Amber Archive Sep 2024: by date

Sunday, 1 September 2024
- Re: [AMBER] Regarding REUS simulations Carlos Simmerling via AMBER
Wednesday, 4 September 2024
- Re: [AMBER] Error to run constant pH replica exchange in explicit solvent in amber18 Dulal Mondal via AMBER
- Re: [AMBER] Error to run constant pH replica exchange in explicit solvent in amber18 Vinicius Cruzeiro via AMBER
Thursday, 5 September 2024
- [AMBER] OPC3 water and ff19SB forcefield for constant pH simulations Nikolay Kuzmich via AMBER
- Re: [AMBER] Custom AA residue missing parameters Téletchéa Stéphane via AMBER
- [AMBER] Possible error in tiMerge Osman, Roman via AMBER
- [AMBER] Using Drude with Amber Abraham, Rhea C via AMBER
Friday, 6 September 2024
- Re: [AMBER] Regarding REUS simulations Carlos Simmerling via AMBER
- Re: [AMBER] Regarding REUS simulations Carlos Simmerling via AMBER
- Re: [AMBER] Modification of MMPBSA electrostatic energy David A Case via AMBER
- Re: [AMBER] Using Drude with Amber David A Case via AMBER
- Re: [AMBER] About making Amber code a more standard David A Case via AMBER
- [AMBER] protein-DNA complex model mohamed marzouk via AMBER
Saturday, 7 September 2024
- [AMBER] Problem with Miniconda after executing ./run_cmake Nikolay Kuzmich via AMBER
- [AMBER] Error while running antechamber on the server Ramesh M via AMBER
Sunday, 8 September 2024
- Re: [AMBER] Error while running antechamber on the server Dr. Anselm Horn via AMBER
- [AMBER] Positive value of MM-GBSA computations Maciej Spiegel via AMBER
- Re: [AMBER] Positive value of MM-GBSA computations Carlos Simmerling via AMBER
- [AMBER] Error while running equilibrium step Ramesh M via AMBER
Monday, 9 September 2024
- Re: [AMBER] Custom AA residue missing parameters Téletchéa Stéphane via AMBER
- Re: [AMBER] Error while running equilibrium step Téletchéa Stéphane via AMBER
- [AMBER] QM/MM error: No parameter for sulfur atom SUBHASMITA MAHAPATRA MAHAPATRA via AMBER
- [AMBER] Regarding a problem with TI calculation Weerawarna Kurukulasooriy, Sandaruwani Tharaka \[CHEM\] via AMBER
- Re: [AMBER] Regarding a problem with TI calculation Timothy Giese via AMBER
- Re: [AMBER] Problem with Miniconda after executing ./run_cmake Daniel Roe via AMBER
- Re: [AMBER] QM/MM error: No parameter for sulfur atom Goetz, Andreas via AMBER
Tuesday, 10 September 2024
- [AMBER] atom does not have a type error, ff15ipq Rosa Teijeiro Juiz via AMBER
- [AMBER] Regarding DiscoverEdges.py script to get xml files for Advanced TI calculation analysis: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Regarding DiscoverEdges.py script to get xml files for Advanced TI calculation analysis: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Regarding DiscoverEdges.py script to get xml files for Advanced TI calculation analysis: Kankana Bhattacharjee via AMBER
- [AMBER] Cuda problems - Error: invalid device ordinal Pertschy, Florian via AMBER
- Re: [AMBER] Regarding DiscoverEdges.py script to get xml files for Advanced TI calculation analysis: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Cuda problems - Error: invalid device ordinal Pertschy, Florian via AMBER
- [AMBER] Cannot find pmemd in $AMBERHOME/bin/ Wu, Ming Hsiu via AMBER
- Re: [AMBER] Cannot find pmemd in $AMBERHOME/bin/ Carlos Simmerling via AMBER
- [AMBER] Possible error in tiMerge Osman, Roman via AMBER
- [AMBER] Fraction in native contacts out file Debarati DasGupta via AMBER
- Re: [AMBER] Cannot find pmemd in $AMBERHOME/bin/ Shiyu Wang via AMBER
- Re: [AMBER] atom does not have a type error, ff15ipq 王世玉 via AMBER
- Re: [AMBER] Positive value of MM-GBSA computations 王世玉 via AMBER
Wednesday, 11 September 2024
- [AMBER] amber24 (cuda) installation compilation error Dulal Mondal via AMBER
- Re: [AMBER] Positive value of MM-GBSA computations Maciej Spiegel via AMBER
- Re: [AMBER] atom does not have a type error, ff15ipq Rosa Teijeiro Juiz via AMBER
- [AMBER] distance command issues Debarati DasGupta via AMBER
- Re: [AMBER] distance command issues Carlos Simmerling via AMBER
- [AMBER] tutorial to run ABFE calculation Justice Josiah Mallen via AMBER
Thursday, 12 September 2024
- [AMBER] atom type error in antechamber 홍종희 via AMBER
- Re: [AMBER] amber24 (cuda) installation compilation error Dulal Mondal via AMBER
- Re: [AMBER] amber24 (cuda) installation compilation error Li, Zhen via AMBER
- Re: [AMBER] Error while running equilibrium step David A Case via AMBER
- Re: [AMBER] Regarding a problem with TI calculation David A Case via AMBER
- Re: [AMBER] amber24 (cuda) installation compilation error David A Case via AMBER
- Re: [AMBER] distance command issues David A Case via AMBER
- Re: [AMBER] atom type error in antechamber David A Case via AMBER
- [AMBER] Announcement: Release of DOCK 6.12 Scott Brozell via AMBER
- Re: [AMBER] atom type error in antechamber Shiyu Wang via AMBER
Friday, 13 September 2024
- [AMBER] Possible error in TiMerge Osman, Roman via AMBER
- [AMBER] Saving a frame of a trajectory in pdbqt format. saverio lemme via AMBER
- Re: [AMBER] Saving a frame of a trajectory in pdbqt format. Daniel Roe via AMBER
Sunday, 15 September 2024
- [AMBER] TI simulation with "covalent ligands" for relative binding energy? King Wang via AMBER
- [AMBER] Forcefield Builder analogs in Amber Nikolay Kuzmich via AMBER
- [AMBER] Regarding a Problem in TI calculation Weerawarna Kurukulasooriy, Sandaruwani Tharaka \[CHEM\] via AMBER
- [AMBER] Some comments about vlimit David A Case via AMBER
- Re: [AMBER] Forcefield Builder analogs in Amber David A Case via AMBER
- Re: [AMBER] Regarding a Problem in TI calculation David A Case via AMBER
Monday, 16 September 2024
- [AMBER] patched plumed with amber24 Dulal Mondal via AMBER
- Re: [AMBER] patched plumed with amber24 SATYAJIT KHATUA via AMBER
- Re: [AMBER] amber24 (cuda) installation compilation error Li, Zhen via AMBER
- Re: [AMBER] amber24 (cuda) installation compilation error Dulal Mondal via AMBER
- [AMBER] reduce command Debarati DasGupta via AMBER
- Re: [AMBER] reduce command Carlos Simmerling via AMBER
- Re: [AMBER] reduce command Debarati DasGupta via AMBER
- [AMBER] Issue with Bonds after Ligand Parameterization for MD Simulation Maciej Spiegel via AMBER
- Re: [AMBER] Issue with Bonds after Ligand Parameterization for MD Simulation Carlos Simmerling via AMBER
- Re: [AMBER] Issue with Bonds after Ligand Parameterization for MD Simulation Carlos Simmerling via AMBER
- [AMBER] Zn2+ bond angle parameter related error Debarati DasGupta via AMBER
- Re: [AMBER] Zn2+ bond angle parameter related error Carlos Simmerling via AMBER
- Re: [AMBER] Zn2+ bond angle parameter related error SATYAJIT KHATUA via AMBER
- Re: [AMBER] Zn2+ bond angle parameter related error SATYAJIT KHATUA via AMBER
- Re: [AMBER] Issue with Bonds after Ligand Parameterization for MD Simulation Carlos Simmerling via AMBER
Tuesday, 17 September 2024
- Re: [AMBER] Forcefield Builder analogs in Amber Jones de Andrade via AMBER
Wednesday, 18 September 2024
- Re: [AMBER] patched plumed with amber24 SATYAJIT KHATUA via AMBER
- [AMBER] Modifying Topology to Use OPC Water Instead of TIP3P Maciej Spiegel via AMBER
- Re: [AMBER] Modifying Topology to Use OPC Water Instead of TIP3P haiyangzhong via AMBER
- Re: [AMBER] Modifying Topology to Use OPC Water Instead of TIP3P Carlos Simmerling via AMBER
- [AMBER] GAFF2 publication with c5 parameterization Intravaia, Lauren E via AMBER
Thursday, 19 September 2024
- [AMBER] MMPBSA error : cpptraj failed with prmtop ../../prep/com.top 홍종희 via AMBER
- Re: [AMBER] Forcefield Builder analogs in Amber David A Case via AMBER
- Re: [AMBER] MMPBSA error : cpptraj failed with prmtop ../../prep/com.top David A Case via AMBER
- Re: [AMBER] Forcefield Builder analogs in Amber Carlos Simmerling via AMBER
- Re: [AMBER] MMPBSA error : cpptraj failed with prmtop ../../prep/com.top 홍종희 via AMBER
- [AMBER] MMPBSA error: LengthError: length mismatch in energy vectors 홍종희 via AMBER
- Re: [AMBER] MMPBSA error : cpptraj failed with prmtop ../../prep/com.top 홍종희 via AMBER
Friday, 20 September 2024
- [AMBER] cannot properly run sqm on antechamber Teijeiro Juiz, Rosa via AMBER
- [AMBER] Issue with Heating a Solvated Membrane Bilayer System in AMBER Maciej Spiegel via AMBER
- Re: [AMBER] Issue with Heating a Solvated Membrane Bilayer System in AMBER Carlos Simmerling via AMBER
- Re: [AMBER] cannot properly run sqm on antechamber David Case via AMBER
- Re: [AMBER] Issue with Heating a Solvated Membrane Bilayer System in AMBER Carlos Simmerling via AMBER
- [AMBER] An error in TiMerge? Osman, Roman via AMBER
- Re: [AMBER] An error in TiMerge? Carlos Simmerling via AMBER
- Re: [AMBER] An error in TiMerge? Ryan Snyder via AMBER
- [AMBER] Calculating the number of replicas for h-remd Liyanage, Risi $MU-Student$ via AMBER
- [AMBER] fusing or tiling simulation boxes Ryan Woltz via AMBER
Saturday, 21 September 2024
- Re: [AMBER] Calculating the number of replicas for h-remd Carlos Simmerling via AMBER
- [AMBER] Water not recgnized correctly by atomtypes in Antechamber Husak Michal via AMBER
Sunday, 22 September 2024
- [AMBER] tleap changes HETATM to ATOM Maciej Spiegel via AMBER
- Re: [AMBER] tleap changes HETATM to ATOM Carlos Simmerling via AMBER
- Re: [AMBER] Water not recgnized correctly by atomtypes in Antechamber Carlos Simmerling via AMBER
- Re: [AMBER] Water not recgnized correctly by atomtypes in Antechamber Carlos Simmerling via AMBER
- [AMBER] Problem in TI output Tamalika Ash via AMBER
Monday, 23 September 2024
- [AMBER] CpH MD in explicit solvent: no switch for CYS although it was in the titratable residues list Nikolay Kuzmich via AMBER
- [AMBER] Packmol-Memgen tleap error - FATAL: Atom .R<LYS 233>.A<OXT 23> does not have a type. Maciej Spiegel via AMBER
- Re: [AMBER] Calculating the number of replicas for h-remd Carlos Simmerling via AMBER
- [AMBER] Question about the use of MCPB.py(Handling of proteins with non-standard residues in the chain) 郑逸非 via AMBER
Tuesday, 24 September 2024
- [AMBER] Installation Amber24 Enrico Martinez via AMBER
- Re: [AMBER] Installation Amber24 Enrico Martinez via AMBER
- Re: [AMBER] Installation Amber24 Enrico Martinez via AMBER
- Re: [AMBER] CpH MD in explicit solvent: no switch for CYS although it was in the titratable residues list Jason Swails via AMBER
- Re: [AMBER] MMPBSA error: LengthError: length mismatch in energy vectors Jason Swails via AMBER
- [AMBER] problem with Python.h while compiling amber24 Luis Simon via AMBER
- Re: [AMBER] Water not recgnized correctly by atomtypes in Antechamber David A Case via AMBER
Wednesday, 25 September 2024
- [AMBER] Bug in parmchck2 code (antechamber engine) ... Michal Husak via AMBER
- [AMBER] Minimisation Error: LINMIN FAILURE SUBHASMITA MAHAPATRA MAHAPATRA via AMBER
- Re: [AMBER] Minimisation Error: LINMIN FAILURE Carlos Simmerling via AMBER
- Re: [AMBER] problem with Python.h while compiling amber24 Timothy Giese via AMBER
- Re: [AMBER] Minimisation Error: LINMIN FAILURE Carlos Simmerling via AMBER
- Re: [AMBER] CpH MD in explicit solvent: no switch for CYS although it was in the titratable residues list Jason Swails via AMBER
- Re: [AMBER] CpH MD in explicit solvent: no switch for CYS although it was in the titratable residues list Adrian Roitberg via AMBER
- Re: [AMBER] problem with Python.h while compiling amber24 LUIS MANUEL SIMÓN RUBIO via AMBER
- [AMBER] Direct contact to Antechamber developers ? Husak Michal via AMBER
- Re: [AMBER] CpH MD in explicit solvent: no switch for CYS although it was in the titratable residues list Jason Swails via AMBER
- Re: [AMBER] problem with Python.h while compiling amber24 David A Case via AMBER
- [AMBER] Failed minimization for membrane system using pmemd.MPI Pengfei Li via AMBER
- Re: [AMBER] Question about the use of MCPB.py(Handling of proteins with non-standard residues in the chain) Li, Zhen via AMBER
- Re: [AMBER] Failed minimization for membrane system using pmemd.MPI David A Case via AMBER
Thursday, 26 September 2024
- Re: [AMBER] Calculating the number of replicas for h-remd Carlos Simmerling via AMBER
- Re: [AMBER] Calculating the number of replicas for h-remd Carlos Simmerling via AMBER
Friday, 27 September 2024
- [AMBER] Molecules minimized by amber + gaff or gaff2 requiest (for code testing) Michal Husak via AMBER
- [AMBER] Error testing pmemd.cuda: "Illegal instruction (core dumped)" Skanda Sastry via AMBER
Sunday, 29 September 2024
- [AMBER] help 张丹阳 via AMBER
- Re: [AMBER] Molecules minimized by amber + gaff or gaff2 requiest (for code testing) David A Case via AMBER
- Re: [AMBER] help David A Case via AMBER
Monday, 30 September 2024
- Re: [AMBER] problem with Python.h while compiling amber24 Timothy Giese via AMBER
- [AMBER] Some dihedral parameters for HID (ff19SB) Peng Zhang via AMBER

Last message date: Mon Sep 30 2024 - 14:30:02 PDT
Archived on: Fri Dec 20 2024 - 05:56:21 PST

Amber Archive Sep 2024 by date