Amber Archive Dec 2021: by date

Wednesday, 1 December 2021
- [AMBER] A bug in phishi Amber20? 余青芬
- [AMBER] bond equilibrium achieved with sander but not with pmemd, Amber 20 Qinghua Liao
- Re: [AMBER] A bug in phishi Amber20? Daniel Roe
- Re: [AMBER] Problems with RMSD of different proteins. Daniel Roe
- Re: [AMBER] How to interpret clustering Daniel Roe
- Re: [AMBER] closest ions radiation distribution Daniel Roe
- Re: [AMBER] Equilibrate and Production Run Membrane-protein complex Daniel Roe
- Re: [AMBER] Protein in mixed of solvents Daniel Roe
- Re: [AMBER] Summit compile and "Attempted to read inpcrd as a NetCDF restart file, but failed" Daniel Roe
- Re: [AMBER] Dynamic cross correlation matrices in AMBER20 Daniel Roe
- Re: [AMBER] Dynamic cross correlation matrices in AMBER20 Debarati DasGupta
- Re: [AMBER] GIST: Entropy calculations Daniel Roe
- Re: [AMBER] How to generate mol2 file with topology and crd file? Daniel Roe
- Re: [AMBER] water box corrupted by minimization Daniel Roe
- Re: [AMBER] Amber calculate RMSF Daniel Roe
- Re: [AMBER] Reg: Cpptraj-Hierarchical Agglomerative Reference paper for methodology and result analysis Daniel Roe
- Re: [AMBER] How is correlation computed in cpptraj Daniel Roe
- Re: [AMBER] RMSD of residues within 3A of ligand Daniel Roe
- Re: [AMBER] Equilibrate and Production Run Membrane-protein complex King Wu
- [AMBER] size (info) difference in traj file format: nc vs mdcrd King Wu
- Re: [AMBER] open mpi compiler error Ayesha Fatima
- Re: [AMBER] size (info) difference in traj file format: nc vs mdcrd Thomas Cheatham
- [AMBER] TiMergeError: Cannot have dihedral cross through softcore region. Saikat Pal
- Re: [AMBER] Some errors for the membrane system Monsurat M. Lawal
- Re: [AMBER] Equilibrate and Production Run Membrane-protein complex Dickson, Callum
- [AMBER] Missing DNA base pair in cpptraj analysis Abhilash J
- Re: [AMBER] installation error amber 18 in ubuntu 20.04 David A Case
- [AMBER] Non-periodic boundry condition simulation Nagar, Hemant
- Re: [AMBER] Missing DNA base pair in cpptraj analysis Abhilash J
- [AMBER] Installation error amber 20 in ubuntu 20.04 Joanna Michelle E. Chua
Thursday, 2 December 2021
- [AMBER] Fortran runtime error during 1D-RISM analysis to generate .xvv file Alexis Azucena
- [AMBER] Zn ion coordination Aravind R
- Re: [AMBER] Installation error amber 20 in ubuntu 20.04 David A Case
- Re: [AMBER] Fortran runtime error during 1D-RISM analysis to generate .xvv file David A Case
- [AMBER] TiMergeError: Cannot have dihedral cross through softcore region. Saikat Pal
- Re: [AMBER] TiMergeError: Cannot have dihedral cross through softcore region. Carlos Simmerling
- Re: [AMBER] TiMergeError: Cannot have dihedral cross through softcore region. Saikat Pal
- Re: [AMBER] Fortran runtime error during 1D-RISM analysis to generate .xvv file tluchko
- [AMBER] Amber Installation Error Suguna Sakkiah
- Re: [AMBER] Amber Installation Error David A Case
- Re: [AMBER] Fortran runtime error during 1D-RISM analysis to generate .xvv file Alexis Azucena
- [AMBER] numpy error with pdb4amber on cluster Vaibhav Dixit
Friday, 3 December 2021
- [AMBER] problem loading the trajectory files in vmd ankita mehta
- [AMBER] Problem loading crd file in vmd ankita mehta
- Re: [AMBER] problem loading the trajectory files in vmd Priya Dey
- Re: [AMBER] problem loading the trajectory files in vmd Mohamed Aboelnga
- Re: [AMBER] problem loading the trajectory files in vmd Mohamed Aboelnga
- Re: [AMBER] numpy error with pdb4amber on cluster David A Case
- Re: [AMBER] problem loading the trajectory files in vmd Carlos Simmerling
- Re: [AMBER] problem loading the trajectory files in vmd Daniel Roe
Saturday, 4 December 2021
- [AMBER] Error during 1D-RISM run Alexis Azucena
- [AMBER] Mmpbsa inp=1 or inp=2 Fabian Glaser
- Re: [AMBER] Mmpbsa inp=1 or inp=2 Fabian Glaser
- [AMBER] What if MM Energy > QM Energy Even Vn=0 Erdem Yeler
- Re: [AMBER] What if MM Energy > QM Energy Even Vn=0 David A Case
- [AMBER] run_cmake error for installing the GPU version of Amber20 jinfeng liu
Sunday, 5 December 2021
- Re: [AMBER] run_cmake error for installing the GPU version of Amber20 David A Case
- [AMBER] Addendum on problems about finding CUDA David A Case
- Re: [AMBER] Mmpbsa inp=1 or inp=2 David A Case
- Re: [AMBER] Error during 1D-RISM run David A Case
- [AMBER] Meaning of "Multiple 'e' in NUMBER-like thing" Matthew Guberman-Pfeffer
- Re: [AMBER] run_cmake error for installing the GPU version of Amber20 jinfeng liu
- [AMBER] about RAMD 田佳琪
Monday, 6 December 2021
- Re: [AMBER] run_cmake error for installing the GPU version of Amber20 Tru Huynh
- Re: [AMBER] problem loading the trajectory files in vmd ankita mehta
- Re: [AMBER] problem loading the trajectory files in vmd Carlos Simmerling
- Re: [AMBER] about RAMD Charles Lin
- Re: [AMBER] problem loading the trajectory files in vmd Matias Machado
- [AMBER] Error with MMPBSA Kehinde Idowu
Tuesday, 7 December 2021
- Re: [AMBER] about RAMD 田佳琪
- Re: [AMBER] Mmpbsa inp=1 or inp=2 Fabian Glaser
- Re: [AMBER] Error with MMPBSA David A Case
- Re: [AMBER] Error with MMPBSA Monsurat M. Lawal
- Re: [AMBER] Zn ion coordination Aravind R
- Re: [AMBER] Error with MMPBSA Debarati DasGupta
- Re: [AMBER] Error with MMPBSA Kehinde Idowu
- Re: [AMBER] about RAMD Charles Lin
- [AMBER] Error for installing the GPU version of Amber20 jinfeng liu
Wednesday, 8 December 2021
- [AMBER] GAFF2 "ho" atoms have non-bonded 0 Stefan Doerr
- Re: [AMBER] GAFF2 "ho" atoms have non-bonded 0 David A Case
- Re: [AMBER] Error with MMPBSA Monsurat M. Lawal
- Re: [AMBER] Error for installing the GPU version of Amber20 David A Case
- Re: [AMBER] Mmpbsa inp=1 or inp=2 Fabian Glaser
Friday, 10 December 2021
- [AMBER] install error for GPU version of Amber20 on A100 GPU card jinfeng liu
- Re: [AMBER] install error for GPU version of Amber20 on A100 GPU card David A Case
- Re: [AMBER] install error for GPU version of Amber20 on A100 GPU card jinfeng liu
Saturday, 11 December 2021
- [AMBER] Electrostatic energy in TI at lambda=1 for a toy system Ali Morshedi
- [AMBER] Error with Zn ion Coordination Aravind R
- [AMBER] README script from CHARMM-GUI to run PMEDE.CUDA King Wu
- Re: [AMBER] README script from CHARMM-GUI to run PMEDE.CUDA David A Case
- Re: [AMBER] numpy error with pdb4amber on cluster Vaibhav Dixit
Sunday, 12 December 2021
- Re: [AMBER] Error with Zn ion Coordination Maria Nagan
- [AMBER] permission error installing amber20 Vaibhav Dixit
Monday, 13 December 2021
- Re: [AMBER] numpy error with pdb4amber on cluster David A Case
- Re: [AMBER] GAFF2 "ho" atoms have non-bonded 0 Stefan Doerr
- Re: [AMBER] What if MM Energy > QM Energy Even Vn=0 David Cerutti
- Re: [AMBER] How to add an amidated residue at the C-terminal in AMBER tleap ? Yen Nguyen
- [AMBER] Neutralizing a protein with unknown charge? Gustavo Seabra
- [AMBER] Q-Chem and GPU use James Kress
- Re: [AMBER] Neutralizing a protein with unknown charge? Carlos Simmerling
- Re: [AMBER] Neutralizing a protein with unknown charge? Debarati DasGupta
- Re: [AMBER] Neutralizing a protein with unknown charge? Matias Machado
- [AMBER] Peptide's charge is not 0 when getting parm7 and rst7 files Yen Nguyen
- Re: [AMBER] Peptide's charge is not 0 when getting parm7 and rst7 files Carlos Simmerling
- Re: [AMBER] Neutralizing a protein with unknown charge? Gustavo Seabra
- Re: [AMBER] Peptide's charge is not 0 when getting parm7 and rst7 files Carlos Simmerling
- Re: [AMBER] Peptide's charge is not 0 when getting parm7 and rst7 files Yen Nguyen
- Re: [AMBER] Peptide's charge is not 0 when getting parm7 and rst7 files Carlos Simmerling
- Re: [AMBER] Peptide's charge is not 0 when getting parm7 and rst7 files Yen Nguyen
- [AMBER] Thermodynamic integration in tutorial 9 鱼翔
- [AMBER] CHAMBER prmtops cannot be used with NMODE 周丽萍
Tuesday, 14 December 2021
- [AMBER] Old Amber Force Fields Niransha Kumarachchi
- Re: [AMBER] Old Amber Force Fields Carlos Simmerling
- [AMBER] Question about build Amber20 with Intel compiler 2019 Chen, Guoquan
- [AMBER] Parallel test stuck at Run.dhfr.noboxinfo Yu Chen
- Re: [AMBER] Error for installing the GPU version of Amber20 Joanna Michelle E. Chua
Wednesday, 15 December 2021
- [AMBER] loadpdb and SSBOND Alan
- [AMBER] tleap: tab complete, highlight, cmd history etc. Alan
- [AMBER] ISSUE About Abmer prep file can not recoganized by TAO package 辛志宏
- Re: [AMBER] Parallel test stuck at Run.dhfr.noboxinfo David A Case
- Re: [AMBER] Parallel test stuck at Run.dhfr.noboxinfo Yu Chen
- [AMBER] amber pmemd.cuda for implicit solvent simulations Prithviraj Nandigrami
- [AMBER] Non periodic system in Amber Nagar, Hemant
- [AMBER] Inquiry about an error message when I constructing the frcmod file for my organometallic complex Yi Ren
Thursday, 16 December 2021
- Re: [AMBER] numpy error with pdb4amber on cluster Vaibhav Dixit
- Re: [AMBER] numpy error with pdb4amber on cluster David A Case
- Re: [AMBER] loadpdb and SSBOND David A Case
- [AMBER] How to restart a MMPBSA job Sadaf Rani
- Re: [AMBER] numpy error with pdb4amber on cluster Vaibhav Dixit
- [AMBER] Help parameterizing iron citrate Matthew Guberman-Pfeffer
Friday, 17 December 2021
- [AMBER] Improving our options for pre-compiled AmberTools? David A Case
- Re: [AMBER] Question about build Amber20 with Intel compiler 2019 David A Case
- [AMBER] second structure Sepideh Jafari
- [AMBER] Amber20 installation error on Centos 7 Suguna Sakkiah
- Re: [AMBER] second structure Carlos Simmerling
- Re: [AMBER] Improving our options for pre-compiled AmberTools? Matias Machado
- Re: [AMBER] Zn ion coordination Pengfei Li
- Re: [AMBER] Amber -log4J impact ? David A Case
- [AMBER] Adding atom types to gaff.dat Sam Walsworth (Researcher)
Saturday, 18 December 2021
- Re: [AMBER] Adding atom types to gaff.dat David A Case
Sunday, 19 December 2021
- [AMBER] Atom types and atom order of lib files and pdb files Sam Walsworth (Researcher)
Monday, 20 December 2021
- [AMBER] Hydrogen Bonding Analysis Huimin Tian
- Re: [AMBER] Atom types and atom order of lib files and pdb files Carlos Simmerling
- Re: [AMBER] Atom types and atom order of lib files and pdb files Sam Walsworth (Researcher)
- Re: [AMBER] Hydrogen Bonding Analysis Daniel Roe
- Re: [AMBER] Amber20 installation error on Centos 7 David A Case
- [AMBER] Constant PH simulations Sruthi Sudhakar
- Re: [AMBER] Constant PH simulations Carlos Simmerling
- [AMBER] CPPTRAJ Segmentation Fault with modified topology file Chris Lee
- Re: [AMBER] CPPTRAJ Segmentation Fault with modified topology file Daniel Roe
- [AMBER] Amber20 installation error - Centos 7 Suguna Sakkiah
- Re: [AMBER] CPPTRAJ Segmentation Fault with modified topology file Chris Lee
- [AMBER] Error running TI with pmemd.cuda: "Error: an illegal memory access was encountered launching kernel kClearTIKinEnergy_kernel" Ali Morshedi
- Re: [AMBER] CPPTRAJ Segmentation Fault with modified topology file Daniel Roe
- Re: [AMBER] Amber20 installation error - Centos 7 David A Case
- Re: [AMBER] Error running TI with pmemd.cuda: "Error: an illegal memory access was encountered launching kernel kClearTIKinEnergy_kernel" Rafał Madaj
Tuesday, 21 December 2021
- Re: [AMBER] Error running TI with pmemd.cuda: "Error: an illegal memory access was encountered launching kernel kClearTIKinEnergy_kernel" Ali Morshedi
- Re: [AMBER] Atom types and atom order of lib files and pdb files Carlos Simmerling
- Re: [AMBER] amber20 - test suite picks up the wrong libgfortran Mark Dixon
- Re: [AMBER] Adding atom types to gaff.dat Pengfei Li
- [AMBER] Amber installation error on Centos 7 Suguna Sakkiah
- Re: [AMBER] Amber installation error on Centos 7 David A Case
- [AMBER] Amber20 installation error on Centos 7 Suguna Sakkiah
- [AMBER] Problems with mdgx - torsional parameters fitting Casalini Tommaso
- [AMBER] Creating library files - optimised or docked structure? Sam Walsworth (Researcher)
- [AMBER] Thermodynamic integration in tutorial 9 鱼翔
- Re: [AMBER] Amber20 installation error on Centos 7 David A Case
Wednesday, 22 December 2021
- Re: [AMBER] Amber20 installation error on Centos 7 Suguna Sakkiah
- [AMBER] Issue with defining angle parameters in frcmod files Sam Walsworth (Researcher)
- Re: [AMBER] Issue with defining angle parameters in frcmod files Carlos Simmerling
- [AMBER] Query regarding minimization in AMBER 20 Arooma Maryam
- Re: [AMBER] Query regarding minimization in AMBER 20 Carlos Simmerling
- [AMBER] prmtop file generated with CLOSEST in cpptraj James Kress
- Re: [AMBER] Issue with defining angle parameters in frcmod files Sam Walsworth (Researcher)
- Re: [AMBER] Amber20 installation error on Centos 7 David A Case
- [AMBER] Problems about quasi-harmonic 周丽萍
- [AMBER] Parameters for Boron nitride Rituparna Roy
Thursday, 23 December 2021
- Re: [AMBER] prmtop file generated with CLOSEST in cpptraj Daniel Roe
- [AMBER] Handling new atom types - bonded Sam Walsworth (Researcher)
- [AMBER] Call for papers - 17th German Conference on Cheminformatics and EuroSAMPL Satellite Workshop, May 8 -12, 2022 in Garmisch-Partenkirchen/Germany Guessregen, Stefan /DE
- [AMBER] Frequency unit used for Oscillating electric field Surajit Kalita
- Re: [AMBER] Amber20 installation error on Centos 7 Suguna Sakkiah
- Re: [AMBER] prmtop file generated with CLOSEST in cpptraj James Kress
- [AMBER] Adjust system in certain axis mohamed marzouk
Friday, 24 December 2021
- Re: [AMBER] Amber20 installation error on Centos 7 David A Case
- Re: [AMBER] Amber20 installation error on Centos 7 Suguna Sakkiah
- [AMBER] Amber20 CUDA installation error Centos 7 Suguna Sakkiah
- Re: [AMBER] Amber20 CUDA installation error Centos 7 David A Case
- [AMBER] How to build one metal ions surrounding with two ligands by MCPB.py ning
Saturday, 25 December 2021
- [AMBER] Non-standard residue parameterization quesitons Matthew Guberman-Pfeffer
- [AMBER] MCPB, how to treat protein-attached Ru-dye Matthew Guberman-Pfeffer
Sunday, 26 December 2021
- [AMBER] Extending constant pH to additional titratable groups 王金玉
- [AMBER] CUDA installation error - CENTOS 7 Suguna Sakkiah
- Re: [AMBER] CUDA installation error - CENTOS 7 David A Case
- Re: [AMBER] scientific issue Alexander Izvorski
- [AMBER] DE Shaw RNA parameters error Alexander Izvorski
- [AMBER] TIP4PD water box error Alexander Izvorski
Tuesday, 28 December 2021
- [AMBER] Ligand problem in system preparation Ch Bilal
- [AMBER] Problem in installation Guodong
- [AMBER] How to generate coordinate and parameter files for OXY bind with copper ions in the protein structure 辛志宏
- [AMBER] what is origin in DX from 3DRISM angad sharma
- Re: [AMBER] Ligand problem in system preparation David A Case
- Re: [AMBER] Problem in installation David A Case
- [AMBER] Li salt parameterisation issue Damiano Spadoni
- [AMBER] 【Error on testing benz_water_md.reaxff and openMPI】 Shang-Wei Li (TMU)
- [AMBER] Non-standard residue parameterization questions Matthew Guberman-Pfeffer
Wednesday, 29 December 2021
- Re: [AMBER] Non-standard residue parameterization questions Dr. Anselm Horn
- [AMBER] amber docker container Fabian Glaser
- Re: [AMBER] amber docker container Carlos Simmerling
- Re: [AMBER] 【Error on testing benz_water_md.reaxff and openMPI】 David A Case
- Re: [AMBER] Non-standard residue parameterization questions Matthew Guberman-Pfeffer
- [AMBER] Advice on Simulated Annealing Matthew Guberman-Pfeffer
- Re: [AMBER] Advice on Simulated Annealing Carlos Simmerling
- Re: [AMBER] 【Error on testing benz_water_md.reaxff and openMPI】 David A Case
- Re: [AMBER] Advice on Simulated Annealing David A Case
Thursday, 30 December 2021
- [AMBER] A10 cards Fabian Glaser
- Re: [AMBER] A10 cards Jason Hogrefe
- Re: [AMBER] Advice on Simulated Annealing Matthew Guberman-Pfeffer
- Re: [AMBER] Advice on Simulated Annealing Hector A. Baldoni
- Re: [AMBER] Advice on Simulated Annealing Matthew Guberman-Pfeffer
- [AMBER] MCPB, how to treat protein-attached Ru-dye Matthew Guberman-Pfeffer
- Re: [AMBER] what is origin in DX from 3DRISM tluchko
- [AMBER] Dihedral restraint on a C=N double bond Liao
- Re: [AMBER] Dihedral restraint on a C=N double bond Carlos Simmerling
- Re: [AMBER] Dihedral restraint on a C=N double bond Liao
- [AMBER] sqm performance: does it run in parallel? Alan
Friday, 31 December 2021
- Re: [AMBER] sqm performance: does it run in parallel? David A Case

Last message date: Fri Dec 31 2021 - 05:30:02 PST
Archived on: Fri Apr 26 2024 - 05:56:13 PDT

Amber Archive Dec 2021 by date