Amber Archive Oct 2023: by thread

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

Amber Archive Oct 2023 by thread