Amber Archive May 2016 by thread
- Re: [AMBER] on antechamber Brett (Sat Apr 30 2016 - 20:51:58 PDT)
- [AMBER] help identifying dihedral parameters for paracetemol using Antechamber conor parks (Sat Apr 30 2016 - 21:13:49 PDT)
- [AMBER] water residence time calculation maryam azimzadehirani (Sun May 01 2016 - 05:59:57 PDT)
- [AMBER] Query about amber 16, external electric field support Kshatresh Dutta Dubey (Sun May 01 2016 - 06:54:50 PDT)
- [AMBER] cpptraj mask command Saman Yousuf ali (Sun May 01 2016 - 08:29:43 PDT)
- [AMBER] angle between normals to dna bases? Bill Ross (Sun May 01 2016 - 20:00:50 PDT)
- [AMBER] Paramfit trajectory read error David Poole (Sun May 01 2016 - 21:28:56 PDT)
- [AMBER] Ewald force using debugf Zhenyu Meng (Mon May 02 2016 - 04:07:17 PDT)
- [AMBER] iwrap=1 issue Hirdesh Kumar (Mon May 02 2016 - 04:57:07 PDT)
- [AMBER] on antechamber of AMBER Brett (Mon May 02 2016 - 06:02:48 PDT)
- [AMBER] Amber 8 on RHEL 6 boyken.divms.uiowa.edu (Mon May 02 2016 - 09:30:41 PDT)
- [AMBER] Rotating the protein along x-axis Aishani Prem (Mon May 02 2016 - 14:53:27 PDT)
- [AMBER] rdf cpptraj. Saman Yousuf ali (Tue May 03 2016 - 02:37:48 PDT)
- Re: [AMBER] tleap - protein + ligand + heme group Anna Cebrian Prats (Tue May 03 2016 - 02:47:55 PDT)
- [AMBER] Problem interpreting cpptraj hbond output file maryam azimzadehirani (Tue May 03 2016 - 05:00:03 PDT)
- [AMBER] process_mdout.perl script Ruth Helena Tichauer (Tue May 03 2016 - 06:35:47 PDT)
- [AMBER] DFTB convergence Jacopo Sgrignani (Tue May 03 2016 - 12:23:17 PDT)
- [AMBER] Amber 12 and VMware workstation 12 player Ibrahim Said (Tue May 03 2016 - 13:00:42 PDT)
- [AMBER] non zero net charge on molecule from AM1-BCC charge parameter fit conor parks (Tue May 03 2016 - 20:25:44 PDT)
- [AMBER] cpptraj rms fit to rst file Bill Ross (Tue May 03 2016 - 21:22:04 PDT)
- [AMBER] Thermodynamic Integration introduce charge Johannes Loeffler (Tue May 03 2016 - 22:36:39 PDT)
- [AMBER] bad data error in sander run Mary Varughese (Wed May 04 2016 - 04:07:47 PDT)
- [AMBER] metal ion models for Zn+2 Fabian gmail (Wed May 04 2016 - 06:10:33 PDT)
- [AMBER] DNA Origami Ramkumar B (Wed May 04 2016 - 11:35:27 PDT)
- [AMBER] MMPBSA: question of pairwise per residue decomposition George Tzotzos (Wed May 04 2016 - 12:27:21 PDT)
- [AMBER] xLeap Ramkumar B (Thu May 05 2016 - 00:20:55 PDT)
- [AMBER] HMR with protein-ligand system Alessio Atzori (Thu May 05 2016 - 00:36:26 PDT)
- [AMBER] pdb2pqr PDB processing for Amber force field James Starlight (Thu May 05 2016 - 03:39:49 PDT)
- [AMBER] Regarding RMSF calculation of protein using AMBER Sivanandam M (Thu May 05 2016 - 05:46:34 PDT)
- [AMBER] help: what cause Sandar crash Yang, Hui (Thu May 05 2016 - 06:23:23 PDT)
- [AMBER] Calculating LJ parameters in Amber format anu chandra (Thu May 05 2016 - 06:45:58 PDT)
- Re: [AMBER] Problem with MCPB.py Surya Prakash Tiwari (Thu May 05 2016 - 10:37:59 PDT)
- [AMBER] RESP charges Chi Jin (Thu May 05 2016 - 15:11:16 PDT)
- [AMBER] live dCAT simulation Bill Ross (Thu May 05 2016 - 16:52:40 PDT)
- [AMBER] Paramfit'ing forces David Poole (Thu May 05 2016 - 17:53:53 PDT)
- [AMBER] DNA Origami Ramkumar B (Fri May 06 2016 - 10:26:55 PDT)
- [AMBER] Problems with cpinutil.py in CpHMD as adding a new titratable ligand Yong Wang (Fri May 06 2016 - 13:43:20 PDT)
- [AMBER] Units in dist_vs_t file from SMD simulation Nisler, Collin R. (Fri May 06 2016 - 14:08:34 PDT)
- [AMBER] Hydroxyapatites force field Mijiddorj Batsaikhan (Sat May 07 2016 - 00:00:40 PDT)
- [AMBER] Hydroxyapatites force field Mijiddorj Batsaikhan (Sat May 07 2016 - 00:03:57 PDT)
- [AMBER] Fw: Fatemeh Arabi (Sat May 07 2016 - 00:16:15 PDT)
- [AMBER] How to modify the LENNARD_JONES_BCOEF in amber topology anu chandra (Sat May 07 2016 - 08:52:25 PDT)
- Re: [AMBER] How to modify the LENNARD_JONES_BCOEF in amber topologyer JAIME RUBIO MARTINEZ (Sun May 08 2016 - 06:12:28 PDT)
- [AMBER] Analysis of protein-protein interaction James Starlight (Mon May 09 2016 - 03:10:22 PDT)
- [AMBER] on GAFF Brett (Mon May 09 2016 - 06:55:45 PDT)
- [AMBER] Amber12 install error 유효정 (Mon May 09 2016 - 08:39:11 PDT)
- [AMBER] Restrain a single atom in the residue during minimization, instead of all the atoms in a residue with RES option Vasantha Kumar (Mon May 09 2016 - 13:32:39 PDT)
- [AMBER] Phosphorylated-RNA yhzahsc (Mon May 09 2016 - 17:48:38 PDT)
- [AMBER] acetone as solvent for simulation Shilpa Gupta (Mon May 09 2016 - 22:53:48 PDT)
- [AMBER] VMD visualization of netcdf trajectories through the terminal James Starlight (Tue May 10 2016 - 02:24:57 PDT)
- [AMBER] How adding cluster to a model Damiano Spadoni (Tue May 10 2016 - 04:57:14 PDT)
- [AMBER] Constant pH simulation Tanmoy Paul (Tue May 10 2016 - 06:16:18 PDT)
- [AMBER] Installing AmberTools16 on OSX 10.11 Adams, John E. (Tue May 10 2016 - 07:48:54 PDT)
- [AMBER] Visualization of all-in-one mdcrd file in VMD Trang Nguyen (Tue May 10 2016 - 11:26:02 PDT)
- [AMBER] MMPBSA doubt Mary Varughese (Tue May 10 2016 - 21:01:03 PDT)
- [AMBER] Regarding joining of two pdb file MOHD HOMAIDUR RAHMAN (Tue May 10 2016 - 22:53:14 PDT)
- [AMBER] amber error - reg Arthi Venkat (Wed May 11 2016 - 02:35:17 PDT)
- [AMBER] Problem with closest command in cpptraj Indrajit Deb (Wed May 11 2016 - 07:16:14 PDT)
- [AMBER] Problem in Restarting production run ATUL KUMAR (Thu May 12 2016 - 00:19:04 PDT)
- [AMBER] Error during frames generation from production run Sneha Rai (Thu May 12 2016 - 01:18:34 PDT)
- [AMBER] error in cluster analysis by cpptraj Michael Shokhen (Thu May 12 2016 - 03:06:39 PDT)
- [AMBER] About harmonic restraints on dihedral angle in pmemd.cuda mish (Thu May 12 2016 - 06:58:21 PDT)
- [AMBER] How to deal with Heme? Morteza Chehel Amirani (Thu May 12 2016 - 10:53:44 PDT)
- [AMBER] slinky on a hot tin roof Bill Ross (Fri May 13 2016 - 01:25:12 PDT)
- [AMBER] Parametrisation of ligand with ions julian.zachmann selvita.home.pl (Fri May 13 2016 - 02:30:27 PDT)
- [AMBER] Scripts to gradually remove NMR restraints during MD simulation Vasantha Kumar (Fri May 13 2016 - 02:46:10 PDT)
- [AMBER] Unable to run Antechamber Shreeramesh (Fri May 13 2016 - 05:12:48 PDT)
- [AMBER] Amber compilation fail after plumed patch Fabrício Bracht (Fri May 13 2016 - 13:29:41 PDT)
- [AMBER] Combining .mdvel and .nc(NetCDF) into one file ATUL KUMAR (Sat May 14 2016 - 00:12:55 PDT)
- [AMBER] parmed units and version numbers hannes.loeffler.stfc.ac.uk (Sat May 14 2016 - 06:49:24 PDT)
- [AMBER] Fix dimension of the box throughout the MD simulations Iqbal, Muhammad Sajid (Sat May 14 2016 - 12:49:43 PDT)
- [AMBER] problem in calculating velocity autocorrelation ATUL KUMAR (Sun May 15 2016 - 06:34:09 PDT)
- [AMBER] MMPBSA for homo-dimer system with ligands Kat G (Sun May 15 2016 - 22:03:35 PDT)
- [AMBER] problem installing AmberTools16 pytraj on Mac Marc van der Kamp (Mon May 16 2016 - 08:23:11 PDT)
- [AMBER] No leaprc.ff14SB anymore in AmberTools16 - reason? Marc van der Kamp (Mon May 16 2016 - 08:27:38 PDT)
- [AMBER] Working with pytraj MOHD HOMAIDUR RAHMAN (Mon May 16 2016 - 12:05:00 PDT)
- Re: [AMBER] AMBER Digest, Vol 1578, Issue 1 Iqbal, Muhammad Sajid (Mon May 16 2016 - 22:21:12 PDT)
- [AMBER] MD Output File Wong Li Zhe (Tue May 17 2016 - 00:56:59 PDT)
- [AMBER] problem with new residu in Xleap Muriel Jourdan (Tue May 17 2016 - 07:15:10 PDT)
- [AMBER] tleap: opls-ua parm for an arbitrary molecule Ekaterina Ratkova (Tue May 17 2016 - 07:02:33 PDT)
- [AMBER] issues with NONBOND LIST? Thomas Pochapsky (Tue May 17 2016 - 11:45:32 PDT)
- [AMBER] Problems with pairwise command in cpptraj Osman, Roman (Tue May 17 2016 - 13:24:41 PDT)
- [AMBER] .nc trajectory format Neha Gandhi (Tue May 17 2016 - 21:35:01 PDT)
- [AMBER] Bug: Gasteiger parameters for S(-1) Mahmoud A. A. Ibrahim (Wed May 18 2016 - 00:42:02 PDT)
- [AMBER] Licence Jacopo Sgrignani (Wed May 18 2016 - 08:46:36 PDT)
- [AMBER] mmpbsa Ziba Bahadori (Wed May 18 2016 - 10:37:26 PDT)
- [AMBER] Problems with pairwise command in cpptraj Osman, Roman (Wed May 18 2016 - 10:47:13 PDT)
- [AMBER] GAFF2 setup Hannes Loeffler (Thu May 19 2016 - 02:03:25 PDT)
- [AMBER] MMPBSA Results asdda asa (Thu May 19 2016 - 02:19:45 PDT)
- [AMBER] rms to pdb for a subset of atoms [cpptraj] Eiros Zamora, Juan (Thu May 19 2016 - 06:55:25 PDT)
- [AMBER] Clustering of MD trajectories: ptraj, cpptraj Francesco Gentile (Thu May 19 2016 - 11:41:16 PDT)
- [AMBER] clustering with ptraj Francesco Gentile (Thu May 19 2016 - 17:08:37 PDT)
- [AMBER] Protein moving out of the water box Arati Paudyal (Thu May 19 2016 - 19:11:17 PDT)
- [AMBER] obtain or build parameters for non-natural residues ALINE THOMAS (Fri May 20 2016 - 00:45:10 PDT)
- [AMBER] choice of lipid type in MD simulation Zhang Marc (Fri May 20 2016 - 00:51:40 PDT)
- [AMBER] QM/MM energy minimization Stanislav Simko (Fri May 20 2016 - 03:34:28 PDT)
- [AMBER] Best Linux Choice Robert Molt (Fri May 20 2016 - 06:03:27 PDT)
- [AMBER] Amber coordinates to chemshell coords file (coords.c) Jenner Bonanata (Fri May 20 2016 - 06:10:25 PDT)
- [AMBER] Opening mol2 file in xleap Nikolay N. Kuzmich (Fri May 20 2016 - 06:36:19 PDT)
- [AMBER] MMPBSA.py issue with complex prmtop file Kalenkiewicz, Andrew (NIH/NICHD) [F] (Fri May 20 2016 - 15:23:16 PDT)
- [AMBER] MMPBSA final results of MMPBSA.py different from tutorial LI An-Bang (Fri May 20 2016 - 19:38:17 PDT)
- [AMBER] QM/MM Interface Nisler, Collin R. (Fri May 20 2016 - 22:37:11 PDT)
- [AMBER] Problems with GTX titan-X GPU Elvis Martis (Sat May 21 2016 - 03:19:54 PDT)
- Re: [AMBER] MMPBSA final results of MMPBSA.py different fromtutorial LI An-Bang (Sat May 21 2016 - 06:29:04 PDT)
- [AMBER] MMPBSA- topology files preparation Kat G (Sat May 21 2016 - 19:44:56 PDT)
- [AMBER] optimised corrections to ff03 Neha Gandhi (Sun May 22 2016 - 18:09:04 PDT)
- [AMBER] nativecontacts Neha Gandhi (Mon May 23 2016 - 00:25:36 PDT)
- [AMBER] CUDA MPI issues Biplab Ghosh (Mon May 23 2016 - 03:45:08 PDT)
- [AMBER] RE_POSITION Wong Li Zhe (Mon May 23 2016 - 18:07:15 PDT)
- [AMBER] Amino Acid Residues in QM/MM Simulation Nisler, Collin R. (Mon May 23 2016 - 19:25:23 PDT)
- [AMBER] Organic solvent box - Amber do not see the molecule but its atoms Stregone (Tue May 24 2016 - 04:27:40 PDT)
- [AMBER] MMPBSA Lara rajam (Tue May 24 2016 - 06:15:41 PDT)
- [AMBER] autoimage and TI Khabiri, Morteza (Tue May 24 2016 - 07:44:34 PDT)
- [AMBER] Regarding parameter file not saved Vishal Nemaysh (Tue May 24 2016 - 09:21:10 PDT)
- [AMBER] How to do QHA with outputs after considering every n-frames of trajectory? SHAILESH KUMAR (Tue May 24 2016 - 11:16:56 PDT)
- [AMBER] mmpbsa Ziba Bahadori (Tue May 24 2016 - 11:14:24 PDT)
- [AMBER] Release of FESetup 1.2 Hannes Loeffler (Tue May 24 2016 - 12:55:19 PDT)
- [AMBER] MM-PBSA result asdda asa (Tue May 24 2016 - 15:20:43 PDT)
- [AMBER] Solvation free energy in rism1d Jingyi Yan (Tue May 24 2016 - 15:51:39 PDT)
- [AMBER] query ankita mehta (Tue May 24 2016 - 22:57:07 PDT)
- [AMBER] Can I build parameters of hydroxyapatites? Mijiddorj Batsaikhan (Wed May 25 2016 - 02:34:39 PDT)
- [AMBER] Regarding Force Field Inquiry Vishal Nemaysh (Wed May 25 2016 - 04:22:48 PDT)
- [AMBER] Modified ARG LYS parameters Vlad Cojocaru (Wed May 25 2016 - 04:51:35 PDT)
- [AMBER] adaptive qm/mm NVT not reaching target temperature Stanislav Simko (Wed May 25 2016 - 05:58:39 PDT)
- [AMBER] standard parameter for sialic acid Bisignano, Paola (Wed May 25 2016 - 16:43:53 PDT)
- [AMBER] acetone as solvent for simulation Shilpa Gupta (Wed May 25 2016 - 22:39:22 PDT)
- [AMBER] cpptraj - rmsd/rmsf & reference structure colvin (Thu May 26 2016 - 02:19:16 PDT)
- [AMBER] Amber16: COM's in GPU version Åsmund Røhr Kjendseth (Thu May 26 2016 - 05:50:52 PDT)
- [AMBER] ante-mmpbsa.py: general question George Tzotzos (Thu May 26 2016 - 11:33:44 PDT)
- [AMBER] Replacing water with a H2O2 and restart the simulation Morteza Chehel Amirani (Thu May 26 2016 - 15:21:16 PDT)
- [AMBER] calculating binding free energy Carlos Romero (Thu May 26 2016 - 17:18:56 PDT)
- [AMBER] Simulation of DNA structure with a three-phosphate at 5' M. Reza Ganjalikhany (Fri May 27 2016 - 01:11:30 PDT)
- [AMBER] Constant area simulation Batuhan Kav (Fri May 27 2016 - 02:07:39 PDT)
- [AMBER] nativecontacts resout command change with AmberTools16 [cpptraj] Eiros Zamora, Juan (Fri May 27 2016 - 02:25:23 PDT)
- [AMBER] About AMBER Advanced Tutorial 17 on GPUs mish (Fri May 27 2016 - 07:44:08 PDT)
- [AMBER] Adaptively Biased MD: Problems with executing groupfile Jason Imamoto (Fri May 27 2016 - 10:20:07 PDT)
- [AMBER] mdl file for 1d-rism Jingyi Yan (Fri May 27 2016 - 15:39:41 PDT)
- [AMBER] Choline Chloride Christopher Jesudason (Sun May 29 2016 - 13:06:20 PDT)
- [AMBER] cpptraj clustering based on ligand cavity Neha Gandhi (Sun May 29 2016 - 18:12:10 PDT)
- [AMBER] Magnesium ion in AMBER Shreeramesh (Mon May 30 2016 - 05:03:46 PDT)
- [AMBER] NMR restraints violation limit Vasantha Kumar (Mon May 30 2016 - 07:38:10 PDT)
- [AMBER] calculated rmsd Ziba Bahadori (Tue May 31 2016 - 00:12:29 PDT)
- [AMBER] "sanderf" Odin Zeus (Tue May 31 2016 - 06:37:23 PDT)
- Last message date: Tue May 31 2016 - 12:30:03 PDT
- Archived on: Wed Dec 25 2024 - 05:55:21 PST
