Amber Archive Oct 2022: by date

Saturday, 1 October 2022
- [AMBER] ValueError in MCPB.py at step 3 Dr. Vaibhav Anil Dixit via AMBER
Sunday, 2 October 2022
- [AMBER] New, sander based real life lmod examples Istvan Kolossvary via AMBER
Monday, 3 October 2022
- Re: [AMBER] NUMEXTRA Error Sally Pias via AMBER
- [AMBER] AMBER22 installation on Linux Azurmendi, Hugo via AMBER
- [AMBER] survival or residence time angad sharma via AMBER
Tuesday, 4 October 2022
- [AMBER] How to concatenate long trajs in a decent time Giulia Sormani via AMBER
- [AMBER] MMGBSA with Mn2+ ions Rafał Madaj via AMBER
- Re: [AMBER] How to concatenate long trajs in a decent time Daniel Roe via AMBER
- [AMBER] problem with MMPBSA.py (and/or ante-MMPBSA.py) Artur Hermano via AMBER
- [AMBER] bar-graph of the hydrogen bonds fraction using xm-grace Enrico Martinez via AMBER
- [AMBER] Running the TI code on a single residue results in NaN electrostatics Miroslav Suruzhon via AMBER
- Re: [AMBER] AMBER22 installation on Linux SATYAJIT KHATUA via AMBER
- Re: [AMBER] AMBER22 installation on Linux Scott Brozell via AMBER
- Re: [AMBER] MMGBSA with Mn2+ ions David A Case via AMBER
Wednesday, 5 October 2022
- Re: [AMBER] Running the TI code on a single residue results in NaN electrostatics David A Case via AMBER
- [AMBER] Error in generating parameters for BMT residue in Cyclosporin and Leap Error in Bond command Suchetana Gupta via AMBER
- Re: [AMBER] NUMEXTRA Error Sally Pias via AMBER
Thursday, 6 October 2022
- [AMBER] ANTECHAMBER: parametrization of charged ligand Enrico Martinez via AMBER
- Re: [AMBER] ANTECHAMBER: parametrization of charged ligand Dr. Anselm Horn via AMBER
- Re: [AMBER] ANTECHAMBER: parametrization of charged ligand Enrico Martinez via AMBER
- [AMBER] How to add gaff parameters to PARMCHK.DAT file Jiaan Zhu via AMBER
- [AMBER] Phase space overlap questions in alchemical free energy calculations Liao via AMBER
Friday, 7 October 2022
- Re: [AMBER] ANTECHAMBER: parametrization of charged ligand Enrico Martinez via AMBER
- Re: [AMBER] Phase space overlap questions in alchemical free energy calculations Liao via AMBER
Saturday, 8 October 2022
- [AMBER] parameterization for non-standard nucleotide Moustafa, Ibrahim M. via AMBER
- Re: [AMBER] parameterization for non-standard nucleotide Maria Nagan via AMBER
- Re: [AMBER] How to add gaff parameters to PARMCHK.DAT file David A Case via AMBER
- Re: [AMBER] parameterization for non-standard nucleotide David A Case via AMBER
- Re: [AMBER] parameterization for non-standard nucleotide Moustafa, Ibrahim M. via AMBER
- Re: [AMBER] parameterization for non-standard nucleotide Moustafa, Ibrahim M. via AMBER
Sunday, 9 October 2022
- Re: [AMBER] How to add gaff parameters to PARMCHK.DAT file Jiaan Zhu via AMBER
Monday, 10 October 2022
- Re: [AMBER] Running the TI code on a single residue results in NaN electrostatics Miroslav Suruzhon via AMBER
- Re: [AMBER] parameterization for non-standard nucleotide Dr. Anselm Horn via AMBER
- [AMBER] Ambermd data erasure request - from Priya Dey - request: UFO3NP7F mmv.priya.dey--- via AMBER
Tuesday, 11 October 2022
- Re: [AMBER] parameterization for non-standard nucleotide Moustafa, Ibrahim M. via AMBER
- Re: [AMBER] Phase space overlap questions in alchemical free energy calculations David A Case via AMBER
Wednesday, 12 October 2022
- [AMBER] Question about h-bond analysis via cpptraj Enrico Martinez via AMBER
- [AMBER] PLUMED misformatted output file Tucker Burgin via AMBER
- [AMBER] using MCPB.py ışılay öztürk via AMBER
- Re: [AMBER] using MCPB.py ışılay öztürk via AMBER
- [AMBER] problem regarding "change" command Saikat Pal via AMBER
- [AMBER] Computing electrostatic interaction FyD via AMBER
Thursday, 13 October 2022
- [AMBER] Question about sasa values Sayan Poddar via AMBER
- Re: [AMBER] Question about sasa values SATYAJIT KHATUA via AMBER
- [AMBER] Separation of protein and ligand during TI simulation. Fanyu Zhao via AMBER
- [AMBER] Amber22 on Red Hat Enterprise Linux 8 Carlos Navarro via AMBER
- [AMBER] Multidihedral, average, lost residue numbers Rosellen, Martin via AMBER
- [AMBER] MCPB.py Failing with OPC water? Gustavo Seabra via AMBER
Friday, 14 October 2022
- Re: [AMBER] Multidihedral, average, lost residue numbers Rosellen, Martin via AMBER
- Re: [AMBER] problem regarding "change" command Daniel Roe via AMBER
- [AMBER] RTX4090 Benchmarks Ross Walker via AMBER
- Re: [AMBER] How to add gaff parameters to PARMCHK.DAT file David A Case via AMBER
- Re: [AMBER] Computing electrostatic interaction David A Case via AMBER
- Re: [AMBER] Separation of protein and ligand during TI simulation. David A Case via AMBER
- [AMBER] glycam web server Moustafa, Ibrahim M. via AMBER
- [AMBER] CpHMD and Umbrella sampling Dulal Mondal via AMBER
Saturday, 15 October 2022
- [AMBER] MCPB, wrong bonding pair Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] CpHMD and Umbrella sampling Vinicius Wilian Cruzeiro via AMBER
- [AMBER] "autoimage" function of cpptraj and holding molecule steady Cenk Andac via AMBER
- Re: [AMBER] "autoimage" function of cpptraj and holding molecule steady SATYAJIT KHATUA via AMBER
- [AMBER] Unsubsrcibe Matthew Noto via AMBER
- Re: [AMBER] "autoimage" function of cpptraj and holding molecule steady Carlos Simmerling via AMBER
- [AMBER] mdl file for OPC water model Weronika Bagrowska via AMBER
- Re: [AMBER] Separation of protein and ligand during TI simulation. Fanyu Zhao via AMBER
Sunday, 16 October 2022
- Re: [AMBER] Amber22, no DV/DL value with option gti_lam_sch Domenico Marson via AMBER
- Re: [AMBER] Ambermd data erasure request - from Priya Dey - request: UFO3NP7F Jason Swails via AMBER
- Re: [AMBER] Unsubsrcibe Jason Swails via AMBER
- [AMBER] Issues concerning keyboard on xleap interface Frederico Henrique Ferreira via AMBER
Monday, 17 October 2022
- [AMBER] clustering trajectories based on RMSD cut-off Sorin Draga via AMBER
- Re: [AMBER] clustering trajectories based on RMSD cut-off Carlos Simmerling via AMBER
- Re: [AMBER] clustering trajectories based on RMSD cut-off Sorin Draga via AMBER
- Re: [AMBER] {SPAM?} MCPB, wrong bonding pair Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] mdl file for OPC water model David A Case via AMBER
- Re: [AMBER] Separation of protein and ligand during TI simulation. Fanyu Zhao via AMBER
- Re: [AMBER] Issues concerning keyboard on xleap interface David A Case via AMBER
- [AMBER] Dihedral PCA Cluster Plot Suchetana Gupta via AMBER
- Re: [AMBER] Separation of protein and ligand during TI simulation. Dr. Anselm Horn via AMBER
Tuesday, 18 October 2022
- Re: [AMBER] Antechamber with QM software other than Gaussian Shiji Zhao via AMBER
- [AMBER] GaMD dihedral boosting Amber18 Martin Juhás via AMBER
- [AMBER] Ion counting angad sharma via AMBER
- [AMBER] AmberTools installation issue MacOS Xavier Brazzolotto via AMBER
- Re: [AMBER] AmberTools installation issue MacOS David A Case via AMBER
- Re: [AMBER] AmberTools installation issue MacOS Xavier Brazzolotto via AMBER
- Re: [AMBER] Ion counting George Madalin Giambasu via AMBER
- [AMBER] AmberTools22 installation compilation file comparisons failed wy202210192022 via AMBER
Wednesday, 19 October 2022
- Re: [AMBER] AmberTools22 installation compilation file comparisons failed Daniel Roe via AMBER
- Re: [AMBER] Ion counting Daniel Roe via AMBER
- [AMBER] Forcing a Peptide to be Helical Cianna Calia via AMBER
- [AMBER] Parameterization of magnesium ions binding site using MCPB.py Huang ZiJian via AMBER
Thursday, 20 October 2022
- Re: [AMBER] Forcing a Peptide to be Helical Cianna Calia via AMBER
- [AMBER] mmpbsa.py: error in the decomposition Enrico Martinez via AMBER
- Re: [AMBER] mmpbsa.py: error in the decomposition Rafał Madaj via AMBER
- Re: [AMBER] mmpbsa.py: error in the decomposition Enrico Martinez via AMBER
- Re: [AMBER] Parameterization of magnesium ions binding site using MCPB.py David A Case via AMBER
- Re: [AMBER] AmberTools22 installation compilation file comparisons failed David A Case via AMBER
- Re: [AMBER] mmpbsa.py: error in the decomposition Bill Miller III via AMBER
- [AMBER] Abrupt temperature rise carrying out Transition path sampling Divya Rai via AMBER
- Re: [AMBER] Abrupt temperature rise carrying out Transition path sampling Adrian Roitberg via AMBER
- [AMBER] AMBER GPU version: Segfault error with 12-6-4 parameters Jafari, Majid via AMBER
- [AMBER] Help in Standardizing NEB Aravind R via AMBER
Friday, 21 October 2022
- [AMBER] amber-subscribe Aravind R via AMBER
- Re: [AMBER] Help in Standardizing NEB Christina Bergonzo via AMBER
- [AMBER] How to restraint proteins to an axis Matthew Guberman-Pfeffer via AMBER
Saturday, 22 October 2022
- [AMBER] tiMerge error with ff19SB jinfeng liu via AMBER
- Re: [AMBER] RTX4090 Benchmarks filip fratev via AMBER
Sunday, 23 October 2022
- [AMBER] co-alchemical ion Pietro Vidossich via AMBER
- [AMBER] MCPB: How to make a larger "small model" Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] How to restraint proteins to an axis Matthew Guberman-Pfeffer via AMBER
- [AMBER] Some questiones about Gaussian/Amber QM/MM simulation 张兴赫 via AMBER
Monday, 24 October 2022
- [AMBER] Energy distribution check for REAF simulation kurisaki2013--- via AMBER
- [AMBER] mmpbsa problem with OPC waters Antonija Tomić via AMBER
- Re: [AMBER] mmpbsa problem with OPC waters Carlos Simmerling via AMBER
- Re: [AMBER] co-alchemical ion David A Case via AMBER
- Re: [AMBER] Some questiones about Gaussian/Amber QM/MM simulation David A Case via AMBER
- Re: [AMBER] C4 terms in 12-6-4LJ model David A Case via AMBER
- [AMBER] RESTRAINT versus NMR restraint in output? Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] mmpbsa problem with OPC waters Antonija Tomić via AMBER
- Re: [AMBER] MCPB: How to make a larger "small model" Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] co-alchemical ion accuratefreeenergy--- via AMBER
- [AMBER] How to restrain minimum distance between proteins? Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] MCPB: How to make a larger "small model" Vaibhav Dixit via AMBER
- Re: [AMBER] Energy distribution check for REAF simulation kurisaki2013--- via AMBER
Tuesday, 25 October 2022
- [AMBER] ERROR while using receptor_mask in MMPBSA Amit Sharma \(Asstt. Prof., MCARS\) via AMBER
- Re: [AMBER] MCPB: How to make a larger "small model" ışılay öztürk via AMBER
- [AMBER] Amber 22 serial installation on ubuntu-18.04 without GPU support Dulal Mondal via AMBER
Wednesday, 26 October 2022
- Re: [AMBER] Help in Standardizing NEB Aravind R via AMBER
- Re: [AMBER] RESTRAINT versus NMR restraint in output? David A Case via AMBER
- Re: [AMBER] ERROR while using receptor_mask in MMPBSA David A Case via AMBER
- Re: [AMBER] Help in Standardizing NEB Christina Bergonzo via AMBER
- Re: [AMBER] {SPAM?} Re: RESTRAINT versus NMR restraint in output? Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] How to restrain minimum distance between proteins? Gustavo Seabra via AMBER
- [AMBER] amber Computational problem Ding Shuaiwei via AMBER
Thursday, 27 October 2022
- Re: [AMBER] using MCPB.py Erdem Yeler via AMBER
- Re: [AMBER] using MCPB.py ışılay öztürk via AMBER
- Re: [AMBER] using MCPB.py Barış KURT via AMBER
- Re: [AMBER] using MCPB.py ışılay öztürk via AMBER
- Re: [AMBER] Amber 22 serial installation on ubuntu-18.04 without GPU support David A Case via AMBER
- Re: [AMBER] amber Computational problem David A Case via AMBER
- Re: [AMBER] using MCPB.py ışılay öztürk via AMBER
- [AMBER] Umbrella Sampling at constant pH using amber 22 Dulal Mondal via AMBER
- Re: [AMBER] Umbrella Sampling at constant pH using amber 22 Adrian Roitberg via AMBER
Friday, 28 October 2022
- [AMBER] 你好amber@ambermd.org你好 3163490855--- via AMBER
Saturday, 29 October 2022
- Re: [AMBER] Antechamber with QM software other than Gaussian Alexander Izvorski via AMBER
- Re: [AMBER] Antechamber with QM software other than Gaussian James Kress via AMBER
- Re: [AMBER] Antechamber with QM software other than Gaussian Barış KURT via AMBER
- Re: [AMBER] Antechamber with QM software other than Gaussian Alexander Izvorski via AMBER
- Re: [AMBER] Antechamber with QM software other than Gaussian Alexander Izvorski via AMBER
- Re: [AMBER] Antechamber with QM software other than Gaussian James Kress via AMBER
Sunday, 30 October 2022
- Re: [AMBER] Antechamber with QM software other than Gaussian Shiji Zhao via AMBER
- [AMBER] Simulation of ssDNA folding Jiaan Zhu via AMBER
- Re: [AMBER] Simulation of ssDNA folding Carlos Simmerling via AMBER
- Re: [AMBER] Simulation of ssDNA folding zhujiaan16.mails.ucas.ac.cn via AMBER
- Re: [AMBER] Simulation of ssDNA folding Thomas Cheatham via AMBER
- [AMBER] Occupancy calculation angad sharma via AMBER
Monday, 31 October 2022
- [AMBER] Amber22 GPU installation fails while building NVCC object `pmemd_xray_cuda_generated_BulkMaskGPU.cu.o` Nitin Kulhar via AMBER
- [AMBER] I implore you to fix the problem regarding MMPBSA analysis Subramanian Boopathi via AMBER
- Re: [AMBER] I implore you to fix the problem regarding MMPBSA analysis Bill Miller III via AMBER
- Re: [AMBER] I implore you to fix the problem regarding MMPBSA analysis Carlos Simmerling via AMBER
- [AMBER] Thermostat Question Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Thermostat Question Carlos Simmerling via AMBER
- [AMBER] Problem: Minimization and TI Matthew Guberman-Pfeffer via AMBER
Monday, 24 October 2022
- [AMBER] C4 terms in 12-6-4LJ model Sara Mahmoud via AMBER
Thursday, 20 October 2022
- [AMBER] Help in Standardizing NEB Aravind R via AMBER
Sunday, 16 October 2022
- [AMBER] Best force field and water model for amyloid study maryam ghorbaninia via AMBER

Last message date: Tue Nov 08 2022 - 13:30:05 PST
Archived on: Wed Apr 24 2024 - 05:56:10 PDT

Amber Archive Oct 2022 by date