Amber Archive Oct 2023: by author

accuratefreeenergy--- via AMBER
- Re: [AMBER] TI calculations on AMBER (Thu Oct 19 2023 - 07:04:00 PDT)
Adeleh Mokhles Gerami via AMBER
- [AMBER] Please remove my email from the mailing list, Thank you. (Tue Oct 10 2023 - 06:11:34 PDT)
Adrian Roitberg via AMBER
- Re: [AMBER] Constant pH REMD at explicit solvent (Wed Oct 11 2023 - 08:51:36 PDT)
Andrea H. Kasun via AMBER
- [AMBER] residues lacking connect1/connect0 (Thu Oct 19 2023 - 08:13:29 PDT)
Anila Sebastian via AMBER
- [AMBER] Error in MMGBSA calculation using IGB= 7 and 8 solvent models (Fri Oct 06 2023 - 01:32:52 PDT)
Antoine MARION via AMBER
- Re: [AMBER] bug with nmropt and ntr group restraints (Mon Oct 09 2023 - 09:39:07 PDT)
- [AMBER] bug with nmropt and ntr group restraints (Mon Oct 09 2023 - 09:32:49 PDT)
Carlos Simmerling via AMBER
- Re: [AMBER] why tleap adds TER in the middle of my DNA sequence (Mon Oct 30 2023 - 07:11:59 PDT)
- Re: [AMBER] Request for help with colvar input file for umbrella sampling (Thu Oct 12 2023 - 13:04:34 PDT)
- Re: [AMBER] .rst7 files unreadable (Mon Oct 09 2023 - 11:54:14 PDT)
- Re: [AMBER] bug with nmropt and ntr group restraints (Mon Oct 09 2023 - 09:45:24 PDT)
- Re: [AMBER] Error in MMGBSA calculation using IGB= 7 and 8 solvent models (Fri Oct 06 2023 - 03:06:20 PDT)
Castro Martinez, Camila via AMBER
- [AMBER] Collective variables in Amber (Tue Oct 17 2023 - 03:30:32 PDT)
Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER
- [AMBER] Amber22/AmberTools23: Enabling of libtorch & cudnn libraries breaks pbsa binaries (Tue Oct 31 2023 - 08:28:47 PDT)
Charles Laughton via AMBER
- [AMBER] Analysis of pmemd performance for exascale (Wed Oct 04 2023 - 00:40:49 PDT)
Daniel Roe via AMBER
- Re: [AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE (Fri Oct 27 2023 - 10:21:11 PDT)
- Re: [AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE (Thu Oct 26 2023 - 17:28:34 PDT)
- Re: [AMBER] Memory leak in amber22 pmemd.cuda (Tue Oct 17 2023 - 15:02:03 PDT)
- Re: [AMBER] Converting a PDB trajectory to a NetCDF trajectory (Tue Oct 17 2023 - 14:59:04 PDT)
- Re: [AMBER] Problem with rmsd (Thu Oct 12 2023 - 05:57:03 PDT)
- Re: [AMBER] Problem with rmsd (Wed Oct 11 2023 - 06:28:38 PDT)
- Re: [AMBER] Constant pH REMD at explicit solvent (Wed Oct 11 2023 - 06:26:42 PDT)
- Re: [AMBER] Problem with rmsd (Tue Oct 10 2023 - 11:07:57 PDT)
- Re: [AMBER] Problem with rmsd (Tue Oct 10 2023 - 06:19:52 PDT)
- Re: [AMBER] Behaviour of addIonsRand in leap (Tue Oct 10 2023 - 06:10:43 PDT)
- Re: [AMBER] Constant pH REMD at explicit solvent (Tue Oct 10 2023 - 06:08:55 PDT)
- Re: [AMBER] restart H-REMD simulation (Tue Oct 10 2023 - 05:59:38 PDT)
- Re: [AMBER] Problem with rmsd (Fri Oct 06 2023 - 07:28:01 PDT)
- Re: [AMBER] Error with a cpptraj loop (Sun Oct 01 2023 - 17:31:41 PDT)
Darrin York via AMBER
- Re: [AMBER] Alchemical free energy (Wed Oct 04 2023 - 09:48:22 PDT)
David A Case via AMBER
- Re: [AMBER] why tleap adds TER in the middle of my DNA sequence (Mon Oct 30 2023 - 13:14:46 PDT)
- Re: [AMBER] Regarding GLYCAMM (Mon Oct 30 2023 - 13:11:48 PDT)
- Re: [AMBER] Help with Choosing the Amber Force Field for circular DNA (Thu Oct 19 2023 - 08:43:22 PDT)
- Re: [AMBER] Error with tleap: Atom does not have a type (Thu Oct 19 2023 - 08:38:26 PDT)
- Re: [AMBER] What's the meaning of "SCF energy" and "Total energy" in sqm output (Thu Oct 19 2023 - 08:35:16 PDT)
- Re: [AMBER] Question about Parameters for Cannabidiol (Wed Oct 18 2023 - 20:26:43 PDT)
- Re: [AMBER] Behaviour of addIonsRand in leap (Mon Oct 09 2023 - 10:59:27 PDT)
- Re: [AMBER] Is there a method of hybrid polarizable and additive force field? (Mon Oct 09 2023 - 10:55:50 PDT)
- Re: [AMBER] Analysis of pmemd performance for exascale (Thu Oct 05 2023 - 07:41:51 PDT)
- Re: [AMBER] Analysis of pmemd performance for exascale (Thu Oct 05 2023 - 07:35:53 PDT)
- Re: [AMBER] Alchemical free energy (Wed Oct 04 2023 - 07:32:36 PDT)
- Re: [AMBER] ?==?utf-8?q? Query Regarding PDB2GMX Error with Amber Force Field (Wed Oct 04 2023 - 07:28:24 PDT)
- Re: [AMBER] SSL: CERTIFICATE_VERIFY_FAILED (Tue Oct 03 2023 - 08:08:05 PDT)
- [AMBER] [amber-owner.ambermd.org: Re: Query Regarding PDB2GMX Error with Amber Force Field] (Mon Oct 02 2023 - 10:13:54 PDT)
- Re: [AMBER] Error: Incompatible CUDA and GNU versions 9.4.0] (Mon Oct 02 2023 - 10:12:41 PDT)
David Case via AMBER
- Re: [AMBER] "No babel excutables" error while trying to apply GAFF (Fri Oct 20 2023 - 07:10:51 PDT)
Dr. Anselm Horn via AMBER
- Re: [AMBER] amber22 not running (Mon Oct 30 2023 - 00:52:12 PDT)
- Re: [AMBER] Problem with rmsd (Fri Oct 13 2023 - 00:48:42 PDT)
- Re: [AMBER] .rst7 files unreadable (Tue Oct 10 2023 - 02:05:15 PDT)
- [AMBER] Behaviour of addIonsRand in leap (Fri Oct 06 2023 - 09:08:13 PDT)
Dulal Mondal via AMBER
- [AMBER] Fwd: Constant pH REMD at explicit solvent (Mon Oct 09 2023 - 11:27:00 PDT)
- [AMBER] Constant pH REMD at explicit solvent (Mon Oct 09 2023 - 02:09:45 PDT)
Eleven via AMBER
- [AMBER] Ask about the PMF generated by the ASMD simulation (Mon Oct 30 2023 - 01:29:33 PDT)
Enrico Martinez via AMBER
- [AMBER] mmpbsa.py: Error: Creating complex topology failed! (Mon Oct 23 2023 - 03:58:24 PDT)
- [AMBER] cpptraj: loading several netcdf files using -y (Mon Oct 09 2023 - 06:25:29 PDT)
Fadaei Fatemeh Mgr. via AMBER
- [AMBER] Help with Choosing the Amber Force Field for circular DNA (Mon Oct 16 2023 - 08:18:57 PDT)
- Re: [AMBER] ?==?utf-8?q? Query Regarding PDB2GMX Error with Amber Force Field (Wed Oct 04 2023 - 05:51:00 PDT)
Ferreira, Tarsis G via AMBER
- [AMBER] constant redox potential and cysteine (Fri Oct 27 2023 - 23:13:47 PDT)
Francesca Mocci via AMBER
- Re: [AMBER] Remove from mailing list (Wed Oct 04 2023 - 08:43:51 PDT)
Hazarika, Saurov via AMBER
- Re: [AMBER] Request for help with colvar input file for umbrella sampling (Thu Oct 12 2023 - 12:57:27 PDT)
He, Amy via AMBER
- Re: [AMBER] Error with tleap: Atom does not have a type (Sun Oct 22 2023 - 22:54:30 PDT)
James Kress via AMBER
- Re: [AMBER] Can we use turbomole ESP data in amber (Mon Oct 09 2023 - 12:01:23 PDT)
Jing Qu via AMBER
- [AMBER] Converting a PDB trajectory to a NetCDF trajectory (Tue Oct 17 2023 - 09:55:09 PDT)
Juraj Dobias via AMBER
- Re: [AMBER] restart H-REMD simulation (Wed Oct 11 2023 - 00:47:43 PDT)
- [AMBER] restart H-REMD simulation (Mon Oct 09 2023 - 23:53:42 PDT)
K A SIVASANKER via AMBER
- [AMBER] "No babel excutables" error while trying to apply GAFF (Fri Oct 20 2023 - 05:13:56 PDT)
- [AMBER] Can we use turbomole ESP data in amber (Mon Oct 09 2023 - 03:47:41 PDT)
Kandhan, Palanisamy via AMBER
- [AMBER] KeyError: 'CMOL' in MCPB.py (Fri Oct 13 2023 - 12:38:14 PDT)
Lachele Foley via AMBER
- Re: [AMBER] Regarding GLYCAMM (Mon Oct 30 2023 - 23:43:20 PDT)
Martin Juhás via AMBER
- [AMBER] RESP in Gaussian: GetVDW: no radius for atom (Mon Oct 09 2023 - 09:50:53 PDT)
- [AMBER] parametrization of cobalt containing dicarbollide (Mon Oct 09 2023 - 04:44:09 PDT)
Maryam Foroozmehr via AMBER
- [AMBER] Error: Incompatible CUDA and GNU versions 9.4.0 (Sun Oct 01 2023 - 18:05:04 PDT)
Matthew Guberman-Pfeffer via AMBER
- [AMBER] What does ivalence set in PBSA? (Mon Oct 30 2023 - 08:47:26 PDT)
maya nair via AMBER
- [AMBER] Fwd: [Sender Not Verified] Query regarding two ligands with one DNA (Wed Oct 04 2023 - 11:01:35 PDT)
- [AMBER] Query regarding two ligands with one DNA (Tue Oct 03 2023 - 03:54:40 PDT)
MD MUZAFFAR UR REHMAN via AMBER
- [AMBER] Error with tleap: Atom does not have a type (Thu Oct 12 2023 - 22:32:56 PDT)
Meyer, Olivia \(meyerok\) via AMBER
- Re: [AMBER] .rst7 files unreadable (Tue Oct 10 2023 - 07:13:17 PDT)
- [AMBER] .rst7 files unreadable (Mon Oct 09 2023 - 11:08:57 PDT)
- [AMBER] Fortran Runtime Error; Computing Binding Enthalpy Tutorial-Minimizing Water Box (Tue Oct 03 2023 - 10:59:32 PDT)
Mirfath Sultana Mesbahuddin via AMBER
- [AMBER] amber22 not running (Fri Oct 27 2023 - 11:14:16 PDT)
Monsurat M. Lawal via AMBER
- Re: [AMBER] Question about Parameters for Cannabidiol (Wed Oct 18 2023 - 15:46:06 PDT)
Natesan Mani via AMBER
- [AMBER] Regarding GLYCAMM (Sun Oct 29 2023 - 14:59:16 PDT)
- [AMBER] Regarding APR in AMBER (Thu Oct 26 2023 - 09:02:35 PDT)
- [AMBER] TI calculations on AMBER (Wed Oct 18 2023 - 10:09:03 PDT)
Nathan Black via AMBER
- [AMBER] Tutorial for Constant pH on Dibasic Nonstandard Residues (Tue Oct 10 2023 - 14:58:57 PDT)
Pedro Guillem via AMBER
- [AMBER] MMPBSA.py - perresidue + pairwise (Mon Oct 30 2023 - 10:39:01 PDT)
Priyasha Majee via AMBER
- [AMBER] why tleap adds TER in the middle of my DNA sequence (Sun Oct 29 2023 - 23:19:38 PDT)
- [AMBER] Regarding 'bond' command in tleap (Thu Oct 12 2023 - 04:58:02 PDT)
Robert Palmere via AMBER
- [AMBER] Question about Parameters for Cannabidiol (Wed Oct 18 2023 - 13:57:12 PDT)
Rodrigo Galindo-Murillo via AMBER
- Re: [AMBER] Regarding 'bond' command in tleap (Thu Oct 12 2023 - 08:49:57 PDT)
- Re: [AMBER] [Sender Not Verified] How to calculate intermolecular H-bonding and pi-pi stacking interaction between solute (Thu Oct 12 2023 - 06:53:12 PDT)
SATYAJIT KHATUA via AMBER
- Re: [AMBER] Converting a PDB trajectory to a NetCDF trajectory (Tue Oct 17 2023 - 10:03:36 PDT)
- [AMBER] About the colvar namelist of NFE module for Steered MD (Sun Oct 08 2023 - 08:27:10 PDT)
- Re: [AMBER] Error with a cpptraj loop (Sun Oct 01 2023 - 13:41:35 PDT)
Sepideh Jafari via AMBER
- [AMBER] Create a DMSO box as solvent (Sun Oct 22 2023 - 04:08:57 PDT)
Setyanto Md via AMBER
- [AMBER] Can Not open ambermd.org (Wed Oct 25 2023 - 20:10:25 PDT)
- [AMBER] error when install Amber22 (Wed Oct 11 2023 - 20:14:21 PDT)
Shakuntala Dhurua via AMBER
- [AMBER] Regarding entropy calculation by using AmberTools: GIST (Sun Oct 15 2023 - 08:00:52 PDT)
Shi Zhang via AMBER
- Re: [AMBER] restart H-REMD simulation (Tue Oct 10 2023 - 16:17:17 PDT)
Sourav Bhowmik via AMBER
- [AMBER] How to calculate intermolecular H-bonding and pi-pi stacking interaction between solute (Wed Oct 11 2023 - 10:01:49 PDT)
- [AMBER] how to determine pi-pi stacking interaction (Fri Oct 06 2023 - 10:02:38 PDT)
Steinbrecher, Thomas via AMBER
- Re: [AMBER] [Sender Not Verified] Error with tleap: Atom does not have a type (Thu Oct 12 2023 - 23:42:48 PDT)
- Re: [AMBER] [Sender Not Verified] How to calculate intermolecular H-bonding and pi-pi stacking interaction between solute (Wed Oct 11 2023 - 23:16:44 PDT)
- Re: [AMBER] [Sender Not Verified] Can we use turbomole ESP data in amber (Mon Oct 09 2023 - 05:14:51 PDT)
- Re: [AMBER] [Sender Not Verified] Alchemical free energy (Wed Oct 04 2023 - 05:09:33 PDT)
- Re: [AMBER] [Sender Not Verified] Fortran Runtime Error; Computing Binding Enthalpy Tutorial-Minimizing Water Box (Tue Oct 03 2023 - 23:13:52 PDT)
Steven Ramsey via AMBER
- Re: [AMBER] Regarding entropy calculation by using AmberTools: GIST (Wed Oct 18 2023 - 10:56:25 PDT)
Suitian Lai via AMBER
- [AMBER] What's the meaning of "SCF energy" and "Total energy" in sqm output (Wed Oct 11 2023 - 19:30:26 PDT)
- [AMBER] DFTB3 level energies calculated by sqm and Gaussian are very different (Sun Oct 08 2023 - 08:36:15 PDT)
Trevor Kramer via AMBER
- [AMBER] SSL: CERTIFICATE_VERIFY_FAILED (Mon Oct 02 2023 - 19:41:25 PDT)
Tucker E. Burgin via AMBER
- [AMBER] GPU Benchmarks: RTX 5000 Ada (Thu Oct 26 2023 - 07:06:00 PDT)
Tuckey, Ryan A via AMBER
- [AMBER] Please remove me from the mailing list (Mon Oct 09 2023 - 08:08:27 PDT)
VERONICA MARTIN HERNANDEZ via AMBER
- Re: [AMBER] Error with tleap: Atom does not have a type (Mon Oct 16 2023 - 01:41:53 PDT)
- [AMBER] Error with a cpptraj loop (Sun Oct 01 2023 - 12:56:49 PDT)
Vinicius Cruzeiro \(Vinny\) via AMBER
- Re: [AMBER] constant redox potential and cysteine (Sat Oct 28 2023 - 10:41:46 PDT)
Xavier Wezen Chee via AMBER
- [AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE (Thu Oct 26 2023 - 15:42:20 PDT)
Xiaoyu Wang via AMBER
- [AMBER] Alchemical free energy (Wed Oct 04 2023 - 04:36:49 PDT)
王伊秋 via AMBER
- [AMBER] Is there a method of hybrid polarizable and additive force field? (Sun Oct 08 2023 - 20:01:18 PDT)
高鹏飞 via AMBER
- [AMBER] Ask about the PMF generated by the ASMD simulation (Mon Oct 30 2023 - 01:42:33 PDT)

Amber Archive Oct 2023 by author