Amber Archive Oct 2017 by thread
- [AMBER] Thermodynamic Integration with pmemd, for explicit solvent models Roma Mukhopadhyay (Sat Sep 30 2017 - 19:48:47 PDT)
- [AMBER] total frames for hbond Thakur, Abhishek (Sun Oct 01 2017 - 12:16:42 PDT)
- Re: [AMBER] leaprc.constph and ff14sb Jason Swails (Sun Oct 01 2017 - 20:29:41 PDT)
- Re: [AMBER] barostat with large coupling constant Jason Swails (Sun Oct 01 2017 - 20:37:57 PDT)
- Re: [AMBER] Amber16 electric field parameters Alessandro Mariani (Mon Oct 02 2017 - 01:18:57 PDT)
- Re: [AMBER] trajout last x frames cpptraj Daniel Roe (Mon Oct 02 2017 - 05:31:23 PDT)
- Re: [AMBER] identiy the step of interaction from an entire trajectory Daniel Roe (Mon Oct 02 2017 - 05:55:48 PDT)
- Re: [AMBER] How to save reimaged trajectory file during MD? Daniel Roe (Mon Oct 02 2017 - 06:05:16 PDT)
- [AMBER] TImask command for PMEMD Roma Mukhopadhyay (Mon Oct 02 2017 - 10:01:12 PDT)
- Re: [AMBER] PyRed FyD (Mon Oct 02 2017 - 23:10:11 PDT)
- [AMBER] Current rmsd from reference in targeted MD Sonia Ziada (Tue Oct 03 2017 - 04:36:33 PDT)
- [AMBER] DPPG lipid bilayer simulation using Lipid17 - too small area per lipid ? Marek Maly (Tue Oct 03 2017 - 08:52:41 PDT)
- [AMBER] Is it possible to simulate Indium (coupled with sulpher and copper) nano material in amber? Charles Mariasoosai (Tue Oct 03 2017 - 09:33:25 PDT)
- [AMBER] Vector math: a couple of questions George Tzotzos (Tue Oct 03 2017 - 11:42:09 PDT)
- [AMBER] force distribution analysis and Ewald Thomas Pochapsky (Tue Oct 03 2017 - 11:57:01 PDT)
- [AMBER] vague error when running constant ph simulations Andrew Schaub (Tue Oct 03 2017 - 21:08:01 PDT)
- [AMBER] TI calculations using pmemd Roma Mukhopadhyay (Wed Oct 04 2017 - 13:00:22 PDT)
- [AMBER] Constant pH Explicit Solvent Pacheco, Sayuri (Wed Oct 04 2017 - 18:22:18 PDT)
- [AMBER] colvar in string methods Chunli Yan (Wed Oct 04 2017 - 19:57:27 PDT)
- [AMBER] Independent MD runs colvin (Wed Oct 04 2017 - 20:11:19 PDT)
- Re: [AMBER] (no subject) Hossein Geraili (Thu Oct 05 2017 - 02:20:22 PDT)
- [AMBER] Generating a dimer starting from monomers using MD jacob wick (Thu Oct 05 2017 - 02:26:48 PDT)
- [AMBER] AMBER Hossein Geraili (Thu Oct 05 2017 - 02:44:50 PDT)
- [AMBER] AmberTools17 and shape.h Christopher Benjamin Coffey (Thu Oct 05 2017 - 07:11:55 PDT)
- Re: [AMBER] Dr. Nick Riviera Junmei Wang (Thu Oct 05 2017 - 08:47:29 PDT)
- [AMBER] AMBER16 parallelisation and fftw3 error Shirin Jamshidi (Thu Oct 05 2017 - 14:41:57 PDT)
- [AMBER] net charge problem of Amber Lipid14 Force Field Xibing He (Thu Oct 05 2017 - 15:03:47 PDT)
- [AMBER] Error in preparation of Zn.lib Anton Perera (Fri Oct 06 2017 - 01:12:44 PDT)
- [AMBER] System preparation for protein with Multiple Zn-CCCC Parthiban Marimuthu (Fri Oct 06 2017 - 09:16:07 PDT)
- [AMBER] Thermodynamic integration/switch off/on cloumbic and vdw interactions Khabiri, Morteza (Fri Oct 06 2017 - 11:05:54 PDT)
- [AMBER] about Paramfit Albert (Fri Oct 06 2017 - 14:03:21 PDT)
- [AMBER] chamber is unavailable from terminal MacOS Sundar (Fri Oct 06 2017 - 15:02:47 PDT)
- [AMBER] striping correctly with ante-MMPBSA.py Sundar (Mon Oct 09 2017 - 01:24:38 PDT)
- [AMBER] Hydrogen Bond ATUL KUMAR (Mon Oct 09 2017 - 04:54:07 PDT)
- [AMBER] How to put anchor_position for RMSD collective variable Value in string methods Chunli Yan (Mon Oct 09 2017 - 05:45:01 PDT)
- [AMBER] Hydrogen Bond ATUL KUMAR (Mon Oct 09 2017 - 05:48:23 PDT)
- [AMBER] MMPBSA error sangita kachhap (Mon Oct 09 2017 - 07:27:26 PDT)
- [AMBER] MCPB.py issue - add_bonded_pairs Szymon Żaczek (Mon Oct 09 2017 - 08:37:38 PDT)
- [AMBER] Question regarding protonated CP in pH dependent REMD Paul Freidhoff (Mon Oct 09 2017 - 09:04:09 PDT)
- [AMBER] Ruthenium complex MD simulation ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not supported! Sanaa ALAbbad (Mon Oct 09 2017 - 16:44:24 PDT)
- [AMBER] Fwd: Error with AMBER/Charmm-GUI output Mac Kevin Braza (Mon Oct 09 2017 - 22:57:33 PDT)
- [AMBER] Fwd: Error with AMBER/Charmm-GUI output Mac Kevin Braza (Mon Oct 09 2017 - 22:57:59 PDT)
- [AMBER] pmemd.cuda and rigid CH2Cl2 Alain Chaumont (Tue Oct 10 2017 - 04:31:12 PDT)
- [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Tue Oct 10 2017 - 05:40:03 PDT)
- [AMBER] REMD job failed Albert (Tue Oct 10 2017 - 07:34:32 PDT)
- [AMBER] Problem with charges - Unable to recover LYS charges from AmberFF Nicolas Cheron (Wed Oct 11 2017 - 03:13:59 PDT)
- [AMBER] output file .out file deleted mistakenly Rana Rehan Khalid (Wed Oct 11 2017 - 10:35:48 PDT)
- [AMBER] getting MC barostat to print less Smith, Louis (Wed Oct 11 2017 - 21:36:58 PDT)
- [AMBER] making 6M GDMCl box ATUL KUMAR (Thu Oct 12 2017 - 02:58:08 PDT)
- [AMBER] Restarting pH-REMD simulations after abnormal termination Eric Lang (Thu Oct 12 2017 - 06:55:28 PDT)
- [AMBER] Error reading Ruthenium complex residue Sanaa ALAbbad (Thu Oct 12 2017 - 08:27:17 PDT)
- [AMBER] parmstrip with cpptraj in Ambertools 17 Li, Wen (Thu Oct 12 2017 - 10:12:37 PDT)
- [AMBER] Wham analysis Thakur, Abhishek (Thu Oct 12 2017 - 14:02:35 PDT)
- [AMBER] help for the installation of Ambertools 17 on Mac huangwc8 (Thu Oct 12 2017 - 22:40:50 PDT)
- [AMBER] Restarting REMD Andreas Tosstorff (Fri Oct 13 2017 - 01:13:54 PDT)
- [AMBER] problem with AMBER TUTORIAL A1 Michael Shokhen (Fri Oct 13 2017 - 05:27:12 PDT)
- [AMBER] Metal site hybrid bonded model Lizelle Lubbe (Fri Oct 13 2017 - 05:45:30 PDT)
- [AMBER] Converting atom names from NAMD to AMBER Eiros Zamora, Juan (Fri Oct 13 2017 - 10:10:54 PDT)
- [AMBER] mdfrc for a single ion in vacuum William Marquardt (Fri Oct 13 2017 - 11:24:46 PDT)
- [AMBER] SCEE incorrectly set for certain dihedral parameter comments Niel Henriksen (Fri Oct 13 2017 - 12:05:00 PDT)
- [AMBER] How to show double bond connection between N=O2 Rana Rehan Khalid (Sat Oct 14 2017 - 07:31:29 PDT)
- [AMBER] Specify amount of memory David Sáez (Sun Oct 15 2017 - 00:20:44 PDT)
- [AMBER] Vector command in cpptraj Pietro Aronica (Sun Oct 15 2017 - 21:14:22 PDT)
- [AMBER] Running Explicit pH MD Pacheco, Sayuri (Mon Oct 16 2017 - 08:26:33 PDT)
- [AMBER] Question on GPUs and OS George Tzotzos (Mon Oct 16 2017 - 11:15:38 PDT)
- [AMBER] RESP charges for a peptide-bound probe with R.E.D. Seth Axen (Mon Oct 16 2017 - 16:00:30 PDT)
- [AMBER] trajout format with cpptraj in Ambertools 17 Li, Wen (Tue Oct 17 2017 - 08:40:28 PDT)
- [AMBER] Cannot create Ru-ligands bonds using genMetalFF.sh Sanaa ALAbbad (Tue Oct 17 2017 - 16:10:44 PDT)
- [AMBER] APR method in CHCl3 Maura Malinska (Wed Oct 18 2017 - 09:34:01 PDT)
- [AMBER] Bias Towards the Periodic Boundary Timothy Schutt (Wed Oct 18 2017 - 10:37:56 PDT)
- [AMBER] How to add the deprotonated SER residue to the ff14SB leap library? Michael Shokhen (Thu Oct 19 2017 - 05:42:38 PDT)
- [AMBER] Protein drift from solvent box Lizelle Lubbe (Thu Oct 19 2017 - 05:44:48 PDT)
- [AMBER] Dummy Atoms in CP Paul Freidhoff (Thu Oct 19 2017 - 06:34:57 PDT)
- [AMBER] WHAM, DHAM, MBAR, BAR, TI... Andreas Tosstorff (Thu Oct 19 2017 - 09:04:22 PDT)
- [AMBER] how we can visualized the bonds after saving on of the MD frame into pdb file. Rana Rehan Khalid (Thu Oct 19 2017 - 11:16:51 PDT)
- [AMBER] effect of MPI problem on MD calculations sangita kachhap (Fri Oct 20 2017 - 01:25:20 PDT)
- [AMBER] Force field parameters for Magnesium and Calcium in Amber Nadine Schwierz-Neumann (Fri Oct 20 2017 - 03:35:06 PDT)
- [AMBER] how to generated data for plot? Albert (Fri Oct 20 2017 - 04:17:17 PDT)
- [AMBER] Independent production runs Lizelle Lubbe (Fri Oct 20 2017 - 04:28:34 PDT)
- [AMBER] Center of mass restraint on GPU? Lin Song (Fri Oct 20 2017 - 08:12:50 PDT)
- [AMBER] hydrogenbond calculations megha vaishnavi (Sun Oct 22 2017 - 20:11:44 PDT)
- [AMBER] difficulty reading a frcmod file in amber Eugene Cha (Sun Oct 22 2017 - 23:41:42 PDT)
- [AMBER] About penalty scores Arun Srikanth (Mon Oct 23 2017 - 17:02:08 PDT)
- [AMBER] Can we use OPLS force field in AMBER Shilpa Gupta (Tue Oct 24 2017 - 05:35:52 PDT)
- [AMBER] MM/PBSA or MM/GBSA sangita kachhap (Tue Oct 24 2017 - 06:47:21 PDT)
- [AMBER] disulfide bonds braking during MD simulation Michael Shokhen (Tue Oct 24 2017 - 07:59:52 PDT)
- [AMBER] Are RNA with ligand system and a GB neck2 protocol compatible Kasprzak, Wojciech (NIH/NCI) [C] (Tue Oct 24 2017 - 10:57:29 PDT)
- [AMBER] About paramfit 1-4 scaling Arun Srikanth (Tue Oct 24 2017 - 17:47:18 PDT)
- [AMBER] Forecefield error Arthi Venkat (Tue Oct 24 2017 - 20:05:28 PDT)
- [AMBER] Cpptraj HBond salt bridge output question Amy Rice (Wed Oct 25 2017 - 08:22:27 PDT)
- [AMBER] error with restraint distance minimization Michael Shokhen (Wed Oct 25 2017 - 09:02:52 PDT)
- [AMBER] STOP PMEMD Terminated Abnormally! Jeyaram R A (Thu Oct 26 2017 - 05:01:21 PDT)
- [AMBER] reference for long-range van der Waals interactions Wook Lee (Thu Oct 26 2017 - 08:16:06 PDT)
- [AMBER] Use of pmemd for minimisation and equilibration Suchetana Gupta (Fri Oct 27 2017 - 05:52:56 PDT)
- [AMBER] parmed.py and xparmed.py problem Michael Shokhen (Fri Oct 27 2017 - 05:58:50 PDT)
- [AMBER] Binding affinity of different small molecules to a complex of metal + protein + DNA Alonso Martinez, Diego (Fri Oct 27 2017 - 06:17:57 PDT)
- [AMBER] MM-PBSA calculation Mustafa Alhaji Isa (Fri Oct 27 2017 - 08:22:33 PDT)
- [AMBER] frozen atoms. danilo gonzalez (Fri Oct 27 2017 - 09:14:30 PDT)
- [AMBER] Error Due to Duplicate residues atoms Rana Rehan Khalid (Fri Oct 27 2017 - 11:15:16 PDT)
- [AMBER] Wrong connectivity after antechamber/Gaussian16 Andreas Tosstorff (Fri Oct 27 2017 - 11:19:04 PDT)
- [AMBER] Error in calculating MM-PBSA Mustafa Alhaji Isa (Sun Oct 29 2017 - 01:11:59 PDT)
- [AMBER] AM1-BCC for charge derivation Shilpa Gupta (Sun Oct 29 2017 - 12:22:40 PDT)
- [AMBER] positive electrostatic energy Sharon D. Morris (Mon Oct 30 2017 - 03:35:18 PDT)
- [AMBER] warning Close contact Shilpa Gupta (Mon Oct 30 2017 - 03:56:13 PDT)
- [AMBER] positional restraint to optimize crystal structure M P (Mon Oct 30 2017 - 04:12:40 PDT)
- [AMBER] restraint_wt applied to wrong atoms sangita kachhap (Mon Oct 30 2017 - 05:14:11 PDT)
- [AMBER] problem with TUTORAL C5: Hydrogen Bond Analysis with CPPTRAJ Setyanto Md (Mon Oct 30 2017 - 05:16:23 PDT)
- [AMBER] disulfide bonds braking during MD simulation Michael Shokhen (Mon Oct 30 2017 - 05:23:00 PDT)
- [AMBER] pdb4amber bug - incorrect "CONECT" between chains Diego Gomes (Mon Oct 30 2017 - 10:49:33 PDT)
- [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Ross Walker (Mon Oct 30 2017 - 11:57:47 PDT)
- [AMBER] Constant temperature is not constant from the beginning David Sáez (Mon Oct 30 2017 - 21:32:29 PDT)
- [AMBER] contributing code Holger Kruse (Tue Oct 31 2017 - 06:19:43 PDT)
- [AMBER] PB Bomb in pb_aaradi() Urszula Uciechowska (Tue Oct 31 2017 - 06:41:15 PDT)
- [AMBER] SCC-DFTB for iron Àngels González Lafont (Tue Oct 31 2017 - 09:04:43 PDT)
- [AMBER] CUDA 9 Weinzierl, Robert O J (Tue Oct 31 2017 - 10:11:52 PDT)
- [AMBER] Test failed after installing Amber Tools 17 Crystal Vander Zanden (Tue Oct 31 2017 - 13:18:24 PDT)
- Last message date: Tue Oct 31 2017 - 18:00:02 PDT
- Archived on: Wed Dec 25 2024 - 05:55:36 PST
