Amber Archive Nov 2018 by thread
- Re: [AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory Dow Hurst (Wed Oct 31 2018 - 21:23:59 PDT)
- [AMBER] CpH simulation- error reading charges in long cpin file Amy Rice (Thu Nov 01 2018 - 09:28:54 PDT)
- Re: [AMBER] the unperturbed charge of the unit is not zero soukaina louerdi (Thu Nov 01 2018 - 12:15:15 PDT)
- Re: [AMBER] CUDA 10.0 vs CUDA 9.2 for Amber18&1080Ti GTX - any gain in performance? Nikolay N. Kuzmich (Fri Nov 02 2018 - 02:12:44 PDT)
- [AMBER] Protein residues CA atoms treated as sidechain in binding energy decomposition? 鲍劲霄 (Fri Nov 02 2018 - 07:58:31 PDT)
- Re: [AMBER] non-bonded params hosein geraili (Fri Nov 02 2018 - 09:50:47 PDT)
- [AMBER] Non-convergence when calculating partial charges for aromatic-adjacent nitriles Jeffrey Wagner (Fri Nov 02 2018 - 10:50:49 PDT)
- [AMBER] Postdoctoral position in the area of FFT-based binding free energy calculations David Minh (Fri Nov 02 2018 - 10:59:01 PDT)
- [AMBER] ligand force field hosein geraili (Fri Nov 02 2018 - 11:22:13 PDT)
- [AMBER] 回复： non-bonded params 201612095.mail.sdu.edu.cn (Fri Nov 02 2018 - 16:06:10 PDT)
- Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Rajbinder Kaur Virk (Sat Nov 03 2018 - 01:01:01 PDT)
- [AMBER] 02_03.rms problem simon chapman (Sat Nov 03 2018 - 02:08:29 PDT)
- [AMBER] regarding ter Charu Sharma (JRF) (Sat Nov 03 2018 - 22:39:15 PDT)
- [AMBER] IR Spectra Abdullah Bin Faheem (Sun Nov 04 2018 - 22:07:16 PST)
- [AMBER] Accelerated MD stopped with Cuda GPU error. M RCC (Sun Nov 04 2018 - 23:10:11 PST)
- Re: [AMBER] Problem regarding radial command Daniel Roe (Mon Nov 05 2018 - 07:12:29 PST)
- [AMBER] Acpype error. No such file or directory neelam wafa (Mon Nov 05 2018 - 07:18:51 PST)
- [AMBER] Implicit solvent simulation effects for the folding Mijiddorj B (Mon Nov 05 2018 - 19:17:47 PST)
- [AMBER] Help regarding AMBER16 CUDA installation Saikat Dutta chowdhury (Tue Nov 06 2018 - 05:13:29 PST)
- [AMBER] amber 18 compilation issue Vlad Cojocaru (Tue Nov 06 2018 - 06:29:54 PST)
- [AMBER] different residue numbering Rosellen, Martin (Tue Nov 06 2018 - 07:27:37 PST)
- [AMBER] Generating topologies with antechamber and acpype neelam wafa (Wed Nov 07 2018 - 01:37:16 PST)
- [AMBER] Geometric hard constraints Charo del Genio (Wed Nov 07 2018 - 02:44:16 PST)
- [AMBER] Generation of velocities depends on conformation? Nicolas Cheron (Wed Nov 07 2018 - 02:44:11 PST)
- [AMBER] MCPB.py Viviani, Lucas (Wed Nov 07 2018 - 02:49:48 PST)
- [AMBER] Files work with sander and not pmemd Nicolas Cheron (Wed Nov 07 2018 - 03:12:38 PST)
- Re: [AMBER] Interplane angles using vector and vectormath in cpptraj Daniel Roe (Wed Nov 07 2018 - 05:54:30 PST)
- [AMBER] REMD: What can I do with much larger replicas than the number of processors Zhonghua Xia (Wed Nov 07 2018 - 07:22:51 PST)
- [AMBER] problem of GPU with ibelly Hadi Rahmaninejad (Wed Nov 07 2018 - 08:05:44 PST)
- [AMBER] Error while using antechamber (AMBER 18) RITUPARNA ROY (Wed Nov 07 2018 - 23:08:13 PST)
- Re: [AMBER] MD_Box_size_and_counterions_counting_general_rule Antonio Amber Carlesso (Thu Nov 08 2018 - 01:43:16 PST)
- [AMBER] Problem with obtaining iodine parameters via R.E.D. Server Markowska (Thu Nov 08 2018 - 04:29:21 PST)
- [AMBER] post-simulation thermodynamic integration calculations Veenis, Andrew Jay (Thu Nov 08 2018 - 12:17:03 PST)
- [AMBER] CPPTRAJ "usefrcascoords" SARAH JEANNE LEFAVE (Thu Nov 08 2018 - 12:33:36 PST)
- Re: [AMBER] phosphorylated peptide with implicit solvent David A Case (Fri Nov 09 2018 - 05:17:44 PST)
- [AMBER] Post-doctoral position in MD at UC Riverside giulia palermo (Fri Nov 09 2018 - 23:57:30 PST)
- [AMBER] tLeap sequence overlap with new residues David Poole (Sat Nov 10 2018 - 06:45:13 PST)
- [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? maryam azimzadehirani (Sun Nov 11 2018 - 04:40:39 PST)
- Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? David Cerutti (Sun Nov 11 2018 - 23:03:04 PST)
- Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? maryam azimzadehirani (Mon Nov 12 2018 - 04:05:02 PST)
- Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? ABEL Stephane (Mon Nov 12 2018 - 05:23:17 PST)
- Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? maryam azimzadehirani (Mon Nov 12 2018 - 06:10:17 PST)
- Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? David Cerutti (Mon Nov 12 2018 - 23:24:20 PST)
- Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? Casalini Tommaso (Mon Nov 12 2018 - 23:39:40 PST)
- Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? maryam azimzadehirani (Mon Nov 12 2018 - 23:41:42 PST)
- Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? David Cerutti (Mon Nov 12 2018 - 23:49:45 PST)
- Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? Dr. Anselm Horn (Tue Nov 13 2018 - 04:50:58 PST)
- Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? Lachele Foley (Tue Nov 13 2018 - 05:57:59 PST)
- Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? maryam azimzadehirani (Tue Nov 13 2018 - 06:06:15 PST)
- Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? maryam azimzadehirani (Tue Nov 13 2018 - 23:10:11 PST)
- Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? David A Case (Mon Nov 12 2018 - 05:26:58 PST)
- Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? Casalini Tommaso (Mon Nov 12 2018 - 05:36:45 PST)
- [AMBER] Preparation of force field of zwitterion glycine molecule euq1702 (Sun Nov 11 2018 - 08:14:49 PST)
- [AMBER] How long should a NPT equilibrium take in QM/MM MD? Meng Wu (Mon Nov 12 2018 - 02:28:14 PST)
- Re: [AMBER] Energies SARAH JEANNE LEFAVE (Mon Nov 12 2018 - 08:14:56 PST)
- [AMBER] how long should a NPT equilibrium take in QM/MM MD? 郭昱 (Mon Nov 12 2018 - 17:17:56 PST)
- [AMBER] regarding tutorials Charu Sharma (JRF) (Mon Nov 12 2018 - 21:41:28 PST)
- [AMBER] query Charu Sharma (JRF) (Mon Nov 12 2018 - 22:27:35 PST)
- [AMBER] RMSD mask selection and closestwater clarification Korey M Reid (Tue Nov 13 2018 - 14:17:06 PST)
- [AMBER] Radial Distribution Function of Waters with respect to a particular Atom diego.soler.uam.es (Wed Nov 14 2018 - 02:11:06 PST)
- [AMBER] regarding MD simulation Charu Sharma (JRF) (Wed Nov 14 2018 - 02:57:36 PST)
- [AMBER] Regarding output file processing of temperature replica exchange Rajarshi Roy (Wed Nov 14 2018 - 04:01:50 PST)
- [AMBER] reconstruction of pH-based trajectory files Elvira Tarasova (Wed Nov 14 2018 - 20:25:15 PST)
- [AMBER] Antechamber with protonated arginine Jose Manuel Granadino Roldán (Wed Nov 14 2018 - 23:05:12 PST)
- [AMBER] Amber 18 memory Beale, John (Thu Nov 15 2018 - 01:05:19 PST)
- [AMBER] GPU card for AMBER Fabian Glaser (Thu Nov 15 2018 - 03:16:43 PST)
- [AMBER] Antechamber for PCBM soukaina louerdi (Thu Nov 15 2018 - 05:07:50 PST)
- [AMBER] very high values of "wrapping mol" when potential boost applied to chloroform solvent system Chetna Tyagi (Thu Nov 15 2018 - 05:24:53 PST)
- [AMBER] Building crystal structures Ali Khodayari (Thu Nov 15 2018 - 11:28:52 PST)
- [AMBER] Problem in designing MD simulation based on Experimental data Bharat Manna (Fri Nov 16 2018 - 07:53:12 PST)
- [AMBER] regarding creation of production MD output Charu Sharma (JRF) (Fri Nov 16 2018 - 08:33:23 PST)
- [AMBER] md production Charu Sharma (JRF) (Fri Nov 16 2018 - 21:07:57 PST)
- [AMBER] xmgrace Charu Sharma (JRF) (Fri Nov 16 2018 - 21:23:11 PST)
- [AMBER] graph Charu Sharma (JRF) (Fri Nov 16 2018 - 22:01:24 PST)
- [AMBER] regarding ambpdb Charu Sharma (JRF) (Sun Nov 18 2018 - 01:22:59 PST)
- [AMBER] cpptraj eroor Rajbinder Kaur Virk (Sun Nov 18 2018 - 05:33:03 PST)
- [AMBER] Post_analysis_Amber_tools_suggestion Antonio Amber Carlesso (Sun Nov 18 2018 - 06:09:51 PST)
- [AMBER] Errors regarding generation of parameter file shivangi agarwal (Sun Nov 18 2018 - 19:15:50 PST)
- [AMBER] CUDA problems in Amber18 Julio Dominguez (Sun Nov 18 2018 - 19:33:30 PST)
- [AMBER] antechamber soukaina louerdi (Mon Nov 19 2018 - 03:29:51 PST)
- [AMBER] cpptraj error Rajbinder Kaur Virk (Mon Nov 19 2018 - 04:59:02 PST)
- [AMBER] About dpeaks implementation in cpptraj Casalini Tommaso (Mon Nov 19 2018 - 05:49:19 PST)
- [AMBER] Correction needed for output of energy action command in cpptraj Veenis, Andrew Jay (Mon Nov 19 2018 - 10:02:18 PST)
- [AMBER] REGARDING TUTORIAL Charu Sharma (JRF) (Tue Nov 20 2018 - 15:39:07 PST)
- [AMBER] CPPTRAJ/PnetCDF error Nikolay N. Kuzmich (Wed Nov 21 2018 - 01:34:37 PST)
- [AMBER] RTX 2080 slower then 1080 Ti with pmemd 18 ? Alain Chaumont (Wed Nov 21 2018 - 11:24:29 PST)
- [AMBER] The interaction energy between substrate molecule and protein Meng Wu (Thu Nov 22 2018 - 02:44:55 PST)
- [AMBER] polymer state hosein geraili (Thu Nov 22 2018 - 07:35:38 PST)
- [AMBER] Getting error for MMPB/GBSA calculaton Saikat Pal (Thu Nov 22 2018 - 07:44:49 PST)
- [AMBER] Obtaining contact maps with cpptraj Stefan Ivanov (Thu Nov 22 2018 - 20:47:59 PST)
- [AMBER] Running tleap for topology generation of a list of pdb files. Leena Aggarwal (Fri Nov 23 2018 - 02:44:39 PST)
- [AMBER] Hamiltonian Replica Exchange with Amber 18 Bruno Falcone (Fri Nov 23 2018 - 07:28:29 PST)
- [AMBER] RMSF Charu Sharma (JRF) (Sat Nov 24 2018 - 03:25:44 PST)
- [AMBER] Parametrs for Targeted MD Mohamad Reza G. (Sat Nov 24 2018 - 03:52:26 PST)
- [AMBER] Latest force field shivangi agarwal (Sat Nov 24 2018 - 09:15:50 PST)
- [AMBER] Ante-MMPBSA.py error jacky zhao (Sat Nov 24 2018 - 19:05:54 PST)
- [AMBER] RMSD Charu Sharma (JRF) (Sun Nov 25 2018 - 22:01:47 PST)
- [AMBER] new amber mailing list for beginner questions/mailing list for advanced users&bug reports Paul Westphälinger (Mon Nov 26 2018 - 01:15:01 PST)
- [AMBER] RESP charge calculation Aashish Bhatt (Mon Nov 26 2018 - 04:43:09 PST)
- [AMBER] Regarding the Targeted MD M. Reza Ganjalikhany (Mon Nov 26 2018 - 12:21:59 PST)
- [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18 Braden Kelly (Tue Nov 27 2018 - 00:10:01 PST)
- [AMBER] Failed to merge the protein-ligand amoeba parameters 王茜茜 (Tue Nov 27 2018 - 00:46:01 PST)
- [AMBER] Why does makeCHIR_RST create restraints for side chains? Stefan Ivanov (Tue Nov 27 2018 - 01:11:39 PST)
- [AMBER] Velocity autocorrelation function(VACF) Aashish Bhatt (Tue Nov 27 2018 - 04:24:28 PST)
- [AMBER] Announcement: Release of DOCK 6.9 Scott Brozell (Tue Nov 27 2018 - 17:29:21 PST)
- [AMBER] thermostat on solvent hosein geraili (Tue Nov 27 2018 - 23:47:19 PST)
- [AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar José Daniel Martinez (Wed Nov 28 2018 - 08:50:38 PST)
- [AMBER] Minimisation and periodic boundaries. Stejskal, Lenka (Wed Nov 28 2018 - 09:56:30 PST)
- [AMBER] equilibration of Packmol generated boxes Arkajyoti Sengupta (Wed Nov 28 2018 - 15:30:31 PST)
- [AMBER] Choosing a temperature schedule for Simulated annealing Rajbinder Kaur Virk (Wed Nov 28 2018 - 23:19:39 PST)
- Re: [AMBER] reminder Chhaya Singh (Thu Nov 29 2018 - 09:13:50 PST)
- [AMBER] free energy calculation for restraining ligand Sukanya Sasmal (Thu Nov 29 2018 - 18:27:53 PST)
- [AMBER] Installation & testing of AMBER18 parallel GPU problem Ibrahim M. Moustafa (Fri Nov 30 2018 - 09:38:11 PST)
- Last message date: Fri Nov 30 2018 - 10:00:01 PST
- Archived on: Wed Dec 25 2024 - 05:55:45 PST
