Amber Archive Mar 2016 by thread
- [AMBER] reading Amber trajectory files with chamber topology file Song-Ho Chong (Mon Feb 29 2016 - 07:31:12 PST)
- Re: [AMBER] more extra points needed David Cerutti (Mon Feb 29 2016 - 21:09:38 PST)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Prayagraj Fandilolu (Mon Feb 29 2016 - 21:37:14 PST)
- [AMBER] Inquiry regarding amber installation Sreemol G (Mon Feb 29 2016 - 22:05:14 PST)
- [AMBER] adding ion zahra khatti (Mon Feb 29 2016 - 22:45:19 PST)
- Re: [AMBER] Bounds command with GIst peter.schmidtke.discngine.servier.com (Mon Feb 29 2016 - 23:18:28 PST)
- [AMBER] Gist calculation on clustered structures peter.schmidtke.discngine.servier.com (Mon Feb 29 2016 - 23:23:01 PST)
- [AMBER] I have a problem when installing GPU version of Pmemd(Amber14). yhzahsc (Tue Mar 01 2016 - 00:44:07 PST)
- Re: [AMBER] Need Amber entropy calculated values Ayesha Kanwal (Tue Mar 01 2016 - 00:51:38 PST)
- [AMBER] Error while creating neutralized topology and coordinates file Sreemol G (Tue Mar 01 2016 - 03:33:44 PST)
- [AMBER] mmpbsa.py question Carlos Romero (Tue Mar 01 2016 - 11:03:44 PST)
- [AMBER] LINMEN Arati Paudyal (Tue Mar 01 2016 - 14:48:58 PST)
- [AMBER] MMPBSA error Hira Jabeen (Tue Mar 01 2016 - 21:56:42 PST)
- [AMBER] calculate free energy binding in presence of ions witn mmpbsa Carlos Romero (Tue Mar 01 2016 - 22:48:03 PST)
- [AMBER] Dihedral angle values from .mdcrd file Vasantha Kumar (Wed Mar 02 2016 - 03:47:21 PST)
- [AMBER] cpptraj molsurf: query on results George Tzotzos (Wed Mar 02 2016 - 13:58:19 PST)
- [AMBER] mmgbsa_error chemjxn (Thu Mar 03 2016 - 00:09:42 PST)
- [AMBER] mmgbsa_error chemjxn (Thu Mar 03 2016 - 00:10:35 PST)
- Re: [AMBER] problem running MD for diphosphoric acid anion necmettin pirinccioglu (Thu Mar 03 2016 - 00:49:28 PST)
- [AMBER] Sign of outputs of MMPBSA.py Aronica, Pietro (Thu Mar 03 2016 - 08:02:58 PST)
- [AMBER] pseudo trajectories with 4 center of mass? Hirdesh Kumar (Thu Mar 03 2016 - 11:49:23 PST)
- [AMBER] GB Parameterization Taylor Harville (Thu Mar 03 2016 - 19:27:13 PST)
- [AMBER] Error while creating topology file after adding ions Sreemol G (Thu Mar 03 2016 - 20:40:03 PST)
- [AMBER] Query regarding NMR refinement Madhura De (Fri Mar 04 2016 - 02:47:15 PST)
- [AMBER] long bond lengths after parmed.py setMolecules command in metal-containing system Arjun Narayanan (Fri Mar 04 2016 - 08:26:36 PST)
- [AMBER] cpptraj surf George Tzotzos (Fri Mar 04 2016 - 13:35:45 PST)
- [AMBER] Analysis of Radius of gyration Iqbal, Muhammad Sajid (Fri Mar 04 2016 - 14:19:26 PST)
- [AMBER] for protein- RNA complex simulation Sreemol G (Fri Mar 04 2016 - 19:49:46 PST)
- [AMBER] regarding mm-pbsa calculation neha chaudhary (Fri Mar 04 2016 - 20:58:10 PST)
- [AMBER] nucleic acid residue representation in leap Sreemol G (Fri Mar 04 2016 - 23:04:00 PST)
- [AMBER] IMPORTANT FOR 12-6-4 USERS Pengfei Li (Sat Mar 05 2016 - 18:30:10 PST)
- [AMBER] cpptraj rmsd error (Orthogonal box), unknown #frames, start=0 offset=1 Saman Yousuf ali (Sun Mar 06 2016 - 22:52:23 PST)
- [AMBER] How to deal with fractional electron unit charges on small molecules?? SHAILESH KUMAR (Mon Mar 07 2016 - 02:30:44 PST)
- [AMBER] tests dont work for serial, parallel or cuda amber instalation. Wesley Alves (Mon Mar 07 2016 - 12:20:05 PST)
- [AMBER] Chamber tool, error using the prmtop and inpcrd files Anna Cebrian Prats (Tue Mar 08 2016 - 02:36:47 PST)
- [AMBER] pseudo trajectories for 4 centers of mass? Hirdesh Kumar (Tue Mar 08 2016 - 06:34:48 PST)
- [AMBER] How to interpret MMGBSA ligand binding free energy decomposition results Zhang Marc (Tue Mar 08 2016 - 09:08:08 PST)
- [AMBER] Production phase for MMPBSA Arati Paudyal (Tue Mar 08 2016 - 11:06:10 PST)
- [AMBER] Diffusion/msd cpptraj bug? Timothy Christopher Schutt (Tue Mar 08 2016 - 13:11:54 PST)
- [AMBER] Does the PBSA Calculation Include the Neutralizing Plasma？ 姜阳 (Tue Mar 08 2016 - 19:27:01 PST)
- [AMBER] How did GAFF get force constants? Ruixing Wang (Tue Mar 08 2016 - 20:01:13 PST)
- [AMBER] Optimize in Gaussian with RESP Jesmita Dhar (Wed Mar 09 2016 - 00:36:50 PST)
- [AMBER] Optimize in Gaussian with RESP Jesmita Dhar (Wed Mar 09 2016 - 00:37:50 PST)
- [AMBER] How to using distance based strip action and generate the corresponding prmtop windy (Wed Mar 09 2016 - 07:02:39 PST)
- Re: [AMBER] tests dont work for serial, parallel or cuda amber instalation Wesley Alves (Wed Mar 09 2016 - 08:57:24 PST)
- [AMBER] geforce 970 versus 780 George Green (Wed Mar 09 2016 - 11:14:04 PST)
- [AMBER] ambpdb could not read restart atoms/time. Bin Wang (Wed Mar 09 2016 - 19:07:31 PST)
- [AMBER] Creating new atom Sreemol G (Wed Mar 09 2016 - 20:25:09 PST)
- Re: [AMBER] velocity auto correlation function Vertika Gautam (Wed Mar 09 2016 - 21:25:02 PST)
- [AMBER] Installation error amber14 Dr. M. K. Yadav (Thu Mar 10 2016 - 00:28:20 PST)
- [AMBER] problem with ionized residues Michael Shokhen (Thu Mar 10 2016 - 02:30:20 PST)
- [AMBER] energy calculation with cpptraj based on chamber topology file Song-Ho Chong (Thu Mar 10 2016 - 04:30:08 PST)
- [AMBER] Failed installation of latest MCPB version anu chandra (Thu Mar 10 2016 - 04:37:18 PST)
- [AMBER] On Amber to Gromacs Parameter Conversion Robert Molt (Thu Mar 10 2016 - 12:55:19 PST)
- [AMBER] On Amber to Gromacs Parameter Conversion Robert Molt (Thu Mar 10 2016 - 12:55:13 PST)
- [AMBER] Paradynamics simulations with Amber lipengfei_mail (Thu Mar 10 2016 - 23:02:13 PST)
- [AMBER] Lower energy frame from summary.EPTOT Vasantha Kumar (Fri Mar 11 2016 - 01:06:47 PST)
- [AMBER] generate frcmod.user file for missing parameters Jesmita Dhar (Fri Mar 11 2016 - 03:03:04 PST)
- [AMBER] protein-RNA complex simulation Sreemol G (Fri Mar 11 2016 - 03:57:51 PST)
- Re: [AMBER] R: R: Fwd: cpinutil.py problem Elisa Pieri (Fri Mar 11 2016 - 04:03:10 PST)
- [AMBER] References Hadeer ELHabashy (Fri Mar 11 2016 - 07:55:29 PST)
- [AMBER] Igb and salt concentration for GBSA Arati Paudyal (Fri Mar 11 2016 - 15:09:02 PST)
- [AMBER] RMSD too high after simulation Arati Paudyal (Fri Mar 11 2016 - 17:41:36 PST)
- [AMBER] How is ΔGnonpolar computed in MMPBSA.py in AMBER 14? (inp=2 in &pb namelist) Stefan Ivanov (Fri Mar 11 2016 - 23:28:32 PST)
- [AMBER] Problem with 'hydrogen' having multiple bonds using SHAKEH alexander.zlobin (Sat Mar 12 2016 - 06:47:28 PST)
- [AMBER] MMPBSA error Arati Paudyal (Sat Mar 12 2016 - 11:07:18 PST)
- [AMBER] ISQBP 2016 meeting - registration opened! Thomas Cheatham (Sun Mar 13 2016 - 22:15:46 PDT)
- Re: [AMBER] AMBER:neutralisation of non integral charges Shilpa Gupta (Mon Mar 14 2016 - 06:22:42 PDT)
- [AMBER] bad atom type with MMPBSA decomposition? Kenneth Huang (Mon Mar 14 2016 - 06:58:25 PDT)
- Re: [AMBER] Problems when trying to improve angle parameters whith paramfit Sigurd Friis Truelsen (Mon Mar 14 2016 - 08:28:52 PDT)
- [AMBER] parmed -setBond command Balaji Selvam (Mon Mar 14 2016 - 11:19:39 PDT)
- [AMBER] Lifetime analysis of backbone hydrogen bonds Krantzman, Kristin D (Mon Mar 14 2016 - 12:28:55 PDT)
- Re: [AMBER] Problems when trying to improve angle parameters whith paramfit Jérémie KNOOPS [531802] (Mon Mar 14 2016 - 14:34:57 PDT)
- [AMBER] Convergence problem with the SCC-DFTB example. Jinfeng Huang (Tue Mar 15 2016 - 01:29:17 PDT)
- [AMBER] A query about using random seed generator in simulations anu chandra (Tue Mar 15 2016 - 05:14:45 PDT)
- [AMBER] Attempting MC barostat change: Failed Michael Shokhen (Tue Mar 15 2016 - 05:51:21 PDT)
- [AMBER] PBSA fails with error message PB Bomb in epsmap(): epsz out of range Bruno Falcone (Tue Mar 15 2016 - 14:55:20 PDT)
- [AMBER] shell script yhzahsc (Tue Mar 15 2016 - 19:27:35 PDT)
- [AMBER] MMPBSA doubt Mary Varughese (Wed Mar 16 2016 - 02:20:21 PDT)
- [AMBER] rmsd y axis value deviation. Saman Yousuf ali (Wed Mar 16 2016 - 02:55:35 PDT)
- [AMBER] topology file for a graphene oxide with repetitive pattern Jesmita Dhar (Wed Mar 16 2016 - 03:07:29 PDT)
- [AMBER] red server error: ddikick.x: Fatal error detected Jesmita Dhar (Wed Mar 16 2016 - 03:44:10 PDT)
- [AMBER] Error with make test.parallel in AmberTools 15 installation anu chandra (Wed Mar 16 2016 - 09:28:10 PDT)
- [AMBER] tests dont work after installation Wesley Alves (Wed Mar 16 2016 - 10:48:02 PDT)
- [AMBER] GROMACS File Conversion Subtlety Robert Molt (Wed Mar 16 2016 - 23:03:10 PDT)
- [AMBER] errors in plumed and amber14 patch jixiaofeng (Thu Mar 17 2016 - 01:06:04 PDT)
- [AMBER] 2016 ISQBP Meeting: early registration / abstract submission deadline approaching Vlad Cojocaru (Thu Mar 17 2016 - 01:50:08 PDT)
- [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" Enrique Frio (Thu Mar 17 2016 - 04:02:29 PDT)
- [AMBER] Training and Innovation Course in Drug Design Thomas Exner (Thu Mar 17 2016 - 08:02:56 PDT)
- [AMBER] nitro tyrosine Wu Xu (Thu Mar 17 2016 - 19:06:00 PDT)
- Re: [AMBER] errors in plumed and amber14 patch (Jason Swails) jixiaofeng (Thu Mar 17 2016 - 19:12:38 PDT)
- [AMBER] The basis for selecting step sizes Bin ZOU (Thu Mar 17 2016 - 22:51:41 PDT)
- [AMBER] restart file error Sidhu, Khushwant (Dr.) (Fri Mar 18 2016 - 03:59:37 PDT)
- [AMBER] Is there a shift of QM energy in a QM/MM simulation? Pengfei Li (Fri Mar 18 2016 - 05:26:47 PDT)
- [AMBER] MPI_ABORT in pH-REMD Elisa Pieri (Fri Mar 18 2016 - 06:05:02 PDT)
- [AMBER] set up for a binding event MD Arnoult, Eric [JRDUS] (Fri Mar 18 2016 - 11:02:17 PDT)
- [AMBER] FW: problem in plotting total energy graph by using perl script Sehrish Naz Aijaz (Sat Mar 19 2016 - 01:20:41 PDT)
- [AMBER] problem in plotting total energy graphs by perl script Sehrish Naz Aijaz (Sat Mar 19 2016 - 01:25:27 PDT)
- [AMBER] Normal Mode Job Allocation Failure Cockroft, Nicholas T. (Mon Mar 21 2016 - 08:18:03 PDT)
- [AMBER] mmpbsa discrepancies George Tzotzos (Mon Mar 21 2016 - 10:05:36 PDT)
- [AMBER] strange output with nativecontacts command Krantzman, Kristin D (Mon Mar 21 2016 - 17:22:06 PDT)
- [AMBER] Calculating pair-wise interaction energy using MMPBSA for Gromacs files Suchetana Gupta (Mon Mar 21 2016 - 22:01:48 PDT)
- [AMBER] Combining parameter of Phosphoserine with 99SBILDN+bsc0 A kS (Mon Mar 21 2016 - 23:25:09 PDT)
- [AMBER] GAFF of Amber 'ff..' force field to prepare ligands? alexander.zlobin (Tue Mar 22 2016 - 03:50:29 PDT)
- [AMBER] Tutorial 18 - CpHMD with pmemd R.G. Mantell (Tue Mar 22 2016 - 05:09:45 PDT)
- [AMBER] interview with David Case Nikolai Skrynnikov (Tue Mar 22 2016 - 22:02:17 PDT)
- [AMBER] Problems running MD simulations with pseudocontact shifts as restraints Francisco Corzana López (Wed Mar 23 2016 - 01:44:12 PDT)
- [AMBER] Fwd: MMPBSA CalceError mmpbsa_py_energy failed with prmtop com.prmtop! Annie Ancy (Wed Mar 23 2016 - 03:49:00 PDT)
- [AMBER] questions about mol2 and pdb file. Hong Sun (Wed Mar 23 2016 - 20:57:22 PDT)
- [AMBER] RMSD of 0 for coordinated ion Francesco Gentile (Wed Mar 23 2016 - 21:25:36 PDT)
- [AMBER] On alphabetizing impropers David Cerutti (Wed Mar 23 2016 - 22:42:52 PDT)
- [AMBER] [Amber] Polarizable ff for vacuum Edwin Aponte (Thu Mar 24 2016 - 07:48:21 PDT)
- [AMBER] Amber parameters for deprotonated threonine anu chandra (Thu Mar 24 2016 - 09:03:54 PDT)
- [AMBER] desc in leap amirhossein taghavi (Thu Mar 24 2016 - 09:05:26 PDT)
- [AMBER] nonnative contacts Krantzman, Kristin D (Thu Mar 24 2016 - 10:27:09 PDT)
- [AMBER] mpirun .... hwloc Marcelo Andrade Chagas (Thu Mar 24 2016 - 11:29:03 PDT)
- [AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not Guqin Shi (Thu Mar 24 2016 - 12:12:11 PDT)
- [AMBER] AT_15 install/osx notes, xleap deselect not working Bill Ross (Thu Mar 24 2016 - 18:27:08 PDT)
- [AMBER] Clustering waleed zalloum (Fri Mar 25 2016 - 02:06:13 PDT)
- [AMBER] MMPBSApy - APBS bug Marek Maly (Sat Mar 26 2016 - 10:09:30 PDT)
- [AMBER] membrane protein problem Michael Shokhen (Sat Mar 26 2016 - 11:35:55 PDT)
- [AMBER] charge membrane Fabian gmail (Mon Mar 28 2016 - 02:18:59 PDT)
- [AMBER] membrane protein complex preparation Fabian gmail (Mon Mar 28 2016 - 04:15:16 PDT)
- [AMBER] problem in nmode calculation by NAB Sanjib Paul (Mon Mar 28 2016 - 07:19:37 PDT)
- [AMBER] Relation between binding affinity and free enegy Sangita Kachhap (Mon Mar 28 2016 - 11:55:34 PDT)
- [AMBER] trajin reads box info from a trajectory with no box info. Jose Borreguero (Mon Mar 28 2016 - 13:21:41 PDT)
- [AMBER] How does one derive parameters to modify GAFF? David Cerutti (Mon Mar 28 2016 - 14:34:11 PDT)
- [AMBER] [AmberTools15] “Cluster” with cpptraj: looking for SSR/SST ratio Guqin Shi (Mon Mar 28 2016 - 14:35:15 PDT)
- [AMBER] amber14 installation Carlos Romero (Mon Mar 28 2016 - 22:52:38 PDT)
- [AMBER] salt concentration KCl Fabian gmail (Tue Mar 29 2016 - 03:33:35 PDT)
- [AMBER] cpptraj mask definition Weinzierl, Robert O J (Tue Mar 29 2016 - 03:51:26 PDT)
- [AMBER] torsion angle rmsd by cpptraj ? Michael Shokhen (Tue Mar 29 2016 - 05:00:49 PDT)
- [AMBER] Amber MD simulation - viewing artifacts in VMD? Enrique Frio (Tue Mar 29 2016 - 05:05:05 PDT)
- [AMBER] General question George Tzotzos (Tue Mar 29 2016 - 09:35:22 PDT)
- [AMBER] aMD simulation of membrane protein ? Michael Shokhen (Wed Mar 30 2016 - 03:18:51 PDT)
- [AMBER] Need python code for the calculation of binding energy Ayesha Kanwal (Wed Mar 30 2016 - 03:21:55 PDT)
- [AMBER] need help for using Re_fit Jesmita Dhar (Wed Mar 30 2016 - 04:45:37 PDT)
- [AMBER] Strange problem of running MD simulation with sander ? Jinfeng Huang (Wed Mar 30 2016 - 08:07:28 PDT)
- [AMBER] Align namelist for direct dipolar coupling restraints Francisco Corzana López (Wed Mar 30 2016 - 08:59:39 PDT)
- [AMBER] Periodicity box Fabian Glaser (Wed Mar 30 2016 - 09:21:02 PDT)
- [AMBER] Hydrophobic solution environment ??? Mijiddorj Batsaikhan (Wed Mar 30 2016 - 09:33:17 PDT)
- [AMBER] Proper nfft* parameters for a very long solvent box? Kasprzak, Wojciech (NIH/NCI) [C] (Wed Mar 30 2016 - 11:14:59 PDT)
- [AMBER] Command to display simulation completion time Sreemol G (Wed Mar 30 2016 - 23:58:48 PDT)
- Last message date: Thu Mar 31 2016 - 22:00:05 PDT
- Archived on: Fri Apr 19 2024 - 05:55:05 PDT
