Amber Archive Aug 2024: by date

Thursday, 1 August 2024
- Re: [AMBER] production run mdin file Dulal Mondal via AMBER
- Re: [AMBER] ff99 and ff14SB - Slight Atom Type Differences Carlos Simmerling via AMBER
- Re: [AMBER] Atom type of DU does not exist in PARMCHK.DAT Abdelrahman, Noureen via AMBER
- Re: [AMBER] MD simulations for 100 ns and PCA Thomas Cheatham via AMBER
Saturday, 3 August 2024
- Re: [AMBER] Effective Born Radius Jaime Rubio Martinez via AMBER
- Re: [AMBER] Effective Born Radius David A Case via AMBER
Sunday, 4 August 2024
- Re: [AMBER] cphstats processing of pH-REMD 'chunks' He, Amy via AMBER
- [AMBER] No QM parameter for a Sulfur atom Sunanda Samanta via AMBER
Monday, 5 August 2024
- Re: [AMBER] No QM parameter for a Sulfur atom Martin Juhás via AMBER
- Re: [AMBER] MCPB.py keyerror Li, Zhen via AMBER
- [AMBER] CHARMM-GUI-provided scripts HAFIDAH ZAKI AL QUDAH via AMBER
- Re: [AMBER] CHARMM-GUI-provided scripts Masoud Keramati via AMBER
- [AMBER] Issues with the Glycoprotein builder on the glycamm website Natesan Mani via AMBER
- Re: [AMBER] Issues with the Glycoprotein builder on the glycamm website Carlos Simmerling via AMBER
- Re: [AMBER] SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f> in QUICK Goetz, Andreas via AMBER
Tuesday, 6 August 2024
- [AMBER] Amber/AmberTools24 installation Apple M2 Xavier Brazzolotto via AMBER
- Re: [AMBER] Amber/AmberTools24 installation Apple M2 Elvis Martis via AMBER
- Re: [AMBER] Amber/AmberTools24 installation Apple M2 Elvis Martis via AMBER
- Re: [AMBER] SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f> in QUICK Timothy Giese via AMBER
- Re: [AMBER] SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f> in QUICK Kriti Shukla via AMBER
- Re: [AMBER] Amber/AmberTools24 installation Apple M2 Elvis Martis via AMBER
- Re: [AMBER] Amber/AmberTools24 installation Apple M2 Elvis Martis via AMBER
- Re: [AMBER] Amber/AmberTools24 installation Apple M2 Elvis Martis via AMBER
- Re: [AMBER] Cmake unable to find Mpich Pertschy, Florian via AMBER
- [AMBER] MPI installation failing. Pertschy, Florian via AMBER
- Re: [AMBER] cphstats processing of pH-REMD 'chunks' Nitin Kulhar via AMBER
- [AMBER] Torsion Term Error Cinar, Sena via AMBER
- [AMBER] Evaluate change in affinity due to mutation Abhilash J via AMBER
- [AMBER] different pH conditions for membrane protein simulations Prithviraj Nandigrami via AMBER
- Re: [AMBER] MPI installation failing. Timothy Giese via AMBER
- Re: [AMBER] Torsion Term Error Carlos Simmerling via AMBER
- Re: [AMBER] cphstats processing of pH-REMD 'chunks' He, Amy via AMBER
- Re: [AMBER] Cmake unable to find Mpich Nil Mu via AMBER
- Re: [AMBER] No QM parameter for a Sulfur atom David A Case via AMBER
- Re: [AMBER] MPI installation failing. David A Case via AMBER
Wednesday, 7 August 2024
- [AMBER] Tleap error Prabir Khatua via AMBER
- Re: [AMBER] Tleap error Carlos Simmerling via AMBER
- [AMBER] parameterize a non-standard residue Peng Zhang via AMBER
- [AMBER] Query about continuous constant pH in amber24 (chapter 28) Dulal Mondal via AMBER
Thursday, 8 August 2024
- Re: [AMBER] Tleap error FyD via AMBER
- [AMBER] Amber24 Cuda installation Pertschy, Florian via AMBER
- [AMBER] Requesting help with Amber TI calculation Weerawarna Kurukulasooriy, Sandaruwani Tharaka \[CHEM\] via AMBER
- Re: [AMBER] Requesting help with Amber TI calculation Carlos Simmerling via AMBER
- [AMBER] How to build own system Sepideh Jafari via AMBER
- [AMBER] Fwd: Regarding Advanced Thermodynamic Integration: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Fwd: Regarding Advanced Thermodynamic Integration: Carlos Simmerling via AMBER
- [AMBER] Surface area of one protein to another King Wang via AMBER
- Re: [AMBER] Regarding Advanced Thermodynamic Integration: He, Amy via AMBER
- Re: [AMBER] Query about continuous constant pH in amber24 (chapter 28) Dulal Mondal via AMBER
- Re: [AMBER] Tleap error Prabir Khatua via AMBER
Friday, 9 August 2024
- [AMBER] Error in ligand paramterisation in tleap Simran Modi via AMBER
- Re: [AMBER] Query about continuous constant pH in amber24 (chapter 28) Carlos Simmerling via AMBER
- Re: [AMBER] Error in ligand paramterisation in tleap Dr. Anselm Horn via AMBER
Saturday, 10 August 2024
- [AMBER] parm10 and PARMCHK.DAT Atom Types Pye, Aaron Wesley via AMBER
- Re: [AMBER] parm10 and PARMCHK.DAT Atom Types Warren, Kyle Benjamin via AMBER
Sunday, 11 August 2024
- [AMBER] Amber 24 encounters freezed jobs Morad Mustafa via AMBER
- Re: [AMBER] Amber 24 encounters freezed jobs Carlos Simmerling via AMBER
- [AMBER] finddgref.py error with manually added titratable ligand Nitin Kulhar via AMBER
- Re: [AMBER] cphstats processing of pH-REMD 'chunks' Nitin Kulhar via AMBER
Monday, 12 August 2024
- Re: [AMBER] finddgref.py error with manually added titratable ligand Vinicius Cruzeiro via AMBER
- Re: [AMBER] finddgref.py error with manually added titratable ligand Nitin Kulhar via AMBER
- Re: [AMBER] QM/MM produces no error but doesn't run successfully Timothy Giese via AMBER
- Re: [AMBER] different pH conditions for membrane protein simulations Prithviraj Nandigrami via AMBER
- Re: [AMBER] finddgref.py error with manually added titratable ligand Vinicius Cruzeiro via AMBER
- [AMBER] Assistance Needed with PCA at Different Temperatures in AMBER ABDELATIF MESSAOUDI via AMBER
- Re: [AMBER] Assistance Needed with PCA at Different Temperatures in AMBER Carlos Simmerling via AMBER
- Re: [AMBER] Assistance Needed with PCA at Different Temperatures in AMBER Carlos Simmerling via AMBER
- Re: [AMBER] cphstats processing of pH-REMD 'chunks' He, Amy via AMBER
Tuesday, 13 August 2024
- [AMBER] Executing absolute binding free energy calculations in Amber Amara Jabeen via AMBER
- [AMBER] illegal memory access Alois Zdrha via AMBER
- [AMBER] QM/MM Energy Decomposition Ge Song via AMBER
- Re: [AMBER] [Sender Not Verified] Re: Requesting help with Amber TI calculation Steinbrecher, Thomas via AMBER
Wednesday, 14 August 2024
- Re: [AMBER] QM/MM Energy Decomposition Timothy Giese via AMBER
Thursday, 15 August 2024
- [AMBER] Compiling CUDA - gpu compatability Alexander Hung Lee via AMBER
Friday, 16 August 2024
- [AMBER] FETookit analysis issue: Kankana Bhattacharjee via AMBER
- [AMBER] query about scaling of nonbonded interactions. Prof. Mark Wilson via AMBER
- Re: [AMBER] query about scaling of nonbonded interactions. Carlos Simmerling via AMBER
- Re: [AMBER] query about scaling of nonbonded interactions. Prof. Mark Wilson via AMBER
- Re: [AMBER] FETookit analysis issue: Timothy Giese via AMBER
- Re: [AMBER] FETookit analysis issue: Shi Zhang via AMBER
- [AMBER] Trouble Calculating Nucleic Pseudo-Torsions Eta and Theta (η-θ) w/ CPPTRAJ Warren, Kyle Benjamin via AMBER
- Re: [AMBER] FETookit analysis issue: Kankana Bhattacharjee via AMBER
- [AMBER] Amber22 cudaGetDeviceCount failed unknown error Gustavo Seabra via AMBER
- Re: [AMBER] FETookit analysis issue: Shi Zhang via AMBER
- Re: [AMBER] Amber22 cudaGetDeviceCount failed unknown error Gustavo Seabra via AMBER
- Re: [AMBER] Trouble Calculating Nucleic Pseudo-Torsions Eta and Theta (η-θ) w/ CPPTRAJ Daniel Roe via AMBER
- [AMBER] Fwd: modifying colvars Gard Nelson via AMBER
Saturday, 17 August 2024
- Re: [AMBER] Compiling CUDA - gpu compatability Daniel Roe via AMBER
- [AMBER] AmberMDPrep.sh finishes after final.1.in step Maciej Spiegel via AMBER
- Re: [AMBER] AmberMDPrep.sh finishes after final.1.in step Daniel Roe via AMBER
Sunday, 18 August 2024
- [AMBER] Multiple Replicas per GPU? Guberman-Pfeffer, Matthew via AMBER
- [AMBER] remlog in cpptraj for pH-REMD Guberman-Pfeffer, Matthew via AMBER
- [AMBER] Multiple Replicas per GPU? Guberman-Pfeffer, Matthew via AMBER
- [AMBER] Unclear cphstats warning Guberman-Pfeffer, Matthew via AMBER
- [AMBER] Missing angle parameter between unconnected atoms Peng Zhang via AMBER
- Re: [AMBER] AmberMDPrep.sh finishes after final.1.in step Daniel Roe via AMBER
- Re: [AMBER] remlog in cpptraj for pH-REMD Daniel Roe via AMBER
- Re: [AMBER] remlog in cpptraj for pH-REMD Daniel Roe via AMBER
- Re: [AMBER] Unclear cphstats warning He, Amy via AMBER
- Re: [AMBER] Unclear cphstats warning Guberman-Pfeffer, Matthew via AMBER
Monday, 19 August 2024
- Re: [AMBER] AmberMDPrep.sh finishes after final.1.in step Daniel Roe via AMBER
- Re: [AMBER] AmberMDPrep.sh finishes after final.1.in step Daniel Roe via AMBER
- Re: [AMBER] Trouble Calculating Nucleic Pseudo-Torsions Eta and Theta (η-θ) w/ CPPTRAJ Daniel Roe via AMBER
- Re: [AMBER] Compiling CUDA - gpu compatability Daniel Roe via AMBER
- Re: [AMBER] AmberMDPrep.sh finishes after final.1.in step Daniel Roe via AMBER
- [AMBER] Custom AA residue missing parameters Javier O Sanlley-hernandez via AMBER
- Re: [AMBER] Custom AA residue missing parameters Daniel Roe via AMBER
- [AMBER] amber19 installation error Dulal Mondal via AMBER
- Re: [AMBER] AmberMDPrep.sh finishes after final.1.in step Daniel Roe via AMBER
- Re: [AMBER] Unclear cphstats warning He, Amy via AMBER
- Re: [AMBER] Unclear cphstats warning Guberman-Pfeffer, Matthew via AMBER
- [AMBER] 回复: Custom AA residue missing parameters Huang ZiJian via AMBER
Tuesday, 20 August 2024
- Re: [AMBER] Error in ligand paramterisation in tleap Simran Modi via AMBER
- [AMBER] Free energy calculation of complex with covalent bond SUBHASMITA MAHAPATRA MAHAPATRA via AMBER
- [AMBER] Cutoff value significantly impacts the electrostatic energy in PME Ge Song via AMBER
- Re: [AMBER] [Sender Not Verified] Cutoff value significantly impacts the electrostatic energy in PME Steinbrecher, Thomas via AMBER
- Re: [AMBER] Error in ligand paramterisation in tleap David A Case via AMBER
- Re: [AMBER] amber19 installation error David A Case via AMBER
- Re: [AMBER] Free energy calculation of complex with covalent bond David A Case via AMBER
- Re: [AMBER] [Sender Not Verified] Cutoff value significantly impacts the electrostatic energy in PME Ge Song via AMBER
- [AMBER] Per residue energy decomposition RAMPRAKASH YADAV via AMBER
Wednesday, 21 August 2024
- Re: [AMBER] Per residue energy decomposition Carlos Simmerling via AMBER
- Re: [AMBER] [Sender Not Verified] Cutoff value significantly impacts the electrostatic energy in PME Ge Song via AMBER
- [AMBER] Regarding an issue with Thermodynamic Integration calculation Weerawarna Kurukulasooriy, Sandaruwani Tharaka \[CHEM\] via AMBER
- Re: [AMBER] Regarding an issue with Thermodynamic Integration calculation Timothy Giese via AMBER
- [AMBER] Convergence checking in Advanced TI calculation: Kankana Bhattacharjee via AMBER
Thursday, 22 August 2024
- Re: [AMBER] Convergence checking in Advanced TI calculation: Kankana Bhattacharjee via AMBER
- Re: [AMBER] [Sender Not Verified] Cutoff value significantly impacts the electrostatic energy in PME David A Case via AMBER
Friday, 23 August 2024
- [AMBER] packmol-memgen: issue with the parametrization of gpcr-ligand system Enrico Martinez via AMBER
- Re: [AMBER] packmol-memgen: issue with the parametrization of gpcr-ligand system Enrico Martinez via AMBER
- [AMBER] Assigning GPUs with pHREMD Guberman-Pfeffer, Matthew via AMBER
- Re: [AMBER] [Sender Not Verified] Cutoff value significantly impacts the electrostatic energy in PME Timothy Giese via AMBER
- [AMBER] Extracting every 10th frame from *.nc file Maciej Spiegel via AMBER
- Re: [AMBER] Extracting every 10th frame from *.nc file Timothy Giese via AMBER
- Re: [AMBER] [Sender Not Verified] Cutoff value significantly impacts the electrostatic energy in PME Ge Song via AMBER
- Re: [AMBER] Extracting every 10th frame from *.nc file Carlos Simmerling via AMBER
- [AMBER] issue using pemed.cuda of AMBER 24 Abhilash J via AMBER
Saturday, 24 August 2024
- [AMBER] Regarding placement of periodic box Natesan Mani via AMBER
- Re: [AMBER] Regarding placement of periodic box David A Case via AMBER
Sunday, 25 August 2024
- [AMBER] combining the results of nab nmode and mmpbsa Siavoush Dastmalchi via AMBER
- [AMBER] Modeling and simulating a cyclic depsipeptide Baker, Joseph via AMBER
- Re: [AMBER] Modeling and simulating a cyclic depsipeptide Carlos Simmerling via AMBER
- [AMBER] run errorn in sander.MPI for constant pH replica exchange in amber18 Dulal Mondal via AMBER
Monday, 26 August 2024
- [AMBER] MMGBSA Calculation Python --version ABDELATIF MESSAOUDI via AMBER
- Re: [AMBER] MMGBSA Calculation Python --version 王世玉 via AMBER
- Re: [AMBER] MMGBSA Calculation Python --version Carlos Simmerling via AMBER
- [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 Dulal Mondal via AMBER
- [AMBER] Continuous constant pH MD with pH replica exchange Nancy Zhu via AMBER
- Re: [AMBER] Error to run constant pH replica exchange in explicit solvent in amber18 Vinicius Cruzeiro via AMBER
- Re: [AMBER] Error to run constant pH replica exchange in explicit solvent in amber18 Dulal Mondal via AMBER
- Re: [AMBER] cphstats processing of pH-REMD 'chunks' Nitin Kulhar via AMBER
- 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
- Re: [AMBER] Error to run constant pH replica exchange in explicit solvent in amber18 Dulal Mondal via AMBER
Tuesday, 27 August 2024
- [AMBER] Lone pair treatment AMBER24 Sorin Draga via AMBER
- Re: [AMBER] Lone pair treatment AMBER24 Juraj Dobias via AMBER
- [AMBER] Amber to Lammps; velocities conversion Meyer, Olivia \(meyerok\) via AMBER
- [AMBER] PCA on Unmodified and Modified Nucleobases within RNA: Different Ribose Atom Ordering Warren, Kyle Benjamin via AMBER
- [AMBER] Protein RNA complex simulation best standards in the field. Debarati DasGupta via AMBER
- Re: [AMBER] Protein RNA complex simulation best standards in the field. Guberman-Pfeffer, Matthew via AMBER
- Re: [AMBER] combining the results of nab nmode and mmpbsa David A Case via AMBER
- Re: [AMBER] Modeling and simulating a cyclic depsipeptide David A Case via AMBER
- Re: [AMBER] Amber to Lammps; velocities conversion David A Case via AMBER
- [AMBER] Reply: Re: combining the results of nab nmode and mmpbsa Siavoush Dastmalchi via AMBER
Wednesday, 28 August 2024
- [AMBER] Amber22_Error: an illegal memory access was encountered launching kernel kNLSkinTest ABDELATIF MESSAOUDI via AMBER
- Re: [AMBER] Amber22_Error: an illegal memory access was encountered launching kernel kNLSkinTest Carlos Simmerling via AMBER
- Re: [AMBER] Protein RNA complex simulation best standards in the field. Reza Khayat via AMBER
- Re: [AMBER] Protein RNA complex simulation best standards in the field. Jiri Sponer via AMBER
- [AMBER] Fwd: TI calculation using pmemd Tamalika Ash via AMBER
- [AMBER] Computing free energy of binding from advanced TI calculation: Kankana Bhattacharjee via AMBER
Thursday, 29 August 2024
- [AMBER] Modification of MMPBSA electrostatic energy Anupaul Baruah via AMBER
- Re: [AMBER] Fwd: TI calculation using pmemd Timothy Giese via AMBER
- Re: [AMBER] Computing free energy of binding from advanced TI calculation: Timothy Giese via AMBER
- [AMBER] Regarding REUS simulations miyagi bunkutu via AMBER
- Re: [AMBER] Fwd: TI calculation using pmemd David A Case via AMBER
- [AMBER] About making Amber code a more standard Vlad via AMBER
- Re: [AMBER] Modification of MMPBSA electrostatic energy Bill Miller III via AMBER
Friday, 30 August 2024
- [AMBER] 回复: Custom AA residue missing parameters Huang ZiJian via AMBER
- Re: [AMBER] Fwd: TI calculation using pmemd Darrin York via AMBER
- [AMBER] Error message : "unsigned long long of length = 42Failed an illegal memory access was encountered" Anna Herz via AMBER
- Re: [AMBER] Error message : "unsigned long long of length = 42Failed an illegal memory access was encountered" Ryan Snyder via AMBER

Last message date: Fri Aug 30 2024 - 08:30:02 PDT
Archived on: Fri Dec 20 2024 - 05:56:21 PST

Amber Archive Aug 2024 by date