Amber Archive Jun 2017 by thread
- Re: [AMBER] external electric field in Amber 16 Charles Lin (Wed May 31 2017 - 19:02:47 PDT)
- Re: [AMBER] amino-cyclopropyl parameters Loris Moretti (Thu Jun 01 2017 - 00:37:05 PDT)
- [AMBER] Error during the installion Jeyaram R A (Thu Jun 01 2017 - 05:25:29 PDT)
- Re: [AMBER] High pressure fluctuation in isothermal-isobaric ensemble Ramin Salimi (Thu Jun 01 2017 - 07:36:39 PDT)
- Re: [AMBER] No Torsion terms Chris Moth (Thu Jun 01 2017 - 08:46:19 PDT)
- Re: [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial Nikolay N. Kuzmich (Thu Jun 01 2017 - 09:50:28 PDT)
- Re: [AMBER] Questions about special periodic boundary conditions. Bill Ross (Thu Jun 01 2017 - 10:11:21 PDT)
- [AMBER] TI free energy calculation errors Sumudu Leelananda (Thu Jun 01 2017 - 11:16:38 PDT)
- [AMBER] TI MD simulation Sowmya Indrakumar (Fri Jun 02 2017 - 03:24:48 PDT)
- [AMBER] center of mass of Guanine Saikat Pal (Fri Jun 02 2017 - 05:25:42 PDT)
- [AMBER] Linear energy decrease in the JAC_production_NVE_4fs benchmark on SDSC Comet (GPU) Marat Talipov (Fri Jun 02 2017 - 07:39:48 PDT)
- [AMBER] How to set substrate concentration gradient difference acorss membrane Meng Wu (Fri Jun 02 2017 - 21:37:19 PDT)
- [AMBER] error in qmmm Ayesha Fatima (Sat Jun 03 2017 - 06:58:44 PDT)
- [AMBER] Accelerated MD: How to reweight secondary structure propensities and radial distribution function? Harshavardhan Khare (Sun Jun 04 2017 - 02:29:55 PDT)
- [AMBER] accelerated molecular dynamics when iamd=1 or iamd=3 Sonia Ziada (Sun Jun 04 2017 - 08:39:21 PDT)
- [AMBER] cuda vs. mpi vs. mpi-cuda Robert Wohlhueter (Sun Jun 04 2017 - 12:17:34 PDT)
- [AMBER] MMPBSA.py with non-standard residues? Marc van der Kamp (Mon Jun 05 2017 - 07:35:19 PDT)
- Re: [AMBER] AMBER Digest, Vol 1946, Issue 1 Gabriel Jara (Mon Jun 05 2017 - 08:33:43 PDT)
- Re: [AMBER] AMBER Digest, Vol 1951, Issue 1 Gabriel Jara (Mon Jun 05 2017 - 11:28:49 PDT)
- [AMBER] RMSD Thakur, Abhishek (Mon Jun 05 2017 - 14:19:23 PDT)
- [AMBER] set substrate concentration gradient difference acorss membrane Meng Wu (Mon Jun 05 2017 - 18:07:47 PDT)
- Re: [AMBER] AMBER Digest, Vol 1932, Issue 1 Garima Singh (Tue Jun 06 2017 - 01:54:36 PDT)
- [AMBER] MD simulation of the whole protein or just its ligand-binding domain Nikolay N. Kuzmich (Tue Jun 06 2017 - 02:02:51 PDT)
- [AMBER] Weighting factors in multi conformational resp fitting Eiros Zamora, Juan (Tue Jun 06 2017 - 04:05:16 PDT)
- [AMBER] average no. of H bond between ligand-solvent. Saman Yousuf ali (Tue Jun 06 2017 - 05:02:31 PDT)
- [AMBER] Calculation of Volume fraction Supriyo Naskar (Tue Jun 06 2017 - 06:12:51 PDT)
- [AMBER] Center of mass Saikat Pal (Tue Jun 06 2017 - 07:56:22 PDT)
- [AMBER] Regarding empty lig.frcmod file Vishal Nemaysh (Tue Jun 06 2017 - 09:27:45 PDT)
- [AMBER] pmemd: posixio...failed Andreas Tosstorff (Tue Jun 06 2017 - 09:49:26 PDT)
- [AMBER] Normal mode entropy calculations for active site residues Manjula Saravanan (Tue Jun 06 2017 - 19:22:01 PDT)
- [AMBER] External electric fields support for GPU and how to set the parameters in mdin files? Jianing Song (Tue Jun 06 2017 - 21:49:45 PDT)
- [AMBER] Is explicit solvent more accurate than implicit solvent? Dd H (Wed Jun 07 2017 - 01:06:46 PDT)
- [AMBER] Center of mass Saikat Pal (Wed Jun 07 2017 - 03:51:55 PDT)
- [AMBER] Velocity autocorrelation ATUL KUMAR (Wed Jun 07 2017 - 04:22:37 PDT)
- [AMBER] Neutral N-terminal proline in AMBER force field Yue Qian (Wed Jun 07 2017 - 07:48:51 PDT)
- [AMBER] TI in dimeric enzyme carmine marco morgillo (Wed Jun 07 2017 - 09:44:00 PDT)
- Re: [AMBER] pmemd.MPI error on lonestar5 super comp. Miguel Rivera (Wed Jun 07 2017 - 12:19:24 PDT)
- Re: [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber. Miguel Rivera (Wed Jun 07 2017 - 12:22:21 PDT)
- [AMBER] Poor performance of REMD simulation MOHD HOMAIDUR RAHMAN (Wed Jun 07 2017 - 13:54:23 PDT)
- [AMBER] ERROR: nfft1 must be in the range of 6 to 512! Andreas Tosstorff (Thu Jun 08 2017 - 05:38:36 PDT)
- [AMBER] PCA analysis Thakur, Abhishek (Thu Jun 08 2017 - 09:52:06 PDT)
- [AMBER] visualizing first mode of motion from PCA analysis in chimera or vmd Thakur, Abhishek (Thu Jun 08 2017 - 14:16:38 PDT)
- Re: [AMBER] set substrate concentration gradient difference Meng Wu (Thu Jun 08 2017 - 19:26:45 PDT)
- [AMBER] SASA calculation Garima Singh (Thu Jun 08 2017 - 22:40:05 PDT)
- [AMBER] Retrieve amd.log/ gamd.log files Kat G (Fri Jun 09 2017 - 21:00:52 PDT)
- [AMBER] How restart md simulation Mustafa Alhaji Isa (Sat Jun 10 2017 - 03:48:55 PDT)
- [AMBER] Problem in creating topology and coordinate files Mustafa Alhaji Isa (Sat Jun 10 2017 - 22:49:59 PDT)
- [AMBER] Accelerated MD when iamd=1 or 3 Sonia Ziada (Sun Jun 11 2017 - 02:38:56 PDT)
- [AMBER] Split trajectory Shafaq Muzammal (Sun Jun 11 2017 - 05:32:43 PDT)
- [AMBER] RNA parameters for wc_helix Supriyo Naskar (Mon Jun 12 2017 - 02:11:53 PDT)
- [AMBER] mdgx extracting energies Charles-Alexandre Mattelaer (Mon Jun 12 2017 - 06:36:27 PDT)
- [AMBER] Formula/reference for ambertools native contact calculations Julio Dominguez (Mon Jun 12 2017 - 09:27:54 PDT)
- [AMBER] inpcrd file format in AmberTools16 Dr. Robert Molt (Mon Jun 12 2017 - 10:45:33 PDT)
- Re: [AMBER] Neutral N-terminal proline parameter in AMBER force field David Case (Tue Jun 13 2017 - 07:00:37 PDT)
- [AMBER] NFE dihedral Fabrício Bracht (Tue Jun 13 2017 - 13:55:15 PDT)
- [AMBER] LAMMPS data file to PDB file (off topic) Sushi Shilpa (Tue Jun 13 2017 - 21:29:22 PDT)
- [AMBER] convert .nc trajectories to .xyz Shafaq Muzammal (Wed Jun 14 2017 - 01:29:15 PDT)
- [AMBER] A conceptual question on MMGBSA binding and RMSF analysis Abhilash J (Wed Jun 14 2017 - 04:42:23 PDT)
- [AMBER] Fwd: test serial amber 14 and ambertool15 co nguyentruong (Wed Jun 14 2017 - 07:58:38 PDT)
- [AMBER] deleting water with ParmEd Hector A. Baldoni (Wed Jun 14 2017 - 12:44:36 PDT)
- [AMBER] Warning during minimization Ramin Salimi (Wed Jun 14 2017 - 18:14:57 PDT)
- [AMBER] problem regarding ACE capping of the protein terminal of the PDB Saikat Pal (Thu Jun 15 2017 - 00:29:46 PDT)
- Re: [AMBER] How to solve the unfilled valence problem in antechamber Ashish Radadiya (Thu Jun 15 2017 - 06:23:31 PDT)
- [AMBER] Selecting histidine Protonation state for simulation Jag Silwal (Thu Jun 15 2017 - 08:43:53 PDT)
- [AMBER] Weired behaviour during Heating Ramin Salimi (Thu Jun 15 2017 - 21:55:02 PDT)
- [AMBER] Ramin Salimi wants to share the file Heat.tar.gz with you Ramin Salimi (Thu Jun 15 2017 - 21:55:14 PDT)
- [AMBER] Issue installing Amber16 cuda Alexander Martin Spring-Connell (Fri Jun 16 2017 - 05:05:38 PDT)
- [AMBER] Specific GPU for running pmemd.cuda Krantzman, Kristin D (Fri Jun 16 2017 - 12:48:05 PDT)
- [AMBER] relaxation time to maintain quasi-static condition Ramin Salimi (Mon Jun 19 2017 - 18:06:12 PDT)
- [AMBER] Free energy path waleed zalloum (Mon Jun 19 2017 - 18:22:28 PDT)
- [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Chris Moth (Tue Jun 20 2017 - 11:29:41 PDT)
- Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps David Cerutti (Tue Jun 20 2017 - 11:39:52 PDT)
- Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Adrian Roitberg (Tue Jun 20 2017 - 11:45:43 PDT)
- Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Chris Moth (Tue Jun 20 2017 - 12:27:08 PDT)
- Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Bill Ross (Tue Jun 20 2017 - 12:34:45 PDT)
- Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Adrian Roitberg (Tue Jun 20 2017 - 12:38:41 PDT)
- Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps David Case (Tue Jun 20 2017 - 13:20:28 PDT)
- Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Adrian Roitberg (Tue Jun 20 2017 - 13:30:00 PDT)
- Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Bill Ross (Tue Jun 20 2017 - 13:51:50 PDT)
- Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Bill Ross (Tue Jun 20 2017 - 13:50:18 PDT)
- Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Bill Ross (Tue Jun 20 2017 - 13:55:08 PDT)
- Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Bill Ross (Tue Jun 20 2017 - 13:57:37 PDT)
- Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Bill Ross (Tue Jun 20 2017 - 16:41:56 PDT)
- Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Daniel Roe (Wed Jun 21 2017 - 05:42:11 PDT)
- Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Chris Moth (Wed Jun 21 2017 - 14:37:43 PDT)
- [AMBER] LEAP Merging Atom Types Govind Hegde (Tue Jun 20 2017 - 14:10:25 PDT)
- [AMBER] Hydrogen bond Average distance Jag Silwal (Tue Jun 20 2017 - 19:14:12 PDT)
- [AMBER] Question about ergodicity and MD Andreas Tosstorff (Wed Jun 21 2017 - 02:09:34 PDT)
- [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes Maryam Hamzehee (Wed Jun 21 2017 - 02:23:10 PDT)
- [AMBER] "Abort trap 6" error message with tLeap and xLeap Xichong Liu (Wed Jun 21 2017 - 04:36:11 PDT)
- [AMBER] issue in antechamber17 bcc charges with mopac Alessandro Contini (Wed Jun 21 2017 - 04:48:17 PDT)
- [AMBER] What nVidia driver for GTX 1080TI? Hadházi Ádám (Wed Jun 21 2017 - 06:22:46 PDT)
- [AMBER] " possible FAILURE " messages Núbia Prates (Wed Jun 21 2017 - 06:41:16 PDT)
- [AMBER] Leap: Periodic Boundary of DNA Johannes Kalliauer (Wed Jun 21 2017 - 06:44:45 PDT)
- [AMBER] A question about handling constraints/restraints with AMBER Jewgeni Starikow (Wed Jun 21 2017 - 06:51:08 PDT)
- [AMBER] convert psf to top of gmx with parmed Qinghua Liao (Wed Jun 21 2017 - 09:42:48 PDT)
- [AMBER] correlated dihedrals in ff parameterization Bala subramanian (Thu Jun 22 2017 - 01:42:58 PDT)
- [AMBER] Amber md in HPC : Job terminated Garima Singh (Thu Jun 22 2017 - 03:26:49 PDT)
- [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time SHAILESH KUMAR (Thu Jun 22 2017 - 06:51:00 PDT)
- [AMBER] error running mmpbsa giulia palermo (Fri Jun 23 2017 - 13:32:54 PDT)
- [AMBER] Problem of running ANTECHAMBER Mustafa Alhaji Isa (Fri Jun 23 2017 - 21:19:30 PDT)
- [AMBER] problem in creating topology and coordinate files Mustafa Alhaji Isa (Fri Jun 23 2017 - 21:51:35 PDT)
- [AMBER] Download and installing cpptraj sub-application Mustafa Alhaji Isa (Sat Jun 24 2017 - 03:56:01 PDT)
- [AMBER] Download and installing cpptraj sub-application Mustafa Alhaji Isa (Sat Jun 24 2017 - 03:56:00 PDT)
- [AMBER] AMber trajectory to Gromacs trajectory Saikat Pal (Sat Jun 24 2017 - 04:55:25 PDT)
- [AMBER] mbondi set up Jag Silwal (Sun Jun 25 2017 - 04:45:15 PDT)
- [AMBER] An off topic survey request Karl Kirschner (Mon Jun 26 2017 - 04:36:29 PDT)
- [AMBER] SN is required in naa_mol2files but not provided Eugene Cha (Mon Jun 26 2017 - 06:04:14 PDT)
- [AMBER] how heme force field combine with amber 99 ff Rana Rehan Khalid (Mon Jun 26 2017 - 13:44:56 PDT)
- [AMBER] mmpbsa Baker, Joseph (Mon Jun 26 2017 - 14:50:30 PDT)
- [AMBER] can't mutated Pro to Ala correctly during generating snapshots 刘兰茹 (Mon Jun 26 2017 - 20:32:30 PDT)
- [AMBER] Parabolic restraint with nmropt Ramin Salimi (Tue Jun 27 2017 - 02:07:50 PDT)
- [AMBER] using mmgbsa for dna/protein Baker, Joseph (Tue Jun 27 2017 - 20:18:11 PDT)
- [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Tue Jun 27 2017 - 20:54:07 PDT)
- [AMBER] ambpdb- Segmentation fault (core dumped) Jag Silwal (Wed Jun 28 2017 - 05:16:12 PDT)
- [AMBER] Cluster analysis Elisa Pieri (Wed Jun 28 2017 - 08:51:00 PDT)
- [AMBER] sander do not write rst and mdcrd files Núbia Prates (Wed Jun 28 2017 - 10:19:01 PDT)
- [AMBER] Force LEaP to use impose on atoms with LOOP or improper torsions in prep file Gorday, Kent M. (Wed Jun 28 2017 - 11:55:12 PDT)
- [AMBER] steps to prepare prmtop and inpcrd for heme containing protein (ff for fe----O2 is present ) Rana Rehan Khalid (Wed Jun 28 2017 - 12:03:02 PDT)
- [AMBER] antechamber Rana Rehan Khalid (Wed Jun 28 2017 - 15:37:12 PDT)
- [AMBER] Heme parameter error Rana Rehan Khalid (Wed Jun 28 2017 - 17:58:03 PDT)
- [AMBER] MCPB step 2 local variable 'ban' referenced before assignment Eugene Cha (Wed Jun 28 2017 - 23:15:55 PDT)
- [AMBER] constant pH MD question Michael Shokhen (Thu Jun 29 2017 - 02:17:58 PDT)
- Re: [AMBER] AMBER Digest, Vol 1973, Issue 1 Garima Singh (Thu Jun 29 2017 - 04:31:19 PDT)
- [AMBER] Parametrization of a phosphorylated small molecule Andreas Tosstorff (Thu Jun 29 2017 - 05:31:54 PDT)
- [AMBER] Is there any analysis of the stability of DNA in presence of Divalent cation?? Saikat Pal (Thu Jun 29 2017 - 06:58:11 PDT)
- [AMBER] adding dummy atom using Parmed API Thomas Evangelidis (Thu Jun 29 2017 - 16:08:52 PDT)
- [AMBER] kindly see the leap.log for fe---02 Rana Rehan Khalid (Thu Jun 29 2017 - 17:16:42 PDT)
- [AMBER] MCPB.py warning meaning is this mol2 file correct?? Rana Rehan Khalid (Thu Jun 29 2017 - 18:07:09 PDT)
- [AMBER] how we can find that metal residue protonation state Rana Rehan Khalid (Thu Jun 29 2017 - 19:15:48 PDT)
- [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Thu Jun 29 2017 - 19:44:36 PDT)
- [AMBER] Mm_pbsa.pl using netcdf trajectory Elvis Martis (Fri Jun 30 2017 - 01:18:14 PDT)
- [AMBER] amber installations error in cygwin venkat (Fri Jun 30 2017 - 06:30:01 PDT)
- [AMBER] problem of installing amber17 in window 10 using cygwin Mustafa Alhaji Isa (Fri Jun 30 2017 - 08:28:55 PDT)
- [AMBER] TI/FEP on GPU in Amber? Hadházi Ádám (Fri Jun 30 2017 - 09:15:48 PDT)
- [AMBER] Amber14 compatible with TITAN X Pascal? Thakur, Abhishek (Fri Jun 30 2017 - 09:43:38 PDT)
- [AMBER] problem in setting AMBERHOME environment variable using cygwin Mustafa Alhaji Isa (Fri Jun 30 2017 - 10:08:10 PDT)
- [AMBER] cphstats Error: Could not open or parse cpin file Vincent Ustach (Fri Jun 30 2017 - 15:54:52 PDT)
- Last message date: Fri Jun 30 2017 - 23:00:03 PDT
- Archived on: Fri Nov 15 2024 - 05:55:35 PST
