Amber Archive Feb 2024: by date

Friday, 2 February 2024
- Re: [AMBER] QUICK QM/MM problem/bug Juraj Dobias via AMBER
- [AMBER] Question about amber mask for restrains Enrico Martinez via AMBER
- [AMBER] Two questions about CPPTRAJ processing Enrico Martinez via AMBER
- Re: [AMBER] Two questions about CPPTRAJ processing Enrico Martinez via AMBER
- Re: [AMBER] QUICK QM/MM problem/bug David A Case via AMBER
- Re: [AMBER] Generating tleap input files for an organomtallic complex David A Case via AMBER
- [AMBER] Calculating RMSD between apoprotein and protein-ligand complex Alexander Hung Lee via AMBER
Saturday, 3 February 2024
- [AMBER] Question about λ adjustable acceleration parameter in aMD 李美玲 via AMBER
- [AMBER] Fw: non superuser installation Joel Gallardo via AMBER
Monday, 5 February 2024
- Re: [AMBER] QUICK QM/MM problem/bug Juraj Dobias via AMBER
- Re: [AMBER] AMBER22 and AmberTools23 installation issue Todd Minehardt via AMBER
- Re: [AMBER] Fw: non superuser installation David A Case via AMBER
- Re: [AMBER] QUICK QM/MM problem/bug David A Case via AMBER
Tuesday, 6 February 2024
- [AMBER] AMBER 20 installation error on Rockey Linux 8 Michael Shokhen via AMBER
- [AMBER] Issue with running NPT ensemble simulations on AMBER 22 using RTX 4500 ada Abhilash J via AMBER
- [AMBER] CM parameters missing in Amber Noureen Abdelrahman via AMBER
- Re: [AMBER] CM parameters missing in Amber Carlos Simmerling via AMBER
- [AMBER] GPU perf: RTX3060TI < RTX2060 Super < RTX4090 ? Thomas C. Bishop via AMBER
- Re: [AMBER] Issue with running NPT ensemble simulations on AMBER 22 using RTX 4500 ada Abhilash J via AMBER
- [AMBER] constant pH protonation states Yang, Li-Yen via AMBER
- Re: [AMBER] constant pH protonation states He, Amy via AMBER
- Re: [AMBER] constant pH protonation states Yang, Li-Yen via AMBER
- Re: [AMBER] constant pH protonation states He, Amy via AMBER
- [AMBER] Amber installation Karis Jimenes via AMBER
- Re: [AMBER] Amber installation haiyangzhong via AMBER
Wednesday, 7 February 2024
- [AMBER] Error in incorporating a modified nucleoside into the 1BNA template Sruthi Sudhakar via AMBER
- [AMBER] AMBER installation error on Rocky Linux 8 Michael Shokhen via AMBER
- Re: [AMBER] AMBER installation error on Rocky Linux 8 Todd Minehardt via AMBER
- Re: [AMBER] constant pH protonation states Yang, Li-Yen via AMBER
- Re: [AMBER] constant pH protonation states He, Amy via AMBER
Thursday, 8 February 2024
- [AMBER] dev/shm memory errors in Amber 22 Waqqas Zia via AMBER
- [AMBER] Computational Chemistry summer intern position. Rodrigo Galindo-Murillo via AMBER
- [AMBER] Error parametrizing ligand covalently bound to cysteine using GAFF Noureen Abdelrahman via AMBER
- [AMBER] Masking backbone interactions Prithviraj Nandigrami via AMBER
Friday, 9 February 2024
- [AMBER] Compiling AmberTools on OSX-arm64 Istvan Kolossvary via AMBER
- [AMBER] PSU residue parameters Debarati DasGupta via AMBER
- Re: [AMBER] PSU residue parameters Rodrigo Galindo-Murillo via AMBER
Sunday, 11 February 2024
- Re: [AMBER] AMBER 20 installation error on Rockey Linux 8 David A Case via AMBER
- Re: [AMBER] GPU perf: RTX3060TI < RTX2060 Super < RTX4090 ? David A Case via AMBER
- Re: [AMBER] Amber installation David A Case via AMBER
- Re: [AMBER] Error parametrizing ligand covalently bound to cysteine using GAFF David A Case via AMBER
Monday, 12 February 2024
- [AMBER] Fwd: dev/shm memory errors in Amber 22 Waqqas Zia via AMBER
- [AMBER] Query regarding Temperature Replica Exchange Molecular Dynamics? Munazzah Fatima Ansari via AMBER
- Re: [AMBER] Query regarding Temperature Replica Exchange Molecular Dynamics? Carlos Simmerling via AMBER
Tuesday, 13 February 2024
- Re: [AMBER] Fwd: dev/shm memory errors in Amber 22 David A Case via AMBER
- [AMBER] Dihedral Parametrization in Amber19: Same QM level as for 94? Jones De Andrade via AMBER
- [AMBER] Residues Naming Advice Kaleem Arshad via AMBER
- Re: [AMBER] Residues Naming Advice He, Amy via AMBER
Wednesday, 14 February 2024
- [AMBER] Using AM1-BCC charges for Organometalls Miriam Sprick via AMBER
- Re: [AMBER] Dihedral Parametrization in Amber19: Same QM level as for 94? Carlos Simmerling via AMBER
- Re: [AMBER] Issue with running NPT ensemble simulations on AMBER 22 using RTX 4500 ada Abhilash J via AMBER
- [AMBER] Solvation models with RNA Debarati DasGupta via AMBER
- Re: [AMBER] Issue with running NPT ensemble simulations on AMBER 22 using RTX 4500 ada Abhilash J via AMBER
- Re: [AMBER] Issue with running NPT ensemble simulations on AMBER 22 using RTX 4500 ada Tru Huynh via AMBER
- [AMBER] Prmtop Parmed and CPPTRAJ Check-Energy Minimization Failure Kaleem Arshad via AMBER
Thursday, 15 February 2024
- Re: [AMBER] Dihedral Parametrization in Amber19: Same QM level as for 94? Jones de Andrade via AMBER
- Re: [AMBER] Dihedral Parametrization in Amber19: Same QM level as for 94? Jones de Andrade via AMBER
- Re: [AMBER] Dihedral Parametrization in Amber19: Same QM level as for 94? He, Amy via AMBER
Friday, 16 February 2024
- [AMBER] failed to minimize after solvation from glycam web BILASH MAITY via AMBER
- Re: [AMBER] Dihedral Parametrization in Amber19: Same QM level as for 94? Jones De Andrade via AMBER
- Re: [AMBER] Prmtop Parmed and CPPTRAJ Check-Energy Minimization Failure David A Case via AMBER
- Re: [AMBER] Dihedral Parametrization in Amber19: Same QM level as for 94? David A Case via AMBER
- Re: [AMBER] failed to minimize after solvation from glycam web David A Case via AMBER
- Re: [AMBER] Dihedral Parametrization in Amber19: Same QM level as for 94? He, Amy via AMBER
Monday, 19 February 2024
- [AMBER] MMPBSA.py: entropy calculation options Dr. Anselm Horn via AMBER
- [AMBER] Force field parameters for modified RNA Jenny 148 via AMBER
- Re: [AMBER] Prmtop Parmed and CPPTRAJ Check-Energy Minimization Failure David A Case via AMBER
- Re: [AMBER] MMPBSA.py: entropy calculation options Bill Miller III via AMBER
- [AMBER] CUDA Toolkit Installation for WSL (Ubuntu 22.04) Kaleem Arshad via AMBER
Tuesday, 20 February 2024
- [AMBER] Constant pH remd Dulal Mondal via AMBER
- Re: [AMBER] MMPBSA.py: entropy calculation options Dr. Anselm Horn via AMBER
- Re: [AMBER] Constant pH remd Adrian Roitberg via AMBER
- [AMBER] Insufficient frames generated Godbole, Shivani via AMBER
- [AMBER] CHARMM Dual Membranes Thompson, Emma via AMBER
- [AMBER] Converting CGenFF CHARMM parameters in tleap Collin Nisler via AMBER
- Re: [AMBER] Converting CGenFF CHARMM parameters in tleap He, Amy via AMBER
- Re: [AMBER] CUDA Toolkit Installation for WSL (Ubuntu 22.04) David A Case via AMBER
- Re: [AMBER] Converting CGenFF CHARMM parameters in tleap David A Case via AMBER
- Re: [AMBER] Insufficient frames generated He, Amy via AMBER
- Re: [AMBER] CHARMM Dual Membranes Stephan Schott via AMBER
- Re: [AMBER] Converting CGenFF CHARMM parameters in tleap Collin Nisler via AMBER
- Re: [AMBER] Converting CGenFF CHARMM parameters in tleap He, Amy via AMBER
- [AMBER] Energy decomposition of TI results using cpptraj. Fanyu Zhao via AMBER
- [AMBER] issue performing heating of protein in implicit solvent Ildar Garipov via AMBER
- Re: [AMBER] Constant pH remd Dulal Mondal via AMBER
Wednesday, 21 February 2024
- Re: [AMBER] issue performing heating of protein in implicit solvent Carlos Simmerling via AMBER
- Re: [AMBER] Constant pH remd Skanda Sastry via AMBER
- Re: [AMBER] Insufficient frames generated Godbole, Shivani via AMBER
- Re: [AMBER] issue performing heating of protein in implicit solvent Carlos Simmerling via AMBER
- Re: [AMBER] Converting CGenFF CHARMM parameters in tleap Collin Nisler via AMBER
- Re: [AMBER] Constant pH remd He, Amy via AMBER
- Re: [AMBER] Best practises for running MD with RNA structures Debarati DasGupta via AMBER
- Re: [AMBER] Constant pH remd Dulal Mondal via AMBER
- Re: [AMBER] Constant pH remd Dulal Mondal via AMBER
Thursday, 22 February 2024
- [AMBER] Regarding Problems with Amber22 Installation on M1 & M2 Hoonsung Lee via AMBER
- [AMBER] Final MD Run in Parts Kaleem Arshad via AMBER
- Re: [AMBER] Best practises for running MD with RNA structures Christina Bergonzo via AMBER
- [AMBER] using 12_6_4 ion parameters with OPC water model Giulio RASTELLI via AMBER
- [AMBER] Thermodynamic Integration of Loosening Restraints Helmut Carter via AMBER
- Re: [AMBER] Constant pH remd Skanda Sastry via AMBER
Friday, 23 February 2024
- [AMBER] Converting ff19SB data files for usage with GROMACS Vedran Miletic via AMBER
- Re: [AMBER] Converting ff19SB data files for usage with GROMACS Carlos Simmerling via AMBER
- Re: [AMBER] [Sender Not Verified] Re: Constant pH remd Adrian Roitberg via AMBER
- Re: [AMBER] Regarding Problems with Amber22 Installation on M1 & M2 David A Case via AMBER
- Re: [AMBER] using 12_6_4 ion parameters with OPC water model Carlos Simmerling via AMBER
- Re: [AMBER] Thermodynamic Integration of Loosening Restraints David A Case via AMBER
- Re: [AMBER] Thermodynamic Integration of Loosening Restraints Darrin York via AMBER
- Re: [AMBER] Best practises for running MD with RNA structures Darrin York via AMBER
- Re: [AMBER] Thermodynamic Integration of Loosening Restraints Skanda Sastry via AMBER
- [AMBER] imaging membrane system Romero, Maria via AMBER
- [AMBER] NTWX Value Advice for Final MD Run Kaleem Arshad via AMBER
Saturday, 24 February 2024
- Re: [AMBER] NTWX Value Advice for Final MD Run Carlos Simmerling via AMBER
Sunday, 25 February 2024
- [AMBER] Is it possible to model a protein with a linker covalently attached at a cysteine? Sasha Buzko via AMBER
Monday, 26 February 2024
- Re: [AMBER] Is it possible to model a protein with a linker covalently attached at a cysteine? Dr. Anselm Horn via AMBER
- [AMBER] Too many TI atoms ERROR Mehrnoosh Khodam Hazrati via AMBER
- [AMBER] Simulation of a membrane containing system in implicit solvent Sergey Samsonov via AMBER
- Re: [AMBER] Is it possible to model a protein with a linker covalently attached at a cysteine? Missing angle parameters Sasha Buzko via AMBER
- Re: [AMBER] Is it possible to model a protein with a linker covalently attached at a cysteine? Missing angle parameters David A Case via AMBER
- [AMBER] Improper torsion terms when building covalent bond in leap Nicole Vita via AMBER
- [AMBER] Sander.mpi haults at 999 steps Montalvillo, Fernando via AMBER
- Re: [AMBER] Improper torsion terms when building covalent bond in leap He, Amy via AMBER
Tuesday, 27 February 2024
- [AMBER] Ranges in generated PRMTOP for Atomic Numbers Trevor Kramer via AMBER
- Re: [AMBER] using 12_6_4 ion parameters with OPC water model Giulio RASTELLI via AMBER
- Re: [AMBER] using 12_6_4 ion parameters with OPC water model haiyangzhong via AMBER
- [AMBER] Please remove my email from mailing list. Thank you Adeleh Mokhles Gerami via AMBER
- Re: [AMBER] using 12_6_4 ion parameters with OPC water model Carlos Simmerling via AMBER
- [AMBER] Long Bond length during simulation of nonstandard residue Cao, Dillon P. via AMBER
- Re: [AMBER] Long Bond length during simulation of nonstandard residue Carlos Simmerling via AMBER
- Re: [AMBER] Long Bond length during simulation of nonstandard residue Cao, Dillon P. via AMBER
Wednesday, 28 February 2024
- [AMBER] Constant pH replica exchange Dulal Mondal via AMBER
- Re: [AMBER] Is it possible to model a protein with a linker covalently attached at a cysteine? Mysterious "invisible" torsion parameters? Dr. Anselm Horn via AMBER
- Re: [AMBER] Constant pH replica exchange Dulal Mondal via AMBER
- Re: [AMBER] Ranges in generated PRMTOP for Atomic Numbers Dr. Anselm Horn via AMBER
- [AMBER] Cu2+ and Zn2+ modeling Omar Ben Mariem via AMBER
- [AMBER] make install error related to pmemd xray & MKL Pertschy, Florian via AMBER
- [AMBER] Error building Amber22 with cuda Dhariwal, Rohit via AMBER
- [AMBER] RMSD values are low Godbole, Shivani via AMBER
- Re: [AMBER] [Sender Not Verified] RMSD values are low Steinbrecher, Thomas via AMBER
- [AMBER] Renumber residues (Error: No change type specified) - AMBER MD 18 Daniel Hall via AMBER
- Re: [AMBER] [Sender Not Verified] RMSD values are low Godbole, Shivani via AMBER
- Re: [AMBER] Renumber residues (Error: No change type specified) - AMBER MD 18 Rodrigo Galindo-Murillo via AMBER
- Re: [AMBER] [Sender Not Verified] RMSD values are low Steinbrecher, Thomas via AMBER
- [AMBER] Force field for modified DNA (OL15 or PARMBSC1) Mac Kevin Braza via AMBER
Thursday, 29 February 2024
- [AMBER] uncertainty in atomic positional fluctuations Duggan, Brendan via AMBER
- Re: [AMBER] uncertainty in atomic positional fluctuations Adrian Roitberg via AMBER
- Re: [AMBER] Error building Amber22 with cuda Goetz, Andreas via AMBER

Last message date: Thu Feb 29 2024 - 13:30:02 PST
Archived on: Mon May 06 2024 - 05:56:06 PDT

Amber Archive Feb 2024 by date