Amber Archive Sep 2021: by date

Wednesday, 1 September 2021
- [AMBER] GIST with cosolvents like acetonitrile, ethanol instead of water Debarati DasGupta
- [AMBER] Does AmberTools21 have parameters for I atom? Ming Tang
- Re: [AMBER] Does AmberTools21 have parameters for I atom? Matthew Guberman-Pfeffer
- Re: [AMBER] Does AmberTools21 have parameters for I atom? Ming Tang
- Re: [AMBER] Does AmberTools21 have parameters for I atom? Matthew Guberman-Pfeffer
- Re: [AMBER] Does AmberTools21 have parameters for I atom? Ming Tang
Thursday, 2 September 2021
- [AMBER] how to change residue number of several residues in AMBER trajectories Ming Tang
- Re: [AMBER] how to change residue number of several residues in AMBER trajectories Dr. Anselm Horn
- [AMBER] Hydrogen atoms with negative RESP charges from Antechamber 库米尔
- [AMBER] Esander and multiple topologies Matthew Guberman-Pfeffer
Friday, 3 September 2021
- Re: [AMBER] Esander and multiple topologies Daniel Roe
Saturday, 4 September 2021
- [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 wangwei1669
- Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 David A Case
Sunday, 5 September 2021
- Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 wangwei1669
- Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 wangwei1669
- [AMBER] REMD using multiple gpus jinfeng liu
- Re: [AMBER] REMD using multiple gpus Carlos Simmerling
- [AMBER] Restart Henry Green
- [AMBER] Restart Henry Green
- [AMBER] Restart Henry Green
- [AMBER] Restart Henry Green
Monday, 6 September 2021
- [AMBER] How to print out implicit solvent charges? Matthew Guberman-Pfeffer
- Re: [AMBER] How to print out implicit solvent charges? Carlos Simmerling
- Re: [AMBER] How to print out implicit solvent charges? Matthew Guberman-Pfeffer
- Re: [AMBER] How to print out implicit solvent charges? David A Case
- Re: [AMBER] Restart Henry Green
- Re: [AMBER] Restart Dr. Anselm Horn
- Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 David A Case
- Re: [AMBER] Problem with metalpdb2mol2.py script Pengfei Li
- Re: [AMBER] iron-sulfur clusters parameters Pengfei Li
- Re: [AMBER] Suggestions for Mn3O4 Pengfei Li
- Re: [AMBER] how to set distance restraints in amber Pengfei Li
- Re: [AMBER] Maximum coordination exceeded Pengfei Li
- Re: [AMBER] How to set a replusive force between two drug molecules or two atoms. Pengfei Li
- [AMBER] Restart Henry Green
Tuesday, 7 September 2021
- Re: [AMBER] How to set a replusive force between two drug molecules or two atoms. neildancer
- [AMBER] atom type issue in tleap with ff-nucleic-OL15 Aliakbartehrani Zahra
- [AMBER] Positional restraints in thermodynamic integration 임호철
- Re: [AMBER] how to set distance restraints in amber Daniel Roe
- Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 wangwei1669
Wednesday, 8 September 2021
- [AMBER] Positional restraints in thermodynamic integration LEO LIM
- Re: [AMBER] Positional restraints in thermodynamic integration Carlos Simmerling
- [AMBER] Explicit water molecules in MMPBSA.py: OPC vs TIP3P Lennart Gundelach
- [AMBER] antechamber raises Segmetation fault yinchaofan
- Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 David A Case
- Re: [AMBER] atom type issue in tleap with ff-nucleic-OL15 David A Case
- Re: [AMBER] Explicit water molecules in MMPBSA.py: OPC vs TIP3P Ray Luo
- [AMBER] GIST question Reyes Nuñez Franco
- Re: [AMBER] How to print out implicit solvent charges? Matthew Guberman-Pfeffer
- Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 wangwei1669
Thursday, 9 September 2021
- Re: [AMBER] GIST question Franz Waibl
- Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 David A Case
- [AMBER] ModuleNotFoundError: No module named 'alamdcrd' Sadaf Rani
- Re: [AMBER] Restart David A Case
- [AMBER] TI simulation for ligand vanishing Delwakkada Liyanage, Senal Dinuka
- Re: [AMBER] ModuleNotFoundError: No module named 'alamdcrd' David A Case
- Re: [AMBER] Positional restraints in thermodynamic integration Carlos Simmerling
Friday, 10 September 2021
- [AMBER] guv output file format Priya Dey
- Re: [AMBER] guv output file format David A Case
- Re: [AMBER] Positional restraints in thermodynamic integration LEO LIM
- [AMBER] How to compute pairwise interaction between masks Matthew Guberman-Pfeffer
Sunday, 12 September 2021
- [AMBER] [Amber] gbnsr6 doesn't calculate VDWAALS Rohanizeidanlou, Sahar
Monday, 13 September 2021
- Re: [AMBER] How to compute pairwise interaction between masks Dr. Anselm Horn
- Re: [AMBER] How to compute pairwise interaction between masks Matthew Guberman-Pfeffer
- Re: [AMBER] GIST question Reyes Nuñez Franco
- Re: [AMBER] Amber20 installation, Amber.pip file broken Oscar Conchillo-Solé
- [AMBER] PARMED Charmber User Warning Quesiton Matthew Guberman-Pfeffer
- Re: [AMBER] How to compute pairwise interaction between masks Debarati DasGupta
- Re: [AMBER] Amber20 installation, Amber.pip file broken Oscar Conchillo-Solé
- Re: [AMBER] [Amber] gbnsr6 doesn't calculate VDWAALS David A Case
- Re: [AMBER] Amber20 installation, Amber.pip file broken David A Case
- Re: [AMBER] How to compute pairwise interaction between masks Dr. Anselm Horn
- Re: [AMBER] How to compute pairwise interaction between masks Dr. Anselm Horn
- [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol ARITRA MITRA
- Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol ARITRA MITRA
- Re: [AMBER] Amber20 installation, Amber.pip file broken Oscar Conchillo-Solé
- Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol David A Case
- Re: [AMBER] Amber20 installation, Amber.pip file broken David A Case
- Re: [AMBER] How to compute pairwise interaction between masks Matthew Guberman-Pfeffer
Tuesday, 14 September 2021
- [AMBER] Zinc is escaping position restraint Debostuti Ghoshdastidar
- Re: [AMBER] Zinc is escaping position restraint Carlos Simmerling
- Re: [AMBER] Amber20 installation, Amber.pip file broken Oscar Conchillo-Solé
- Re: [AMBER] GIST question Franz Waibl
- Re: [AMBER] PARMED Charmber User Warning Quesiton Jason Swails
- Re: [AMBER] PARMED Charmber User Warning Quesiton Matthew Guberman-Pfeffer
- Re: [AMBER] Zinc is escaping position restraint Elvis A F Martis
Wednesday, 15 September 2021
- [AMBER] Problem with AMBER20 aMD tutorial Michael Shokhen
- Re: [AMBER] GIST question Reyes Nuñez Franco
- [AMBER] ambermd.org SSL Certificate Ryan Novosielski
- Re: [AMBER] ambermd.org SSL Certificate David A Case
- [AMBER] Lipid21 Alyemni, Saleh
Thursday, 16 September 2021
- Re: [AMBER] Lipid21 Stephan Schott
- [AMBER] Non-integer pbsa surface charge? Matthew Guberman-Pfeffer
- Re: [AMBER] Non-integer pbsa surface charge? David A Case
- Re: [AMBER] Non-integer pbsa surface charge? Matthew Guberman-Pfeffer
- [AMBER] Error while running make install Rodrigo da Silva Bitzer
- [AMBER] Use Amber12 with cuda Rana Rehan Khalid
Friday, 17 September 2021
- Re: [AMBER] Use Amber12 with cuda Dr. Anselm Horn
- Re: [AMBER] Error while running make install David A Case
- Re: [AMBER] Error while running make install Rodrigo da Silva Bitzer
- Re: [AMBER] GIST question Daniel Roe
- Re: [AMBER] Problem with AMBER20 aMD tutorial Daniel Roe
- Re: [AMBER] Error while running make install David A Case
- [AMBER] New In CPPTRAJ (September 2021) Daniel Roe
- [AMBER] Is AMBER multithreaded? James Kress
- Re: [AMBER] Is AMBER multithreaded? David A Case
Saturday, 18 September 2021
- Re: [AMBER] Non-integer pbsa surface charge? David A Case
- [AMBER] Setting compiler flags w/cmake build? Amber20/AmberTools21 Ryan Novosielski
Sunday, 19 September 2021
- Re: [AMBER] cpptraj has stopped working Mike Mazanetz
- Re: [AMBER] Setting compiler flags w/cmake build? Amber20/AmberTools21 David A Case
- Re: [AMBER] cpptraj has stopped working David A Case
- Re: [AMBER] cpptraj has stopped working Daniel Roe
- Re: [AMBER] Setting compiler flags w/cmake build? Amber20/AmberTools21 Ryan Novosielski
- Re: [AMBER] Setting compiler flags w/cmake build? Amber20/AmberTools21 Ryan Novosielski
- [AMBER] cpptraj has stopped working Mike Mazanetz
Monday, 20 September 2021
- Re: [AMBER] cpptraj has stopped working Daniel Roe
- [AMBER] NVIDIA RTX3080s or 3090s for servers? Kevin Hauser
Tuesday, 21 September 2021
- [AMBER] Restart/Reference file for targeted MD Rafał Madaj
- [AMBER] Reduced Units Chloe Jaiswal
Wednesday, 22 September 2021
- Re: [AMBER] Reduced Units David A Case
- Re: [AMBER] Problem with AMBER20 aMD tutorial Michael Shokhen
- [AMBER] How to set up a simulation keeping crystal waters in the binding site Sadaf Rani
- Re: [AMBER] How to set up a simulation keeping crystal waters in the binding site Carlos Simmerling
- [AMBER] Cpptraj hbond criteria Veenis, Andrew Jay
Thursday, 23 September 2021
- Re: [AMBER] GIST question Reyes Nuñez Franco
- [AMBER] Question regarding LIE calculations vs explicit solvent enthalpy calculations? Liao
- [AMBER] Error installing amber macOS M1 Rodrigo da Silva Bitzer
- Re: [AMBER] Error installing amber macOS M1 David A Case
- Re: [AMBER] Question regarding LIE calculations vs explicit solvent enthalpy calculations? David A Case
- Re: [AMBER] Question regarding LIE calculations vs explicit solvent enthalpy calculations? Liao
- Re: [AMBER] Question regarding LIE calculations vs explicit solvent enthalpy calculations? Liao
Friday, 24 September 2021
- [AMBER] Custom Residue frcmod Chloe Jaiswal
- Re: [AMBER] Custom Residue frcmod David A Case
- [AMBER] Co-ordinates switching in CPPTRAJ output Annabelle Hartt
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output Carlos Simmerling
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output Daniel Roe
- Re: [AMBER] Question regarding LIE calculations vs explicit solvent enthalpy calculations? Debarati DasGupta
- Re: [AMBER] Error installing amber macOS M1 Rodrigo da Silva Bitzer
- Re: [AMBER] Error installing amber macOS M1 David A Case
Saturday, 25 September 2021
- [AMBER] Can a PDB be loaded directly into cpptraj without a topology? Matthew Guberman-Pfeffer
- Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology? Carlos Simmerling
- Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology? Matthew Guberman-Pfeffer
- Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology? Carlos Simmerling
- Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology? Matthew Guberman-Pfeffer
- Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology? Thomas Cheatham
- Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology? Matthew Guberman-Pfeffer
- Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology? Daniel Roe
- Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology? Carlos Simmerling
Sunday, 26 September 2021
- [AMBER] parmed for 12-6-4 LJ (Geng Dong) 东庚
- [AMBER] zero torsion in DUMPAVE file in a sander run jamal kazazi
Monday, 27 September 2021
- [AMBER] TI in membrane system Rafał Madaj
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output Annabelle Hartt
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output Carlos Simmerling
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output Annabelle Hartt
- [AMBER] Amber20 installation vivek rabha
- Re: [AMBER] Amber20 installation David A Case
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output Carlos Simmerling
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output Daniel Roe
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output Daniel Roe
- Re: [AMBER] zero torsion in DUMPAVE file in a sander run jamal kazazi
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output Annabelle Hartt
- Re: [AMBER] parmed for 12-6-4 LJ (Geng Dong) Jason Swails
- [AMBER] Seeking advice on computing interaction energies Matthew Guberman-Pfeffer
- [AMBER] problem about the absolutely binding free energy calculation neildancer.sina.com
Tuesday, 28 September 2021
- [AMBER] parmed for 12-6-4 LJ (Geng Dong) 东庚
- Re: [AMBER] Error installing amber macOS M1 Rodrigo da Silva Bitzer
- [AMBER] Atom type of NO does not shown up in PARMCHK.DAT Reza Esmaeeli
- Re: [AMBER] problem about the absolutely binding free energy calculation Song, Lin
- Re: [AMBER] Error installing amber macOS M1 David A Case
- Re: [AMBER] Atom type of NO does not shown up in PARMCHK.DAT David A Case
- Re: [AMBER] Error installing amber macOS M1 Rodrigo da Silva Bitzer
- Re: [AMBER] Error installing amber macOS M1 David A Case
- [AMBER] 回复：Re: problem about the absolutely binding free energy calculation neildancer.sina.com
- [AMBER] How to combine the coordinate and parm7 files of the glycolipid into a protein complex system neildancer.sina.com
- [AMBER] Problem in installing AMBER 20 Ubantu ; configuring molecules from own data obtained from Gaussian Satya Pal Singh
Wednesday, 29 September 2021
- Re: [AMBER] How to combine the coordinate and parm7 files of the glycolipid into a protein complex system David A Case
- Re: [AMBER] Problem in installing AMBER 20 Ubantu ; configuring molecules from own data obtained from Gaussian David A Case
- Re: [AMBER] Atom type of NO does not shown up in PARMCHK.DAT Reza Esmaeeli
Thursday, 30 September 2021
- 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

Last message date: Thu Sep 30 2021 - 14:30:03 PDT
Archived on: Fri Oct 31 2025 - 05:56:06 PDT

Amber Archive Sep 2021 by date