Amber Archive Oct 2021: by date

Friday, 1 October 2021
- [AMBER] buffer overflow in tleap, AmberTools21, gcc 9.3 Alessandro Contini
- Re: [AMBER] Error installing amber macOS M1 David A Case
- [AMBER] Postdoctoral fellowship Computational Drug Discovery Marawan Hussien
- [AMBER] How to reshuffle traj frames Matthew Guberman-Pfeffer
- Re: [AMBER] How to combine the coordinate and parm7 files of the glycolipid into a protein complex system neildancer
Saturday, 2 October 2021
- [AMBER] Distanced-based atom selection from the center of mass Umesh Roy
- Re: [AMBER] How to combine the coordinate and parm7 files of the glycolipid into a protein complex system David A Case
- Re: [AMBER] Distanced-based atom selection from the center of mass Daniel Roe
- Re: [AMBER] How to reshuffle traj frames Daniel Roe
- Re: [AMBER] parmed for 12-6-4 LJ (Geng Dong) Pengfei Li
- [AMBER] TI for DG when only cofactor charge changes Vaibhav Dixit
Sunday, 3 October 2021
- Re: [AMBER] How to combine the coordinate and parm7 files of the glycolipid into a protein complex system neildancer
Monday, 4 October 2021
- [AMBER] Question of Amber_ Sasaki Shiho Ohno
- [AMBER] Atomistic Simulation Center - Invitation to virtual inauguration symposium Dr. Anselm Horn
- [AMBER] Ligand is unstable in simulations Midhun K Madhu
- Re: [AMBER] Question of Amber_ Sasaki David A Case
- Re: [AMBER] Ligand is unstable in simulations David A Case
- [AMBER] How to superpose the solvated box to the original pdb structure? Gao Zhenting
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? Song, Lin
- [AMBER] FixCondaShebang Error Satya Pal Singh
Tuesday, 5 October 2021
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? Dr. Anselm Horn
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? Gao Zhenting
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? Reyes Nuñez Franco
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? Carlos Simmerling
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? David A Case
- Re: [AMBER] Cpptraj hbond criteria Daniel Roe
- Re: [AMBER] FixCondaShebang Error David A Case
- Re: [AMBER] Restart/Reference file for targeted MD Daniel Roe
- Re: [AMBER] Restart/Reference file for targeted MD Rafał Madaj
- [AMBER] Restraint COM between two proteins Mohamed Aboelnga
- Re: [AMBER] Distanced-based atom selection from the center of mass Daniel Roe
- [AMBER] Zn sim Cato, Lee
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? Gao Zhenting
- [AMBER] The silver ion parameter nali
- Re: [AMBER] Error installing amber macOS M1 Rodrigo da Silva Bitzer
- Re: [AMBER] Error installing amber macOS M1 David A Case
- Re: [AMBER] Error installing amber macOS M1 Rodrigo da Silva Bitzer
Wednesday, 6 October 2021
- [AMBER] Regarding xleap error Archana
- Re: [AMBER] Regarding xleap error Dr. Anselm Horn
- [AMBER] CPPTRAJ Rana Rehan Khalid
- Re: [AMBER] CPPTRAJ Daniel Roe
- Re: [AMBER] CPPTRAJ Rana Rehan Khalid
- Re: [AMBER] CPPTRAJ Rana Rehan Khalid
- Re: [AMBER] CPPTRAJ Rana Rehan Khalid
- [AMBER] Symmetrical voids during heating stage Nagar, Hemant
- [AMBER] Question of Amber_ Sasaki Shiho Ohno
- [AMBER] Tohoku Medical and Pharmaceutical University Sasaki　It's resolved Shiho Ohno
- Re: [AMBER] Symmetrical voids during heating stage Thomas Cheatham
- Re: [AMBER] Symmetrical voids during heating stage Thomas Cheatham
- [AMBER] parameters for ions in Amber Małgorzata Kogut
Thursday, 7 October 2021
- [AMBER] parameters for ions Małgorzata Kogut
- Re: [AMBER] parameters for ions in Amber David A Case
- [AMBER] Help with carbohydrate nomenclature Daniel Roe
- Re: [AMBER] Help with carbohydrate nomenclature Hector A. Baldoni
Friday, 8 October 2021
- [AMBER] Calculating viscosity, thermal conductivity and self-diffusion coefficient Chloe Jaiswal
- Re: [AMBER] Help with carbohydrate nomenclature Daniel Roe
- [AMBER] How to set multiple positional restraints during minimization Sadaf Rani
- Re: [AMBER] How to set multiple positional restraints during minimization Carlos Simmerling
- Re: [AMBER] [SPAM] Help with carbohydrate nomenclature Rafael Nunes
- [AMBER] Restraining the distance between two groups of residues? Gustavo Seabra
- Re: [AMBER] [SPAM] Help with carbohydrate nomenclature Daniel Roe
Saturday, 9 October 2021
- [AMBER] VDWAALS = ************* in minimization Sadaf Rani
- Re: [AMBER] VDWAALS = ************* in minimization Ben Roberts
- Re: [AMBER] VDWAALS = ************* in minimization Carlos Simmerling
- [AMBER] Rotation Matrix mohamed marzouk
Sunday, 10 October 2021
- Re: [AMBER] Rotation Matrix David A Case
- Re: [AMBER] Rotation Matrix mohamed marzouk
- [AMBER] How many complex trajectories for mmpbsa computations ? Cenk Andac
- Re: [AMBER] How many complex trajectories for mmpbsa computations ? Thomas Cheatham
- Re: [AMBER] How many complex trajectories for mmpbsa computations ? Liao
- Re: [AMBER] How many complex trajectories for mmpbsa computations ? Liao
Monday, 11 October 2021
- Re: [AMBER] Distanced-based atom selection from the center of mass Umesh Roy
- [AMBER] FixCondaShebang persists German P. Barletta
- [AMBER] How to generate different velocities for same structure during equilibration Sadaf Rani
- [AMBER] How to turn H-bonding point charges Matthew Guberman-Pfeffer
- Re: [AMBER] How to turn H-bonding point charges Carlos Simmerling
- Re: [AMBER] How to generate different velocities for same structure during equilibration Carlos Simmerling
- [AMBER] On Ion Distribution and "Replicates" Robert Molt
- Re: [AMBER] How to turn H-bonding point charges Matthew Guberman-Pfeffer
- [AMBER] Accelerated dissociation events in MD simulation by temperature increase? Liao
- Re: [AMBER] Accelerated dissociation events in MD simulation by temperature increase? Carlos Simmerling
- Re: [AMBER] Accelerated dissociation events in MD simulation by temperature increase? Matthew Guberman-Pfeffer
Tuesday, 12 October 2021
- Re: [AMBER] FixCondaShebang persists David A Case
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? David A Case
- [AMBER] How to depict Atomic Fluctuations of a specific residue Versus Frames by CPPTRAJ Maghsoud, Yazdan
Wednesday, 13 October 2021
- [AMBER] Amber20/AmberTools21 Installation Test Errors Ravi Abrol
- Re: [AMBER] Amber20/AmberTools21 Installation Test Errors David A Case
- Re: [AMBER] buffer overflow in tleap, AmberTools21, gcc 9.3 David A Case
- [AMBER] How to minimize average structure (pdb) using Amber 16 priya murugan
- Re: [AMBER] How to minimize average structure (pdb) using Amber 16 Liao
- [AMBER] How to characterize Binding Sites with cpptraj Matthew Guberman-Pfeffer
Thursday, 14 October 2021
- Re: [AMBER] FixCondaShebang persists German P. Barletta
- Re: [AMBER] Explicit water molecules in MMPBSA.py: OPC vs TIP3P Lennart Gundelach
- Re: [AMBER] Amber20/AmberTools21 Installation Test Errors Ravi Abrol
- [AMBER] parmed for two atom type with the same LJ parameters Qinghua Liao
- Re: [AMBER] Explicit water molecules in MMPBSA.py: OPC vs TIP3P David A Case
- Re: [AMBER] Problems with mm_pbsa tests David A Case
- Re: [AMBER] FixCondaShebang persists David A Case
- Re: [AMBER] FixCondaShebang persists Stephan Schott
- Re: [AMBER] How to depict Atomic Fluctuations of a specific residue Versus Frames by CPPTRAJ Daniel Roe
- Re: [AMBER] How to superpose the solvated box to the original pdb structure? Daniel Roe
- Re: [AMBER] VDWAALS = ************* in minimization Daniel Roe
- Re: [AMBER] FixCondaShebang persists David A Case
- Re: [AMBER] parmed for two atom type with the same LJ parameters Song, Lin
- Re: [AMBER] FixCondaShebang persists Stephan Schott
- Re: [AMBER] FixCondaShebang persists German P. Barletta
- Re: [AMBER] parmed for two atom type with the same LJ parameters Jason Swails
- [AMBER] Automated capping of missing loops? Brian Radak
- [AMBER] Protein-protein binding free energy MMPBSA Rana Rehan Khalid
- Re: [AMBER] FixCondaShebang persists David A Case
- Re: [AMBER] Automated capping of missing loops? David A Case
- Re: [AMBER] Protein-protein binding free energy MMPBSA David A Case
- Re: [AMBER] Problems with mm_pbsa tests Ravi Abrol
Friday, 15 October 2021
- [AMBER] calculate potential energies with imin=5 Richard Kullmann
- Re: [AMBER] Problems with mm_pbsa tests David A Case
- Re: [AMBER] calculate potential energies with imin=5 David A Case
- [AMBER] Mutation by pdb4amber mohamed marzouk
- [AMBER] MMGBSA error help Debarati DasGupta
- Re: [AMBER] Automated capping of missing loops? Brian Radak
- Re: [AMBER] FixCondaShebang persists German P. Barletta
Saturday, 16 October 2021
- Re: [AMBER] Rotation Matrix mohamed marzouk
- Re: [AMBER] FixCondaShebang persists David A Case
- Re: [AMBER] Rotation Matrix David A Case
- Re: [AMBER] Rotation Matrix mohamed marzouk
- [AMBER] Unwanted water protein interaction mohamed marzouk
- [AMBER] Regarding entropy calculations in MMPBSA.py when enthalpy is either from GBSA or PBSA? Liao
- [AMBER] cpptraj RMSD reference Mac Kevin Braza
- Re: [AMBER] cpptraj RMSD reference Mac Kevin Braza
Sunday, 17 October 2021
- [AMBER] trajectory of mutation generation (Geng Dong) 东庚
- Re: [AMBER] Unwanted water protein interaction David A Case
- Re: [AMBER] Unwanted water protein interaction mohamed marzouk
- Re: [AMBER] Regarding entropy calculations in MMPBSA.py when enthalpy is either from GBSA or PBSA? David A Case
- [AMBER] Meaning of 3D-RISM output files? Gao Zhenting
- Re: [AMBER] {SPAM?} trajectory of mutation generation (Geng Dong) Matthew Guberman-Pfeffer
- Re: [AMBER] Automated capping of missing loops? Matias Machado
Monday, 18 October 2021
- Re: [AMBER] Automated capping of missing loops? Jason Swails
- [AMBER] What is the default value of tishake Suitian Lai
- Re: [AMBER] Automated capping of missing loops? Brian Radak
- Re: [AMBER] Meaning of 3D-RISM output files? tluchko
- [AMBER] Parameters for non-standard residues Nagar, Hemant
- Re: [AMBER] Automated capping of missing loops? David A Case
- Re: [AMBER] Parameters for non-standard residues Carlos Simmerling
- Re: [AMBER] Parameters for non-standard residues David A Case
- [AMBER] How I can Remove dna form .rst files Rana Rehan Khalid
Tuesday, 19 October 2021
- Re: [AMBER] How I can Remove dna form .rst files David A Case
- [AMBER] Error with PDB4AMBER Rangarajan, Amith
- Re: [AMBER] Error with PDB4AMBER Vinicius Wilian Cruzeiro
- Re: [AMBER] Error with PDB4AMBER Rangarajan, Amith
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Rangarajan, Amith
- Re: [AMBER] Error with PDB4AMBER Dr. Anselm Horn
- Re: [AMBER] Parameters for non-standard residues Nagar, Hemant
- [AMBER] Restraining ligand for TI Delwakkada Liyanage, Senal Dinuka
Wednesday, 20 October 2021
- [AMBER] Fwd: topology file and co-ordinate file making by amber tool (gaff.dat) vivek rabha
- Re: [AMBER] Fwd: topology file and co-ordinate file making by amber tool (gaff.dat) Dr. Anselm Horn
- Re: [AMBER] Fwd: topology file and co-ordinate file making by amber tool (gaff.dat) vivek rabha
- Re: [AMBER] Fwd: topology file and co-ordinate file making by amber tool (gaff.dat) Dr. Anselm Horn
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered David A Case
- Re: [AMBER] Parameters for non-standard residues David A Case
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Rangarajan, Amith
- [AMBER] Freeze DNA during simulation. Rana Rehan Khalid
- [AMBER] Query regarding missing oxygen atom in RNA sequence Saikat Pal
- Re: [AMBER] Fwd: topology file and co-ordinate file making by amber tool (gaff.dat) vivek rabha
Thursday, 21 October 2021
- [AMBER] Ambertools18 tleap scripts not working when run on Ambertools21 Daniel Fowles
- Re: [AMBER] Ambertools18 tleap scripts not working when run on Ambertools21 Jason Swails
- Re: [AMBER] Parameters for non-standard residues Dr. Anselm Horn
- [AMBER] Query regarding not integral charge in RNA Saikat Pal
- Re: [AMBER] Query regarding not integral charge in RNA David A Case
- Re: [AMBER] Query regarding not integral charge in RNA Saikat Pal
- [AMBER] Maximizing GROMACS Throughput with Multiple Simulations per GPU Using MPS and MIG James Kress
- [AMBER] ZAFF Simulation Error Daniel Hall
- Re: [AMBER] Query regarding not integral charge in RNA David A Case
- Re: [AMBER] Rotation Matrix mohamed marzouk
Friday, 22 October 2021
- Re: [AMBER] Fwd: topology file and co-ordinate file making by amber tool (gaff.dat) Dr. Anselm Horn
- [AMBER] RMSD of residues within 3A of ligand Sadaf Rani
- Re: [AMBER] Maximizing GROMACS Throughput with Multiple Simulations per GPU Using MPS and MIG Matias Machado
- [AMBER] Amber20 benchmarks for RTX A4000 Vaibhav Dixit
- Re: [AMBER] Maximizing GROMACS Throughput with Multiple Simulations per GPU Using MPS and MIG Jason Hogrefe
- Re: [AMBER] Maximizing GROMACS Throughput with Multiple Simulations per GPU Using MPS and MIG James Kress
- [AMBER] Query regarding ZAFF Modeling Tutorial Saikat Pal
Saturday, 23 October 2021
- [AMBER] How can I download amber 18？ Hecate Me
- [AMBER] Fwd: Ambertools21 installation problems Victor Nazarychev
- [AMBER] LINMIN ERROR Sumon Naskar
Sunday, 24 October 2021
- Re: [AMBER] How can I download amber 18？ David A Case
- Re: [AMBER] Fwd: Ambertools21 installation problems David A Case
- Re: [AMBER] LINMIN ERROR David A Case
- [AMBER] reasonable GIST griddim values Christian Seitz
- Re: [AMBER] Fwd: Ambertools21 installation problems David A Case
- [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 priya murugan
- [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 priya murugan
- [AMBER] Can I used AMBER 16 CPPTRAJ to perform dynamic cross correlation map? priya murugan
Monday, 25 October 2021
- [AMBER] How is correlation computed in cpptraj Matthew Guberman-Pfeffer
- Re: [AMBER] Fwd: Ambertools21 installation problems Victor Nazarychev
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 Dr. Anselm Horn
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 priya murugan
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 Hector A. Baldoni
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 priya murugan
- Re: [AMBER] Fwd: Ambertools21 installation problems David A Case
- Re: [AMBER] Can I used AMBER 16 CPPTRAJ to perform dynamic cross correlation map? Daniel Roe
- Re: [AMBER] Fwd: Ambertools21 installation problems Victor Nazarychev
- Re: [AMBER] reasonable GIST griddim values Daniel Roe
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 Adrian Roitberg
- Re: [AMBER] How is correlation computed in cpptraj Matthew Guberman-Pfeffer
- [AMBER] Several postdoctoral positions available in EU Jan Brezovsky
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 James Kress
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 Adrian Roitberg
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 Robert Molt
- [AMBER] bug in pmemd/src/cuda/gpu.cpp line 2852? Thomas Zeiser
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 James Kress
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 Robert Molt
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 Thomas Cheatham
- Re: [AMBER] bug in pmemd/src/cuda/gpu.cpp line 2852? David A Case
- [AMBER] Reg: Cpptraj-Hierarchical Agglomerative Reference paper for methodology and result analysis Lara rajam
- Re: [AMBER] Can I used AMBER 16 CPPTRAJ to perform dynamic cross correlation map? priya murugan
- Re: [AMBER] bug in pmemd/src/cuda/gpu.cpp line 2852? thomas.zeiser.rrze.uni-erlangen.de
Tuesday, 26 October 2021
- Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 priya murugan
- [AMBER] Amber21 installation using Docker will be Parallel or Serial? Erdem Yeler
- [AMBER] Regarding Amber20 installation Rajarshi Roy
- [AMBER] Organometallic RESP charge derivation for use with AmberTools Sam Walsworth (Researcher)
- Re: [AMBER] bug in pmemd/src/cuda/gpu.cpp line 2852? Kellon Belfon
- [AMBER] Atom type does not shown up in PARMCHK.DAT Rohanizeidanlou, Sahar
- Re: [AMBER] Query regarding ZAFF Modeling Tutorial Maria Nagan
- Re: [AMBER] ZAFF Simulation Error Maria Nagan
- Re: [AMBER] Organometallic RESP charge derivation for use with AmberTools Vaibhav Dixit
Wednesday, 27 October 2021
- [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces Umesh Roy
- Re: [AMBER] Atom type does not shown up in PARMCHK.DAT Dr. Anselm Horn
- Re: [AMBER] Fwd: Ambertools21 installation problems Victor Nazarychev
- Re: [AMBER] Regarding Amber20 installation David A Case
- Re: [AMBER] Regarding Amber20 installation Rajarshi Roy
- [AMBER] How to minimize a pdb format file in Amber 16 priya murugan
Thursday, 28 October 2021
- [AMBER] How to handle Ca2+ ion with 8 coordination Geometry in lectin domain for MD simulation. Bhat Zahoor
- [AMBER] Regarding area calculation of protein cavity Athena N
- Re: [AMBER] Regarding area calculation of protein cavity Dr. Anselm Horn
- Re: [AMBER] How to handle Ca2+ ion with 8 coordination Geometry in lectin domain for MD simulation. Dr. Anselm Horn
- Re: [AMBER] How to minimize a pdb format file in Amber 16 Hector A. Baldoni
- Re: [AMBER] How to minimize a pdb format file in Amber 16 Carlos Simmerling
- [AMBER] mm_pbsa and MMPBSA.py zmatovic.kg.ac.rs
- Re: [AMBER] Regarding area calculation of protein cavity Athena N
- [AMBER] Multiple Replicate Trajectories Li,Haoxi
- Re: [AMBER] mm_pbsa and MMPBSA.py Dr. Anselm Horn
- Re: [AMBER] Regarding area calculation of protein cavity Carlos Simmerling
- Re: [AMBER] mm_pbsa and MMPBSA.py zmatovic.kg.ac.rs
- Re: [AMBER] How to minimize a pdb format file in Amber 16 priya murugan
- Re: [AMBER] Regarding Amber20 installation Dow Hurst
Friday, 29 October 2021
- [AMBER] Wrong Angel Given by Cpptraj? Matthew Guberman-Pfeffer
- Re: [AMBER] Amber21 installation using Docker will be Parallel or Serial? Jason Swails
- Re: [AMBER] {SPAM?} trajectory of mutation generation (Geng Dong) Jason Swails
- [AMBER] Constant pH MD simulation Divya Rai
- Re: [AMBER] Constant pH MD simulation Jason Swails
- Re: [AMBER] Constant pH MD simulation Vinicius Wilian Cruzeiro
- Re: [AMBER] Regarding Amber20 installation David A Case
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces David A Case
- [AMBER] weired Ligand conformation during simulation Sadaf Rani
- [AMBER] unable to get response from mailing list Sadaf Rani
Saturday, 30 October 2021
- Re: [AMBER] weired Ligand conformation during simulation David A Case
- Re: [AMBER] unable to get response from mailing list David A Case
- Re: [AMBER] unable to get response from mailing list Carlos Simmerling
- [AMBER] Fwd: Constant pH MD simulation Divya Rai
- [AMBER] Problem measuring angle in CPPTRAJ Matthew Guberman-Pfeffer
- [AMBER] How to Compare RDFs for different systems Matthew Guberman-Pfeffer
- [AMBER] MMPBSA (Unable to read script file because of error: invalid option argument "-O") Rana Rehan Khalid
Sunday, 31 October 2021
- Re: [AMBER] weired Ligand conformation during simulation Sadaf Rani
- Re: [AMBER] weired Ligand conformation during simulation David A Case

Last message date: Sun Oct 31 2021 - 13:30:02 PDT
Archived on: Wed Oct 29 2025 - 05:56:13 PDT

Amber Archive Oct 2021 by date