMBER] regading no tortion terms MIRA JHAWAR
- Re: [AMBER] regading no tortion terms David A Case
- [AMBER] 1D-RISM Convergence ABDUL BASIT
- [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Renato Araujo
- [AMBER] lipid modification to a nucleic acid base Daniel Konstantinovsky
- Re: [AMBER] 1D-RISM Convergence tluchko
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered David A Case
- Re: [AMBER] amber20 - test suite picks up the wrong libgfortran tluchko
Wednesday, 5 January 2022
- [AMBER] How to use MN2+ parameter (.dat and .prp) files downloaded form AMBER parameter database of Bryce group Pranabesh Mandal (PhD, Bioinformatics August-2019)
- Re: [AMBER] How to use MN2+ parameter (.dat and .prp) files downloaded form AMBER parameter database of Bryce group Dr. Anselm Horn
- Re: [AMBER] lipid modification to a nucleic acid base Carlos Simmerling
- Re: [AMBER] Hydrogen Bonding Analysis Daniel Roe
- Re: [AMBER] amber20 - test suite picks up the wrong libgfortran Mark Dixon
- [AMBER] GCC and EuroSAMPL Satellite Workshop 2022 - Submission deadline extension Guessregen, Stefan /DE
- [AMBER] Heating only a region of the system Liao
Thursday, 6 January 2022
- [AMBER] CV_type Ming Tang
- Re: [AMBER] How to use MN2+ parameter (.dat and .prp) files downloaded form AMBER parameter database of Bryce group Pranabesh Mandal (PhD, Bioinformatics August-2019)
- Re: [AMBER] How to use MN2+ parameter (.dat and .prp) files downloaded form AMBER parameter database of Bryce group Dr. Anselm Horn
Friday, 7 January 2022
- Re: [AMBER] CV_type Feng Pan
- Re: [AMBER] Heating only a region of the system David A Case
- [AMBER] RESP doesn't incorporate charge constraint Daniel Konstantinovsky
- Re: [AMBER] RESP doesn't incorporate charge constraint Matthew Guberman-Pfeffer
- Re: [AMBER] RESP doesn't incorporate charge constraint Daniel Konstantinovsky
- Re: [AMBER] RESP doesn't incorporate charge constraint Matthew Guberman-Pfeffer
- Re: [AMBER] tleap error: "expected 'default'" Matthew Guberman-Pfeffer
- Re: [AMBER] tleap error: "expected 'default'" Daniel Konstantinovsky
- Re: [AMBER] Why SANDER can't rotate the dihedral for some angles? [Metal Center] Erdem Yeler
- Re: [AMBER] tleap error: "expected 'default'" Matthew Guberman-Pfeffer
- [AMBER] Problem with reading a mol2 file into tleap David A Case
- [AMBER] Amber20 minimization, the rendered .rst file is corrupted and unreadable Yi Ren
- Re: [AMBER] How to use MN2+ parameter (.dat and .prp) files downloaded form AMBER parameter database of Bryce group Pranabesh Mandal (PhD, Bioinformatics August-2019)
Saturday, 8 January 2022
- Re: [AMBER] Amber20 minimization, the rendered .rst file is corrupted and unreadable David A Case
- [AMBER] MCPB.py error in GAMESS-US calculations ABDUL BASIT
- Re: [AMBER] Amber20 minimization, the rendered .rst file is corrupted and unreadable Carlos Simmerling
- Re: [AMBER] Amber20 minimization, the rendered .rst file is corrupted and unreadable Daniel Roe
- [AMBER] FEP calculation in tutorial 9 xiangyu
- Re: [AMBER] Amber20 minimization, the rendered .rst file is corrupted and unreadable Yi Ren
- [AMBER] RESP VS ESP charge fitting Nagar, Hemant
Sunday, 9 January 2022
- [AMBER] attaching a residue to DNA Daniel Konstantinovsky
- Re: [AMBER] CPPTRAJ Segmentation Fault with modified topology file Chris Lee
- Re: [AMBER] CPPTRAJ Segmentation Fault with modified topology file Daniel Roe
- [AMBER] Multi-GPU oddity James Kress
- [AMBER] Problem in mmpbsa calculation Rakesh Roy
- Re: [AMBER] regading no tortion terms MIRA JHAWAR
- Re: [AMBER] regading no tortion terms MIRA JHAWAR
- [AMBER] Problems with mdgx torsion parameters fitting - possible bug with polymers? Casalini Tommaso
Monday, 10 January 2022
- Re: [AMBER] regading no tortion terms MIRA JHAWAR
- Re: [AMBER] attaching a residue to DNA Christina Bergonzo
- Re: [AMBER] regading no tortion terms David A Case
- Re: [AMBER] regading no tortion terms Dr. Anselm Horn
- Re: [AMBER] regading no tortion terms MIRA JHAWAR
- [AMBER] SMD negative distance Jacopo Sgrignani
- Re: [AMBER] CPPTRAJ Segmentation Fault with modified topology file Daniel Roe
- Re: [AMBER] regading no tortion terms MIRA JHAWAR
- [AMBER] how to stop making terminal residue Daniel Konstantinovsky
- Re: [AMBER] Problems with mdgx torsion parameters fitting - possible bug with polymers? David Cerutti
- [AMBER] Help in ligand preparation_antechamber Arooma Maryam
- [AMBER] Amber21/Orca5.0?==?utf-8?q? QM/MM simulations Antonio Frances Monerris
- [AMBER] Reg: PLP - LYS parameters Lara rajam
- Re: [AMBER] Reg: PLP - LYS parameters Gerald Monard
Tuesday, 11 January 2022
- Re: [AMBER] regading no tortion terms MIRA JHAWAR
- Re: [AMBER] regading no tortion terms David A Case
- Re: [AMBER] how to stop making terminal residue David A Case
- Re: [AMBER] regading no tortion terms MIRA JHAWAR
- Re: [AMBER] how to stop making terminal residue Daniel Konstantinovsky
- Re: [AMBER] Help in ligand preparation_antechamber David A Case
- Re: [AMBER] regading no tortion terms MIRA JHAWAR
- Re: [AMBER] how to stop making terminal residue David A Case
- [AMBER] MCPB, atom mismatch and naming problem Matthew Guberman-Pfeffer
- [AMBER] Multi-GPU Bug in Amber20 James Kress
- Re: [AMBER] Multi-GPU Bug in Amber20 Ross Walker
- [AMBER] RESP giving ridiculous charges Daniel Konstantinovsky
- Re: [AMBER] Multi-GPU Bug in Amber20 James Kress
- Re: [AMBER] Multi-GPU Bug in Amber20 James Kress
- Re: [AMBER] regading no tortion terms David A Case
- Re: [AMBER] Multi-GPU Bug in Amber20 David A Case
- Re: [AMBER] Multi-GPU Bug in Amber20 James Kress
- Re: [AMBER] regading no tortion terms MIRA JHAWAR
- [AMBER] Question on REMD on GPU/CPU Suchetana Gupta
- Re: [AMBER] Question on REMD on GPU/CPU Vinicius Wilian Cruzeiro
Wednesday, 12 January 2022
- [AMBER] SMD Jacopo Sgrignani
- Re: [AMBER] how to stop making terminal residue Dr. Anselm Horn
- [AMBER] Running AmberTools21 on HPC cluster using distributed memory Manuel Fernandez Merino
- Re: [AMBER] RESP giving ridiculous charges Dr. Anselm Horn
- [AMBER] Thermodynamic integration equilibration Gian Marco ELISI
- Re: [AMBER] [External] How to calculate multipole moment？ Scott Boesch
- Re: [AMBER] [External] How to calculate multipole moment？ Scott Boesch
- Re: [AMBER] Running AmberTools21 on HPC cluster using distributed memory David A Case
- [AMBER] About the drug charge _antechamber Arooma Maryam
- [AMBER] Restraint removal doesn't seem to be happening Daniel Burns
- Re: [AMBER] About the drug charge _antechamber David A Case
- [AMBER] number of waters near a mask (K+) cpptraj Vaibhav Dixit
Thursday, 13 January 2022
- Re: [AMBER] Running AmberTools21 on HPC cluster using distributed memory Manuel Fernandez Merino
- [AMBER] Single Point Energy: sander x python sander Alan
- [AMBER] QM / MM module query Aashish Bhatt
- Re: [AMBER] number of waters near a mask (K+) cpptraj Daniel Roe
- Re: [AMBER] Restraint removal doesn't seem to be happening David A Case
- Re: [AMBER] Running AmberTools21 on HPC cluster using distributed memory David A Case
- Re: [AMBER] Single Point Energy: sander x python sander David A Case
- Re: [AMBER] QM / MM module query David A Case
- Re: [AMBER] number of waters near a mask (K+) cpptraj Vaibhav Dixit
- Re: [AMBER] Running AmberTools21 on HPC cluster using distributed memory Manuel Fernandez Merino
- Re: [AMBER] Restraint removal doesn't seem to be happening Daniel Burns
- Re: [AMBER] Single Point Energy: sander x python sander Alan
- Re: [AMBER] Single Point Energy: sander x python sander Ray Luo
- Re: [AMBER] Single Point Energy: sander x python sander David A Case
- [AMBER] CMAP and NBFIX Charmm36 in amber Burns Casamayor, Violeta
- Re: [AMBER] CMAP and NBFIX Charmm36 in amber David A Case
- [AMBER] How to solve Error: an illegal memory access was encountered launching kernel kClearForces on amber? natalia francisca rodriguez cabello
- Re: [AMBER] How to solve Error: an illegal memory access was encountered launching kernel kClearForces on amber? Mohamed Aboelnga
- Re: [AMBER] How to solve Error: an illegal memory access was encountered launching kernel kClearForces on amber? David A Case
- [AMBER] Request for Extra Points Functionality Matthew Guberman-Pfeffer
- [AMBER] The application of QM/MMGBSA in the evaluation of protein stability, is it reasonable? Xinheng He
Friday, 14 January 2022
- Re: [AMBER] Restraint removal doesn't seem to be happening Rafał Madaj
- [AMBER] NETCDF problem Björn Karlsson
- Re: [AMBER] Single Point Energy: sander x python sander Alan
- Re: [AMBER] Single Point Energy: sander x python sander Alan
- Re: [AMBER] How to solve Error: an illegal memory access was encountered launching kernel kClearForces on amber? natalia francisca rodriguez cabello
- Re: [AMBER] NETCDF problem David A Case
- Re: [AMBER] Single Point Energy: sander x python sander David A Case
- Re: [AMBER] NETCDF problem Björn Karlsson
- [AMBER] [MCPB] The force field parameter problem of the MCPB Huimin Tian
- Re: [AMBER] NETCDF problem David A Case
- Re: [AMBER] NETCDF problem Björn Karlsson
- [AMBER] Error in MMPBSA calculation Sruthi Sudhakar
- Re: [AMBER] Restraint removal doesn't seem to be happening Daniel Burns
- Re: [AMBER] Restraint removal doesn't seem to be happening David A Case
- Re: [AMBER] Error in MMPBSA calculation Sruthi Sudhakar
Saturday, 15 January 2022
- Re: [AMBER] Restraint removal doesn't seem to be happening Daniel Burns
- Re: [AMBER] Restraint removal doesn't seem to be happening Daniel Burns
Sunday, 16 January 2022
- [AMBER] Inquiry on LJ parameters in .mdl file for 3D-RISM Alexis Azucena
Monday, 17 January 2022
- [AMBER] Bad atom type error and invalid periodicity error in MMPBSA.py Yi Ren
- [AMBER] Protein + DNA, which FF? Alan
- Re: [AMBER] Protein + DNA, which FF? Alan
- [AMBER] Distorted water molecules in QM partition (possible bug) Antonio Frances Monerris
- [AMBER] Need help with SMD natalia francisca rodriguez cabello
- Re: [AMBER] Need help with SMD Carlos Simmerling
- Re: [AMBER] Inquiry on LJ parameters in .mdl file for 3D-RISM tluchko
- [AMBER] low-water system, bad NPT and NVT Daniel Konstantinovsky
- Re: [AMBER] low-water system, bad NPT and NVT Carlos Simmerling
- Re: [AMBER] Inquiry on LJ parameters in .mdl file for 3D-RISM Alexis Azucena
Tuesday, 18 January 2022
- [AMBER] Converting %FLAG XVV array found in .xvv file into a readable format similar to other .*vv files Daniel Fowles
- Re: [AMBER] Distorted water molecules in QM partition (possible bug) David A Case
- [AMBER] A4500 Benchmarks Ross Walker
- Re: [AMBER] ?==?utf-8?q? Distorted water molecules in QM partition (possible?==?utf-8?q? bug) Antonio Frances Monerris
- [AMBER] how to obtain index of atoms based on residue and atom masks Ming Tang
- [AMBER] Improved speed of CPPTRAJ post-clustering steps for large sets Daniel Roe
- Re: [AMBER] Improved speed of CPPTRAJ post-clustering steps for large sets Robert Molt
- Re: [AMBER] how to obtain index of atoms based on residue and atom masks Matthew Guberman-Pfeffer
Wednesday, 19 January 2022
- Re: [AMBER] how to obtain index of atoms based on residue and atom masks Dr. Anselm Horn
- [AMBER] Converting %FLAG XVV array found in .xvv file into a readable format similar to other .*vv files Daniel Fowles
- Re: [AMBER] Restraint removal doesn't seem to be happening David A Case
- [AMBER] How to compute MM/PB(GB)SA with Extra Points 王世玉
- Re: [AMBER] QM / MM module query Aashish Bhatt
- Re: [AMBER] how to obtain index of atoms based on residue and atom masks Hai Nguyen
- [AMBER] Comparing trajectories Reza Khayat
- Re: [AMBER] Comparing trajectories Thomas Cheatham
- Re: [AMBER] Comparing trajectories Carlos Simmerling
- Re: [AMBER] Comparing trajectories Reza Khayat
- Re: [AMBER] Comparing trajectories Rodrigo Galindo-Murillo
- Re: [AMBER] how to obtain index of atoms based on residue and atom masks Ming Tang
- [AMBER] Parameterize SO4 zz sheng
- [AMBER] Installing amber20 in conda Ming Tang
Thursday, 20 January 2022
- Re: [AMBER] Parameterize SO4 David A Case
- Re: [AMBER] Installing amber20 in conda David A Case
- Re: [AMBER] Parameterize SO4 Matthew Guberman-Pfeffer
- Re: [AMBER] Converting %FLAG XVV array found in .xvv file into a readable format similar to other .*vv files Jason Swails
- [AMBER] Adding on terminal hydrogen/phosphate to nucleosides in ff86? Kenneth Huang
- Re: [AMBER] Parameterize SO4 zz sheng
- Re: [AMBER] Parameterize SO4 Matthew Guberman-Pfeffer
Friday, 21 January 2022
- Re: [AMBER] Parameterize SO4 zz sheng
- [AMBER] Aligning a dimer for PCA analysis Kodituwakku,Dimuthu Nirmani
- [AMBER] GaMD error: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Li,Haoxi
- Re: [AMBER] Aligning a dimer for PCA analysis Daniel Roe
- Re: [AMBER] Archive page Thomas Cheatham
- Re: [AMBER] Improved speed of CPPTRAJ post-clustering steps for large sets Daniel Roe
- Re: [AMBER] Archive page James Kress
- [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Michael Coleman
Saturday, 22 January 2022
- [AMBER] ghost pmemd.cuda process ? Jordi Bujons
Sunday, 23 January 2022
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Gerald Monard
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Gerald Monard
- [AMBER] Distorted average pdb structure from 10 ns trajectory !!! A R
- Re: [AMBER] Distorted average pdb structure from 10 ns trajectory !!! Carlos Simmerling
- [AMBER] hydrogen mass repartitioning with accelerated MD James Kress
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Michael Coleman
- [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark John Chodera
Monday, 24 January 2022
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Karl Kirschner
- Re: [AMBER] Aligning a dimer for PCA analysis Dr. Anselm Horn
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) David A Case
- Re: [AMBER] ghost pmemd.cuda process ? Ross Walker
- Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark David A Case
- Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark Piotr Cieplak
- [AMBER] Restraint file for amber20 with pmemd.cuda implementation Prithviraj Nandigrami
- [AMBER] MEOHBOX/CHCL3BOX not working Daniel Konstantinovsky
- Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark David A Case
- Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation Carlos Simmerling
- Re: [AMBER] MEOHBOX/CHCL3BOX not working Matthew Guberman-Pfeffer
- Re: [AMBER] MEOHBOX/CHCL3BOX not working Daniel Konstantinovsky
- Re: [AMBER] MEOHBOX/CHCL3BOX not working Matthew Guberman-Pfeffer
- Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation Prithviraj Nandigrami
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Michael Coleman
- [AMBER] Regarding targeted md Pranabesh Mandal (PhD, Bioinformatics August-2019)
Tuesday, 25 January 2022
- Re: [AMBER] Regarding targeted md Carlos Simmerling
- Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation David A Case
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) David A Case
- Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation Prithviraj Nandigrami
- Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation Carlos Simmerling
- Re: [AMBER] ghost pmemd.cuda process ? Jordi Bujons
- [AMBER] adding ions to half the water box Daniel Konstantinovsky
- Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation David A Case
- Re: [AMBER] adding ions to half the water box David A Case
- Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark John Chodera
- [AMBER] CPPTRAJ for Buried SA King Wu
- Re: [AMBER] adding ions to half the water box Hai Nguyen
Wednesday, 26 January 2022
- Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark Dr. Anselm Horn
- [AMBER] dihedral restraints slowing down simulation Richard Kullmann
- Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark David A Case
- Re: [AMBER] dihedral restraints slowing down simulation David A Case
- Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark David A Case
- Re: [AMBER] dihedral restraints slowing down simulation Carlos Simmerling
- [AMBER] LIE calculation with distance-based mask - reg. Naveen Kumar Vasudevan
- [AMBER] The effect of water box size for TI free energy calculation zz sheng
- [AMBER] Umbrella Sampling Collective Variable Volkan Findik
- Re: [AMBER] Regarding targeted md Pranabesh Mandal (PhD, Bioinformatics August-2019)
Thursday, 27 January 2022
- Re: [AMBER] dihedral restraints slowing down simulation Kellon Belfon
- Re: [AMBER] dihedral restraints slowing down simulation Richard Kullmann
- Re: [AMBER] dihedral restraints slowing down simulation Carlos Simmerling
- Re: [AMBER] Regarding targeted md Carlos Simmerling
- Re: [AMBER] dihedral restraints slowing down simulation Kellon Belfon
- Re: [AMBER] dihedral restraints slowing down simulation Kellon Belfon
- Re: [AMBER] dihedral restraints slowing down simulation Richard Kullmann
- [AMBER] Calculating energies per residue pair, rather than per residue Tue
- Re: [AMBER] Calculating energies per residue pair, rather than per residue Matthew Guberman-Pfeffer
- [AMBER] Issue concerning the AMBER/TeraChem interface Jiang, Yaoyukun
- Re: [AMBER] Issue concerning the AMBER/TeraChem interface Vinicius Wilian Cruzeiro
Friday, 28 January 2022
- Re: [AMBER] Calculating energies per residue pair, rather than per residue Carlos Simmerling
- [AMBER] Torsion parameters Cenk Andac
- Re: [AMBER] Torsion parameters Karl Kirschner
- Re: [AMBER] Torsion parameters Cenk Andac
- Re: [AMBER] dihedral restraints slowing down simulation Carlos Simmerling
Monday, 31 January 2022
- Re: [AMBER] How to compute MM/PB(GB)SA with Extra Points David A Case
- Re: [AMBER] How to compute MM/PB(GB)SA with Extra Points Ray Luo
- Re: [AMBER] How to compute MM/PB(GB)SA with Extra Points Matthew Guberman-Pfeffer
- Re: [AMBER] How to compute MM/PB(GB)SA with Extra Points David A Case

Last message date: Mon Jan 31 2022 - 18:30:02 PST
Archived on: Fri Apr 26 2024 - 05:56:14 PDT

Amber Archive Jan 2022 by date