Amber Archive Jan 2019 by thread
- Re: [AMBER] Obtaining necessary *.top for MMPBSA.py Elvis Martis (Mon Dec 31 2018 - 21:05:54 PST)
- [AMBER] orca failure in mdgx: QM grid file not found Anthony Bogetti (Tue Jan 01 2019 - 18:10:04 PST)
- [AMBER] error with HEM parm Mohammad Salem (Tue Jan 01 2019 - 20:21:02 PST)
- [AMBER] Understanding Distance Restraint Ara R (Wed Jan 02 2019 - 06:19:54 PST)
- [AMBER] Calculated dipole moment in AMBER Xiaocong Wang (Wed Jan 02 2019 - 07:22:25 PST)
- [AMBER] Amber Restraint output from Kung, Ryan (Wed Jan 02 2019 - 14:29:35 PST)
- [AMBER] DMF Arkajyoti Sengupta (Wed Jan 02 2019 - 15:37:25 PST)
- [AMBER] Error with mdnab from amberlite Sundar (Wed Jan 02 2019 - 17:30:57 PST)
- Re: [AMBER] Testing AMBER16 installation in parallel; possible bug in testing scripts Bellesis, Andrew G (Thu Jan 03 2019 - 08:26:19 PST)
- Re: [AMBER] Literature about magnesium ion parameters in tutorial A8 Zuo, Zhicheng (Thu Jan 03 2019 - 12:19:03 PST)
- [AMBER] Zeolite simulations Sundar (Thu Jan 03 2019 - 21:06:06 PST)
- Re: [AMBER] MMPBSA.py error Pratul Agarwal (Fri Jan 04 2019 - 06:28:09 PST)
- [AMBER] CUDA and Restraint Error Kung, Ryan (Fri Jan 04 2019 - 13:51:18 PST)
- [AMBER] Si and Al parameters Sundar (Sat Jan 05 2019 - 14:17:44 PST)
- [AMBER] QM/MM-GBSA results Sundar (Sat Jan 05 2019 - 14:21:55 PST)
- [AMBER] RMSF in amber Akshay Prabhakant (Sun Jan 06 2019 - 01:23:41 PST)
- [AMBER] Amber installation Yazan Haddad (Mon Jan 07 2019 - 08:07:07 PST)
- [AMBER] average mulliken charges Thakur, Abhishek (Mon Jan 07 2019 - 08:50:35 PST)
- [AMBER] Problem with AMP atom separating in equilibration Kasprzak, Wojciech (NIH/NCI) [C] (Mon Jan 07 2019 - 13:13:57 PST)
- [AMBER] Clipping radius in AddToBox Lucas Bandeira (Tue Jan 08 2019 - 04:02:24 PST)
- [AMBER] "vlimit exceeded" in NVT simulation Lucas Bandeira (Tue Jan 08 2019 - 07:07:03 PST)
- [AMBER] makeDIST_RST Sundar (Tue Jan 08 2019 - 13:51:54 PST)
- [AMBER] steered md at constant force Batuhan Kav (Wed Jan 09 2019 - 03:00:56 PST)
- [AMBER] Cpptraj: std::bad_alloc error Nikolay N. Kuzmich (Wed Jan 09 2019 - 03:33:45 PST)
- [AMBER] How to load and visualize large trajectories? Chetna Tyagi (Wed Jan 09 2019 - 04:22:29 PST)
- [AMBER] TMD and pmemd Sundar (Wed Jan 09 2019 - 12:15:06 PST)
- Re: [AMBER] MCPB.py Modelling Question Pengfei Li (Thu Jan 10 2019 - 07:35:29 PST)
- [AMBER] Virtual Spin Labels in Amber Kari Gaalswyk (Thu Jan 10 2019 - 07:56:30 PST)
- [AMBER] MMPBSA.py- bad atom type "I" Subha Kalyaanamoorthy (Thu Jan 10 2019 - 11:20:33 PST)
- [AMBER] Installation error on cray machine Sundar (Thu Jan 10 2019 - 12:23:58 PST)
- [AMBER] NO and CO parameters from Antechamber Markowska (Thu Jan 10 2019 - 13:17:06 PST)
- [AMBER] Amber energy minimization and the energy unit Vasantha Kumar (Thu Jan 10 2019 - 20:45:10 PST)
- [AMBER] Problems with cutoff (?) Margarita I. Bernal-Uruchurtu (Fri Jan 11 2019 - 01:48:21 PST)
- [AMBER] reweighting aMD Núbia Prates (Fri Jan 11 2019 - 04:17:43 PST)
- [AMBER] "make test" 1 errors occur changseo park (Fri Jan 11 2019 - 04:30:31 PST)
- [AMBER] Constant external force in the given space zone ? Thermostat working just on selected part of simulated system ? Marek Maly (Fri Jan 11 2019 - 06:38:54 PST)
- [AMBER] TMD reporting force profile Sundar (Fri Jan 11 2019 - 08:04:40 PST)
- [AMBER] Modifying mdread2.F90 for bad atom type: "I" MMPBSA error Subha Kalyaanamoorthy (Fri Jan 11 2019 - 10:29:45 PST)
- [AMBER] gpu_shuttle_post_data can't work in the implicit solvent 张浩淼 (Fri Jan 11 2019 - 21:23:22 PST)
- [AMBER] DMF Arkajyoti Sengupta (Sun Jan 13 2019 - 03:59:43 PST)
- [AMBER] calculating am1-bcc charges from user generated mulliken charges Braden Kelly (Sun Jan 13 2019 - 14:32:19 PST)
- [AMBER] Using Distance Restraints in TMD Aravind R (Mon Jan 14 2019 - 06:40:13 PST)
- [AMBER] mutation using pdb4amber Sundar (Mon Jan 14 2019 - 10:51:36 PST)
- [AMBER] RMSD of independent trajectories using cpptraj Hunter Wilson (Mon Jan 14 2019 - 13:24:30 PST)
- [AMBER] Metal center molecule gaohanlu (Mon Jan 14 2019 - 19:22:02 PST)
- [AMBER] Autoimage command not working Martín Pettinati (Tue Jan 15 2019 - 10:40:44 PST)
- [AMBER] Printing distance values to a file Sundar (Tue Jan 15 2019 - 14:18:29 PST)
- [AMBER] simulation with glycans Jacopo Sgrignani (Wed Jan 16 2019 - 02:47:44 PST)
- [AMBER] Separate work values for each restraint in SMD Sundar (Wed Jan 16 2019 - 07:10:17 PST)
- [AMBER] Can't put position restrains on ions Andrea H. Kasun (Wed Jan 16 2019 - 07:33:48 PST)
- [AMBER] Introduction to dummy atoms needed Markowska (Wed Jan 16 2019 - 09:30:54 PST)
- [AMBER] Abrupt peaks in the RMSD plot of heating trajectory Amartya Pradhan (Wed Jan 16 2019 - 10:29:36 PST)
- [AMBER] MCPB.py problem gaohanlu (Wed Jan 16 2019 - 17:46:53 PST)
- [AMBER] Amber parameters for Boron atom Vincenzo Maria D'Amore (Thu Jan 17 2019 - 05:48:46 PST)
- [AMBER] pytraj Error: No reference set, cannot select by distance. Thomas Evangelidis (Thu Jan 17 2019 - 07:48:46 PST)
- [AMBER] time-dependent distance restraints Sundar (Thu Jan 17 2019 - 08:07:47 PST)
- [AMBER] Post to amber mailing list Debarati DasGupta (Thu Jan 17 2019 - 12:31:31 PST)
- [AMBER] LIE calculation in FEW workflow Debarati DasGupta (Thu Jan 17 2019 - 12:46:36 PST)
- [AMBER] How to convert a NetCDF format trajectory to separate PDB files in sequential order frame by frame Li, Dailin (Thu Jan 17 2019 - 15:10:19 PST)
- [AMBER] AMBER v18 on BG/Q Pratul Agarwal (Thu Jan 17 2019 - 15:36:04 PST)
- [AMBER] [MGMS-DS]: Molecular Modelling Workshop + Tim Clark Birthday Symposium: April 08-11, 2019 in Erlangen, Germany Dr. Anselm Horn (Fri Jan 18 2019 - 01:13:18 PST)
- [AMBER] detecting bridging waters and ions with cpptraj Stefan Ivanov (Fri Jan 18 2019 - 02:48:17 PST)
- [AMBER] Water bridge analysis using cpptraj (hbond) Abhilash J (Fri Jan 18 2019 - 06:04:06 PST)
- [AMBER] Xplor file generation Debarati DasGupta (Fri Jan 18 2019 - 07:47:28 PST)
- [AMBER] Entropy calculation with Interaction Entropy (IE) method Fulbabu Sk (Fri Jan 18 2019 - 12:03:36 PST)
- [AMBER] pmemd18 mpi installation error Kateryna Miroshnychenko (Fri Jan 18 2019 - 13:38:18 PST)
- [AMBER] DNA-ligand system maya nair (Sun Jan 20 2019 - 22:42:50 PST)
- [AMBER] regarding change in time Charu Sharma (JRF) (Mon Jan 21 2019 - 00:36:19 PST)
- [AMBER] MD with different velocities. Rinsha Chk (Mon Jan 21 2019 - 04:47:51 PST)
- [AMBER] Suggestions on MM-(GB)PBSA Sundar (Mon Jan 21 2019 - 23:20:56 PST)
- [AMBER] Using Distance Restraints in TMD Aravind R (Tue Jan 22 2019 - 00:30:25 PST)
- [AMBER] PCA Analyze mode evec.pev Shirin Jamshidi (Tue Jan 22 2019 - 03:01:25 PST)
- [AMBER] lipidscd S.D. Stephan Schott (Tue Jan 22 2019 - 06:44:27 PST)
- [AMBER] MCPB.py Error Dylan Novack (Tue Jan 22 2019 - 16:53:40 PST)
- [AMBER] 2 types of Chlorine atom (one charge is -1 and other is -0.8) Saikat Pal (Tue Jan 22 2019 - 22:13:49 PST)
- [AMBER] Creating a coarse-grained trajectory from an all atomistic simulation SARAH JEANNE LEFAVE (Wed Jan 23 2019 - 07:22:01 PST)
- [AMBER] pytraj native contacts Rosellen, Martin (Wed Jan 23 2019 - 07:55:34 PST)
- [AMBER] GPU cards RTX 2080Ti and Nvidia quadro 16GB RTX 5000 madhumalar arumugam (Thu Jan 24 2019 - 03:35:39 PST)
- [AMBER] Lifetime structural waters CPPTRAJ error Pedro Miguel Reis Figueiredo (Thu Jan 24 2019 - 04:24:10 PST)
- [AMBER] Combining CpHMD and aMD Cecilia Lindgren (Thu Jan 24 2019 - 07:37:26 PST)
- [AMBER] Simulation setup for LIE Debarati DasGupta (Thu Jan 24 2019 - 11:27:04 PST)
- [AMBER] Unnatural nucleic acid in DNA chain Anthony Bogetti (Thu Jan 24 2019 - 12:52:19 PST)
- [AMBER] Error in conversion from charmmgui to AMBER format Souvik Dey (Thu Jan 24 2019 - 16:21:03 PST)
- [AMBER] NMOD is not running for MM PBSA Santanu Santra (Thu Jan 24 2019 - 23:20:12 PST)
- [AMBER] Failed to compile mcres.F90 of Amber18+update.10 with ifort Motoshi Kamiya (Fri Jan 25 2019 - 00:58:21 PST)
- [AMBER] questions on VDW parameters Qinghua Liao (Fri Jan 25 2019 - 03:06:02 PST)
- [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Qinghua Liao (Fri Jan 25 2019 - 04:46:20 PST)
- Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water) Debarati DasGupta (Fri Jan 25 2019 - 08:00:31 PST)
- Re: [AMBER] MCPB.py error with HEME containing protein Pengfei Li (Fri Jan 25 2019 - 08:21:16 PST)
- [AMBER] QM/MM dynamics: metal oxides emanuele falbo (Fri Jan 25 2019 - 09:03:49 PST)
- [AMBER] Error Amber18 installation with Intel 19 compiler Bundit BOONYARIT (Fri Jan 25 2019 - 12:56:55 PST)
- [AMBER] Unusual separation between protein and ligand Rajarshi Roy (Fri Jan 25 2019 - 23:11:34 PST)
- [AMBER] Interpreting MM-(GB)PBSA results Sundar (Sat Jan 26 2019 - 17:43:57 PST)
- [AMBER] Calculation of binding energy associated with a single water molecule Leena Aggarwal (Sun Jan 27 2019 - 22:04:40 PST)
- [AMBER] Amber force-filed parameters for amino-acid side chain analogues mish (Mon Jan 28 2019 - 09:15:24 PST)
- [AMBER] Energy Calculation Mathematical Formula. DHEERAJ CHITARA (Tue Jan 29 2019 - 03:57:32 PST)
- [AMBER] Set the correct number of CPUs and GPU - benchmark - Amber 14 Eduardo Almeida Costa (Tue Jan 29 2019 - 10:34:02 PST)
- [AMBER] email MYRIAN TORRES RICO (Wed Jan 30 2019 - 07:22:07 PST)
- [AMBER] dihedral angles MYRIAN TORRES RICO (Wed Jan 30 2019 - 07:49:46 PST)
- [AMBER] Error while running MMPBSA.py Shagun Krishna (Wed Jan 30 2019 - 10:08:37 PST)
- [AMBER] Problem regarding RMSD Saikat Pal (Thu Jan 31 2019 - 06:50:03 PST)
- [AMBER] pytraj time Shayna Hilburg (Thu Jan 31 2019 - 11:44:26 PST)
- Last message date: Thu Jan 31 2019 - 13:00:02 PST
- Archived on: Fri Dec 20 2024 - 05:55:48 PST
