Amber Archive Oct 2023: by date

Sunday, 1 October 2023
- [AMBER] Error with a cpptraj loop VERONICA MARTIN HERNANDEZ via AMBER
- Re: [AMBER] Error with a cpptraj loop SATYAJIT KHATUA via AMBER
- Re: [AMBER] Error with a cpptraj loop Daniel Roe via AMBER
- [AMBER] Error: Incompatible CUDA and GNU versions 9.4.0 Maryam Foroozmehr via AMBER
Monday, 2 October 2023
- Re: [AMBER] Error: Incompatible CUDA and GNU versions 9.4.0] David A Case via AMBER
- [AMBER] [amber-owner.ambermd.org: Re: Query Regarding PDB2GMX Error with Amber Force Field] David A Case via AMBER
- [AMBER] SSL: CERTIFICATE_VERIFY_FAILED Trevor Kramer via AMBER
Tuesday, 3 October 2023
- [AMBER] Query regarding two ligands with one DNA maya nair via AMBER
- Re: [AMBER] SSL: CERTIFICATE_VERIFY_FAILED David A Case via AMBER
- [AMBER] Fortran Runtime Error; Computing Binding Enthalpy Tutorial-Minimizing Water Box Meyer, Olivia \(meyerok\) via AMBER
- Re: [AMBER] [Sender Not Verified] Fortran Runtime Error; Computing Binding Enthalpy Tutorial-Minimizing Water Box Steinbrecher, Thomas via AMBER
Wednesday, 4 October 2023
- [AMBER] Analysis of pmemd performance for exascale Charles Laughton via AMBER
- [AMBER] Alchemical free energy Xiaoyu Wang via AMBER
- Re: [AMBER] [Sender Not Verified] Alchemical free energy Steinbrecher, Thomas via AMBER
- Re: [AMBER] ?==?utf-8?q? Query Regarding PDB2GMX Error with Amber Force Field Fadaei Fatemeh Mgr. via AMBER
- Re: [AMBER] ?==?utf-8?q? Query Regarding PDB2GMX Error with Amber Force Field David A Case via AMBER
- Re: [AMBER] Alchemical free energy David A Case via AMBER
- Re: [AMBER] Remove from mailing list Francesca Mocci via AMBER
- Re: [AMBER] Alchemical free energy Darrin York via AMBER
- [AMBER] Fwd: [Sender Not Verified] Query regarding two ligands with one DNA maya nair via AMBER
Thursday, 5 October 2023
- Re: [AMBER] Analysis of pmemd performance for exascale David A Case via AMBER
- Re: [AMBER] Analysis of pmemd performance for exascale David A Case via AMBER
Friday, 6 October 2023
- [AMBER] Error in MMGBSA calculation using IGB= 7 and 8 solvent models Anila Sebastian via AMBER
- Re: [AMBER] Error in MMGBSA calculation using IGB= 7 and 8 solvent models Carlos Simmerling via AMBER
- Re: [AMBER] Problem with rmsd Daniel Roe via AMBER
- [AMBER] Behaviour of addIonsRand in leap Dr. Anselm Horn via AMBER
- [AMBER] how to determine pi-pi stacking interaction Sourav Bhowmik via AMBER
Sunday, 8 October 2023
- [AMBER] About the colvar namelist of NFE module for Steered MD SATYAJIT KHATUA via AMBER
- [AMBER] DFTB3 level energies calculated by sqm and Gaussian are very different Suitian Lai via AMBER
- [AMBER] Is there a method of hybrid polarizable and additive force field? 王伊秋 via AMBER
Monday, 9 October 2023
- [AMBER] Constant pH REMD at explicit solvent Dulal Mondal via AMBER
- [AMBER] Can we use turbomole ESP data in amber K A SIVASANKER via AMBER
- [AMBER] parametrization of cobalt containing dicarbollide Martin Juhás via AMBER
- Re: [AMBER] [Sender Not Verified] Can we use turbomole ESP data in amber Steinbrecher, Thomas via AMBER
- [AMBER] cpptraj: loading several netcdf files using -y Enrico Martinez via AMBER
- [AMBER] Please remove me from the mailing list Tuckey, Ryan A via AMBER
- [AMBER] bug with nmropt and ntr group restraints Antoine MARION via AMBER
- Re: [AMBER] bug with nmropt and ntr group restraints Antoine MARION via AMBER
- Re: [AMBER] bug with nmropt and ntr group restraints Carlos Simmerling via AMBER
- [AMBER] RESP in Gaussian: GetVDW: no radius for atom Martin Juhás via AMBER
- Re: [AMBER] Is there a method of hybrid polarizable and additive force field? David A Case via AMBER
- Re: [AMBER] Behaviour of addIonsRand in leap David A Case via AMBER
- [AMBER] .rst7 files unreadable Meyer, Olivia \(meyerok\) via AMBER
- [AMBER] Fwd: Constant pH REMD at explicit solvent Dulal Mondal via AMBER
- Re: [AMBER] .rst7 files unreadable Carlos Simmerling via AMBER
- Re: [AMBER] Can we use turbomole ESP data in amber James Kress via AMBER
- [AMBER] restart H-REMD simulation Juraj Dobias via AMBER
Tuesday, 10 October 2023
- Re: [AMBER] .rst7 files unreadable Dr. Anselm Horn via AMBER
- Re: [AMBER] restart H-REMD simulation Daniel Roe via AMBER
- Re: [AMBER] Constant pH REMD at explicit solvent Daniel Roe via AMBER
- Re: [AMBER] Behaviour of addIonsRand in leap Daniel Roe via AMBER
- [AMBER] Please remove my email from the mailing list, Thank you. Adeleh Mokhles Gerami via AMBER
- Re: [AMBER] Problem with rmsd Daniel Roe via AMBER
- Re: [AMBER] .rst7 files unreadable Meyer, Olivia \(meyerok\) via AMBER
- Re: [AMBER] Problem with rmsd Daniel Roe via AMBER
- [AMBER] Tutorial for Constant pH on Dibasic Nonstandard Residues Nathan Black via AMBER
- Re: [AMBER] restart H-REMD simulation Shi Zhang via AMBER
Wednesday, 11 October 2023
- Re: [AMBER] restart H-REMD simulation Juraj Dobias via AMBER
- Re: [AMBER] Constant pH REMD at explicit solvent Daniel Roe via AMBER
- Re: [AMBER] Problem with rmsd Daniel Roe via AMBER
- Re: [AMBER] Constant pH REMD at explicit solvent Adrian Roitberg via AMBER
- [AMBER] How to calculate intermolecular H-bonding and pi-pi stacking interaction between solute Sourav Bhowmik via AMBER
- [AMBER] What's the meaning of "SCF energy" and "Total energy" in sqm output Suitian Lai via AMBER
- [AMBER] error when install Amber22 Setyanto Md via AMBER
- Re: [AMBER] [Sender Not Verified] How to calculate intermolecular H-bonding and pi-pi stacking interaction between solute Steinbrecher, Thomas via AMBER
Thursday, 12 October 2023
- [AMBER] Regarding 'bond' command in tleap Priyasha Majee via AMBER
- Re: [AMBER] Problem with rmsd Daniel Roe via AMBER
- Re: [AMBER] [Sender Not Verified] How to calculate intermolecular H-bonding and pi-pi stacking interaction between solute Rodrigo Galindo-Murillo via AMBER
- Re: [AMBER] Regarding 'bond' command in tleap Rodrigo Galindo-Murillo via AMBER
- Re: [AMBER] Request for help with colvar input file for umbrella sampling Hazarika, Saurov via AMBER
- Re: [AMBER] Request for help with colvar input file for umbrella sampling Carlos Simmerling via AMBER
- [AMBER] Error with tleap: Atom does not have a type MD MUZAFFAR UR REHMAN via AMBER
- Re: [AMBER] [Sender Not Verified] Error with tleap: Atom does not have a type Steinbrecher, Thomas via AMBER
Friday, 13 October 2023
- Re: [AMBER] Problem with rmsd Dr. Anselm Horn via AMBER
- [AMBER] KeyError: 'CMOL' in MCPB.py Kandhan, Palanisamy via AMBER
Sunday, 15 October 2023
- [AMBER] Regarding entropy calculation by using AmberTools: GIST Shakuntala Dhurua via AMBER
Monday, 16 October 2023
- Re: [AMBER] Error with tleap: Atom does not have a type VERONICA MARTIN HERNANDEZ via AMBER
- [AMBER] Help with Choosing the Amber Force Field for circular DNA Fadaei Fatemeh Mgr. via AMBER
Tuesday, 17 October 2023
- [AMBER] Collective variables in Amber Castro Martinez, Camila via AMBER
- [AMBER] Converting a PDB trajectory to a NetCDF trajectory Jing Qu via AMBER
- Re: [AMBER] Converting a PDB trajectory to a NetCDF trajectory SATYAJIT KHATUA via AMBER
- Re: [AMBER] Converting a PDB trajectory to a NetCDF trajectory Daniel Roe via AMBER
- Re: [AMBER] Memory leak in amber22 pmemd.cuda Daniel Roe via AMBER
Wednesday, 18 October 2023
- [AMBER] TI calculations on AMBER Natesan Mani via AMBER
- Re: [AMBER] Regarding entropy calculation by using AmberTools: GIST Steven Ramsey via AMBER
- [AMBER] Question about Parameters for Cannabidiol Robert Palmere via AMBER
- Re: [AMBER] Question about Parameters for Cannabidiol Monsurat M. Lawal via AMBER
- Re: [AMBER] Question about Parameters for Cannabidiol David A Case via AMBER
Thursday, 19 October 2023
- Re: [AMBER] TI calculations on AMBER accuratefreeenergy--- via AMBER
- [AMBER] residues lacking connect1/connect0 Andrea H. Kasun via AMBER
- Re: [AMBER] What's the meaning of "SCF energy" and "Total energy" in sqm output David A Case via AMBER
- Re: [AMBER] Error with tleap: Atom does not have a type David A Case via AMBER
- Re: [AMBER] Help with Choosing the Amber Force Field for circular DNA David A Case via AMBER
Friday, 20 October 2023
- [AMBER] "No babel excutables" error while trying to apply GAFF K A SIVASANKER via AMBER
- Re: [AMBER] "No babel excutables" error while trying to apply GAFF David Case via AMBER
Sunday, 22 October 2023
- [AMBER] Create a DMSO box as solvent Sepideh Jafari via AMBER
- Re: [AMBER] Error with tleap: Atom does not have a type He, Amy via AMBER
Monday, 23 October 2023
- [AMBER] mmpbsa.py: Error: Creating complex topology failed! Enrico Martinez via AMBER
Wednesday, 25 October 2023
- [AMBER] Can Not open ambermd.org Setyanto Md via AMBER
Thursday, 26 October 2023
- [AMBER] GPU Benchmarks: RTX 5000 Ada Tucker E. Burgin via AMBER
- [AMBER] Regarding APR in AMBER Natesan Mani via AMBER
- [AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE Xavier Wezen Chee via AMBER
- Re: [AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE Daniel Roe via AMBER
Friday, 27 October 2023
- Re: [AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE Daniel Roe via AMBER
- [AMBER] amber22 not running Mirfath Sultana Mesbahuddin via AMBER
- [AMBER] constant redox potential and cysteine Ferreira, Tarsis G via AMBER
Saturday, 28 October 2023
- Re: [AMBER] constant redox potential and cysteine Vinicius Cruzeiro \(Vinny\) via AMBER
Sunday, 29 October 2023
- [AMBER] Regarding GLYCAMM Natesan Mani via AMBER
- [AMBER] why tleap adds TER in the middle of my DNA sequence Priyasha Majee via AMBER
Monday, 30 October 2023
- Re: [AMBER] amber22 not running Dr. Anselm Horn via AMBER
- [AMBER] Ask about the PMF generated by the ASMD simulation Eleven via AMBER
- [AMBER] Ask about the PMF generated by the ASMD simulation 高鹏飞 via AMBER
- Re: [AMBER] why tleap adds TER in the middle of my DNA sequence Carlos Simmerling via AMBER
- [AMBER] What does ivalence set in PBSA? Matthew Guberman-Pfeffer via AMBER
- [AMBER] MMPBSA.py - perresidue + pairwise Pedro Guillem via AMBER
- Re: [AMBER] Regarding GLYCAMM David A Case via AMBER
- Re: [AMBER] why tleap adds TER in the middle of my DNA sequence David A Case via AMBER
- Re: [AMBER] Regarding GLYCAMM Lachele Foley via AMBER
Tuesday, 31 October 2023
- [AMBER] Amber22/AmberTools23: Enabling of libtorch & cudnn libraries breaks pbsa binaries Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER

Last message date: Tue Oct 31 2023 - 09:00:02 PDT
Archived on: Wed May 08 2024 - 05:56:04 PDT

Amber Archive Oct 2023 by date