Amber Archive May 2019 by thread
- [AMBER] Vina Zinc Beale, John (Wed May 01 2019 - 04:05:56 PDT)
- Re: [AMBER] Library for Phosphate ion David A Case (Wed May 01 2019 - 04:44:06 PDT)
- [AMBER] SMD using contact number Chem Jubilant (Wed May 01 2019 - 07:40:46 PDT)
- Re: [AMBER] mol2 files for FEW David A Case (Wed May 01 2019 - 10:50:43 PDT)
- Re: [AMBER] Simulation with Protein, cofactor and Ligand David A Case (Wed May 01 2019 - 10:53:53 PDT)
- [AMBER] CPPTRAJ average residue-wise contact map anu chandra (Wed May 01 2019 - 12:06:24 PDT)
- [AMBER] Error using mm_pbsa.pl binding energy calculations Jaimes, Luis (Wed May 01 2019 - 17:44:23 PDT)
- [AMBER] Random segfaults (invalid memory reference) in sander Charo del Genio (Thu May 02 2019 - 01:43:19 PDT)
- [AMBER] FEW not producing *.lib file for ligand ali akbar (Thu May 02 2019 - 02:50:12 PDT)
- Re: [AMBER] CPPTRAJ gnu extension not working Daniel Roe (Thu May 02 2019 - 05:34:12 PDT)
- [AMBER] Distance calculation and distance matrix giving discrepant results Jonathan Huihui (Thu May 02 2019 - 09:25:55 PDT)
- Re: [AMBER] Novel Force Field Parameters for Aromatic Dihedrals Carlos Simmerling (Thu May 02 2019 - 09:36:00 PDT)
- [AMBER] Force field for nucleobases, nucleosides and nucleotides Elisa Pieri (Thu May 02 2019 - 14:10:06 PDT)
- [AMBER] Random segfaults (invalid memory reference) in sander Margarita I. Bernal-Uruchurtu (Fri May 03 2019 - 02:11:59 PDT)
- [AMBER] Files for Tutorial 32 (Deriving bonded parameters with mdgx) Michiel de Hoon (Fri May 03 2019 - 02:26:58 PDT)
- [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Erdem Yeler (Fri May 03 2019 - 02:36:48 PDT)
- Re: [AMBER] Guidance on WHAM Ruth Helena Tichauer (Fri May 03 2019 - 08:09:38 PDT)
- [AMBER] FLAG_POINTERS in prmtop file Feng, Zimin (Fri May 03 2019 - 08:10:33 PDT)
- Re: [AMBER] [mjldehoon.yahoo.com: Files for Tutorial 32 (Deriving bonded parameters with mdgx)] David Cerutti (Fri May 03 2019 - 08:30:40 PDT)
- [AMBER] Are R.E.D. tools still a thing? Luca Codutti (Fri May 03 2019 - 10:17:35 PDT)
- [AMBER] Question regarding compatibility of Temperature replica exchange MD (TREMD) with constant pH MD Pacheco, Sayuri (Fri May 03 2019 - 11:48:35 PDT)
- Re: [AMBER] issues with pmemd.cuda Veenis, Andrew Jay (Fri May 03 2019 - 12:20:43 PDT)
- [AMBER] SIRAH force field goes quantum in AMBER Matias Machado (Fri May 03 2019 - 13:12:34 PDT)
- [AMBER] FEW- an issue generating *.lib for ligand ali akbar (Sat May 04 2019 - 00:39:44 PDT)
- [AMBER] AmberTools hardcodes library names into binaries viktor drobot (Sat May 04 2019 - 03:57:57 PDT)
- [AMBER] check version Akshay Prabhakant (Sun May 05 2019 - 05:29:29 PDT)
- [AMBER] umbrella sampling using pmemd in amber/2016 Akshay Prabhakant (Sun May 05 2019 - 08:30:04 PDT)
- [AMBER] Ambertools2018/SQM installation Sina (Mon May 06 2019 - 01:59:31 PDT)
- [AMBER] matching energies betwen amber-md and gromacs using amber parameters in both Akshay Prabhakant (Mon May 06 2019 - 02:59:06 PDT)
- Re: [AMBER] Any help on how to implement it in cpptraj? Debarati DasGupta (Mon May 06 2019 - 13:27:46 PDT)
- [AMBER] three letter code for unprotonated carboxyglutamates Tanusree S (Tue May 07 2019 - 02:45:25 PDT)
- [AMBER] running qsub files in a single standalone workstation ali akbar (Tue May 07 2019 - 03:28:21 PDT)
- [AMBER] different energy values from mdout and cpptraj Batuhan Kav (Tue May 07 2019 - 05:24:18 PDT)
- [AMBER] SPAM bulk solvent free energy parameters Debarati DasGupta (Tue May 07 2019 - 06:36:51 PDT)
- Re: [AMBER] cuda test failing after installation Ravi Abrol (Tue May 07 2019 - 10:26:54 PDT)
- [AMBER] NVidia backwards compatibility James Kress (Tue May 07 2019 - 12:43:34 PDT)
- [AMBER] Unequal distribution of water Piotr Fajer (Tue May 07 2019 - 14:26:29 PDT)
- [AMBER] distance restraint failed in minimization and MD wujue (Tue May 07 2019 - 19:38:40 PDT)
- Re: [AMBER] AMBER Digest, Vol 2638, Issue 1 ali akbar (Tue May 07 2019 - 22:07:54 PDT)
- [AMBER] running qsub files in a single standalone workstation ali akbar (Tue May 07 2019 - 22:32:49 PDT)
- [AMBER] Thermostat question Markowska (Tue May 07 2019 - 23:51:52 PDT)
- [AMBER] CPPTRAJ OPENMP - MPI Lorenzo Gontrani (Wed May 08 2019 - 02:51:34 PDT)
- [AMBER] Capping a dipeptide with Boc Saikat Pal (Wed May 08 2019 - 04:04:50 PDT)
- [AMBER] pmemd.cuda "cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered" Akshay Prabhakant (Wed May 08 2019 - 08:50:21 PDT)
- [AMBER] AMBER 16 vs 18 on different cuda Xiaoyu Wang (Wed May 08 2019 - 13:08:11 PDT)
- [AMBER] continuous DNA Qinghua Liao (Thu May 09 2019 - 06:39:00 PDT)
- [AMBER] GPU versions: pmemd.cuda* Yin, Guowei (Thu May 09 2019 - 08:11:05 PDT)
- [AMBER] Energy shifted energy term Debarati DasGupta (Thu May 09 2019 - 13:48:42 PDT)
- [AMBER] Fwd: August 5-8.SBU: 2019 Summer School Parallel Computing in Molecular Sciences Carlos Simmerling (Fri May 10 2019 - 07:09:40 PDT)
- [AMBER] Regarding GTX 1050 Ti Rajarshi Roy (Fri May 10 2019 - 20:22:09 PDT)
- [AMBER] Fwd: The unperturbed charge of the unit: 4.003000 is not zero Sadaf Rani (Sat May 11 2019 - 04:16:07 PDT)
- [AMBER] Failed to generate parameters Sadaf Rani (Sat May 11 2019 - 08:48:41 PDT)
- [AMBER] MC barostat cause the system to stuck indefinitely Zhiyi Wu (Sat May 11 2019 - 14:10:13 PDT)
- [AMBER] Problem with preparing parameters with antechamber for modified amino acid Saikat Dutta chowdhury (Sat May 11 2019 - 23:40:19 PDT)
- [AMBER] Residence time around ions Reber, David (Sun May 12 2019 - 03:58:43 PDT)
- [AMBER] Center of mass velocity autocorrelation function Reber, David (Sun May 12 2019 - 18:29:33 PDT)
- [AMBER] tleap split lipid when it shouldn't Maximilien BERNE (Mon May 13 2019 - 05:41:42 PDT)
- [AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016 Akshay Prabhakant (Mon May 13 2019 - 06:53:49 PDT)
- [AMBER] Atom type (C.2) is not in PARMCHK.DAT Segmentation fault (core dumped) Sadaf Rani (Mon May 13 2019 - 08:56:06 PDT)
- [AMBER] MMPBSA radiopt effect on EDISPER Thomas Gaillard (Mon May 13 2019 - 09:40:57 PDT)
- [AMBER] amber18 parallel cpu make test hanging at first test Ravi Abrol (Mon May 13 2019 - 11:47:18 PDT)
- [AMBER] Average structure vs Individual frames Yin, Guowei (Mon May 13 2019 - 18:16:59 PDT)
- Re: [AMBER] Building inpcrd and prmtop for a non-standard residue containing cyclic peptide Pietro Aronica (Tue May 14 2019 - 02:19:31 PDT)
- [AMBER] Solute free non-water solvent razie yousefi (Tue May 14 2019 - 08:01:17 PDT)
- [AMBER] 3D-RISM options Ryan Pavlovicz (Tue May 14 2019 - 14:45:27 PDT)
- [AMBER] Entropy calculation for a protein homodimerization Rakesh Srivastava (Wed May 15 2019 - 01:47:53 PDT)
- [AMBER] hbond lifetime filesize issues Reber, David (Wed May 15 2019 - 02:53:13 PDT)
- [AMBER] set RA, RT and n_partition in adQM/MM run Ruth Helena Tichauer (Wed May 15 2019 - 03:57:38 PDT)
- [AMBER] Crashed dynamics : connectivity emanuele falbo (Wed May 15 2019 - 05:59:49 PDT)
- [AMBER] nvidia tesla-t4 and amber Luca Codutti (Wed May 15 2019 - 08:46:36 PDT)
- [AMBER] Missing file amber tutorial Sadaf Rani (Wed May 15 2019 - 11:06:10 PDT)
- [AMBER] NetCDF trajectory file does not contain information about time/timestep Markowska (Wed May 15 2019 - 11:12:57 PDT)
- [AMBER] Releasing SIRAH lipids! A complete coarse-grained force field running on AMBER Matias Machado (Wed May 15 2019 - 11:30:57 PDT)
- [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file Gargi Borgohain (Thu May 16 2019 - 02:38:29 PDT)
- [AMBER] Bubbles during NPT and NVT simulations Stefano Motta (Thu May 16 2019 - 02:56:24 PDT)
- [AMBER] RMSF of combined trajectory Rinsha Chk (Thu May 16 2019 - 04:43:37 PDT)
- [AMBER] Simulating Water Exchange to Buried Binding Sites Debarati DasGupta (Thu May 16 2019 - 06:21:44 PDT)
- [AMBER] Error in step 3 of MCPB.py Shahila Muhammed (Fri May 17 2019 - 01:02:55 PDT)
- [AMBER] Selecting number of waters in tleap Elena Gomez (Fri May 17 2019 - 01:09:35 PDT)
- [AMBER] Open position for doctoral candidate in biomolecular simulations Jan Brezovsky (Fri May 17 2019 - 02:17:10 PDT)
- [AMBER] Suggestion about proper ANTECHAMBER usage Saikat Dutta chowdhury (Fri May 17 2019 - 04:38:52 PDT)
- [AMBER] Velocity rescaling between different temperatures? Kenneth Huang (Fri May 17 2019 - 12:18:15 PDT)
- [AMBER] DRMSD utility in cpptraj Debarati DasGupta (Fri May 17 2019 - 13:45:30 PDT)
- [AMBER] Force field for intrinsically disordered proteins Markowska (Sat May 18 2019 - 05:11:46 PDT)
- [AMBER] Catalysis mechanism of ATPase sunyeping (Sun May 19 2019 - 04:29:35 PDT)
- [AMBER] Regarding building of parallel version of AMBER18 in centos 7 Rajarshi Roy (Tue May 21 2019 - 20:49:41 PDT)
- [AMBER] Temperature variation in QM/MM simulation with AMBER18/G09 Abhilash J (Wed May 22 2019 - 11:38:05 PDT)
- [AMBER] amber inputs Sina (Thu May 23 2019 - 06:44:31 PDT)
- [AMBER] Volmap command in cpptraj followed by SPAM Debarati DasGupta (Thu May 23 2019 - 06:59:28 PDT)
- [AMBER] Lennard Jones parameters in frcmod Stefano Motta (Thu May 23 2019 - 07:31:17 PDT)
- [AMBER] Different potential energies between recomputed and original simulations from PMEMD? 杨明俊 (Fri May 24 2019 - 03:14:32 PDT)
- [AMBER] Qm minimization, Sina (Fri May 24 2019 - 03:22:47 PDT)
- [AMBER] Some basic question Sina (Fri May 24 2019 - 09:18:41 PDT)
- [AMBER] jobs getting cancelled on cuda7 gpus maryam azimzadehirani (Fri May 24 2019 - 22:59:14 PDT)
- [AMBER] PCA with a really giant trajectory David Cerutti (Sat May 25 2019 - 12:31:54 PDT)
- [AMBER] Print Hessian matrix in (3,3) dimension Bouibes Amine (Sun May 26 2019 - 01:03:55 PDT)
- [AMBER] How to generate the correct force field parameter for a large molecule? xmgign.126.com (Sun May 26 2019 - 23:27:44 PDT)
- [AMBER] graph Charu Sharma (JRF) (Mon May 27 2019 - 04:06:01 PDT)
- [AMBER] compiling Amber Tools 19 Vlad Cojocaru (Mon May 27 2019 - 04:42:38 PDT)
- [AMBER] Protein-Lipid Bilayer PDB preparation Issue(s) Abhishek Sirohiwal (Mon May 27 2019 - 09:48:32 PDT)
- [AMBER] rmsd Hirdesh Kumar (Mon May 27 2019 - 11:35:16 PDT)
- [AMBER] GCC 2019, November 3-5 in Mainz, Deadline extendend to June 23, 2019 Stefan.Guessregen.sanofi.com (Mon May 27 2019 - 23:20:14 PDT)
- [AMBER] Problem in simulating peptide with modified amino acid - vlimit exceeded Saikat Dutta chowdhury (Tue May 28 2019 - 04:07:07 PDT)
- [AMBER] reduce info.log Sadaf Rani (Tue May 28 2019 - 04:38:07 PDT)
- Re: [AMBER] Installation of AMBER 18 regarding David A Case (Tue May 28 2019 - 10:43:50 PDT)
- [AMBER] Changes to AmberTools antechamber Makefile Jocelyn Sunseri (Tue May 28 2019 - 10:58:47 PDT)
- [AMBER] amber 16 installation on Ubuntu 18 Ming Tang (Tue May 28 2019 - 21:45:12 PDT)
- [AMBER] Minimization input Sadaf Rani (Wed May 29 2019 - 03:29:46 PDT)
- [AMBER] problem of srun Albert (Wed May 29 2019 - 05:51:46 PDT)
- [AMBER] phosphor tyrosine bound to C5' terminal DA5 Fabian Glaser (Wed May 29 2019 - 07:04:19 PDT)
- [AMBER] error with loading HEM parameters for constph redox calcuations Vaibhav Dixit (Wed May 29 2019 - 07:53:28 PDT)
- [AMBER] deselect residues for step1 model in MCPB.py SARAH JEANNE LEFAVE (Wed May 29 2019 - 09:39:30 PDT)
- [AMBER] Help compiling AMBER18 GPU Code- Cannot find compiler cl.exe in PATH Jay Spencer (Wed May 29 2019 - 19:01:53 PDT)
- [AMBER] Radgyr or distance averages Reber, David (Wed May 29 2019 - 20:24:20 PDT)
- [AMBER] Optimization of geometry in xleap Shilpa Gupta (Wed May 29 2019 - 23:21:05 PDT)
- [AMBER] anybody has any idea? Albert (Thu May 30 2019 - 00:17:35 PDT)
- [AMBER] How to generate boron atom force field parameters Meng Wu (Thu May 30 2019 - 03:53:24 PDT)
- [AMBER] empty cein file redox potential calculations Vaibhav Dixit (Thu May 30 2019 - 04:36:37 PDT)
- [AMBER] parameter file for dUTP sunyeping (Thu May 30 2019 - 06:03:54 PDT)
- [AMBER] Using a box of organic solvent Alessandro LANDI (Fri May 31 2019 - 03:42:08 PDT)
- [AMBER] Boron QM/MM Pär Håkansson (Fri May 31 2019 - 04:08:00 PDT)
- [AMBER] make test fail Sadaf Rani (Fri May 31 2019 - 09:24:55 PDT)
- [AMBER] Question about sander running parallel Sadaf Rani (Fri May 31 2019 - 09:39:23 PDT)
- Last message date: Fri May 31 2019 - 13:00:02 PDT
- Archived on: Wed Dec 25 2024 - 05:55:49 PST
