Amber Archive Jul 2016 by thread
- [AMBER] cpptraj.hbond: water in the complex chemjxn (Thu Jun 30 2016 - 18:10:42 PDT)
- Re: [AMBER] bad atom type decomp Bruno Falcone (Thu Jun 30 2016 - 20:45:48 PDT)
- [AMBER] Help: make test fails during parallel amber installation Dr. M. K. Yadav (Thu Jun 30 2016 - 20:52:03 PDT)
- Re: [AMBER] Umbrella Sampling bharat gupta (Thu Jun 30 2016 - 22:00:58 PDT)
- Re: [AMBER] Slow performance of Amber12 on cluster bharat gupta (Thu Jun 30 2016 - 22:03:14 PDT)
- [AMBER] Regarding GIST calculation ATUL KUMAR (Thu Jun 30 2016 - 22:51:58 PDT)
- Re: [AMBER] Structural refinement of the protein complexed with metalo-ions James Starlight (Fri Jul 01 2016 - 01:37:14 PDT)
- [AMBER] can MCPB build non amino-acid containing complex? Zhenyu Meng (Fri Jul 01 2016 - 05:37:26 PDT)
- [AMBER] MMPBSA -O: command not found Thakur, Abhishek (Fri Jul 01 2016 - 12:58:38 PDT)
- Re: [AMBER] MCPB Fabrício Bracht (Fri Jul 01 2016 - 16:29:58 PDT)
- Re: [AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt Jose Manuel (Sat Jul 02 2016 - 01:46:09 PDT)
- Re: [AMBER] Regarding ho parameter in gaff David A Case (Sat Jul 02 2016 - 05:51:11 PDT)
- Re: [AMBER] addAtomType problem David A Case (Sat Jul 02 2016 - 05:55:16 PDT)
- [AMBER] convert amber topology and coordinates files into gromacs topology Ming Tang (Sun Jul 03 2016 - 17:27:47 PDT)
- [AMBER] Lipid14 with ntr=1 Himanshu Joshi (Mon Jul 04 2016 - 00:17:39 PDT)
- [AMBER] ParmEd Neha Gandhi (Mon Jul 04 2016 - 01:26:46 PDT)
- [AMBER] Ambertool16 - MCPB.py angle cut off and Error with Pdbsearcher.py Bilal Nizami (Mon Jul 04 2016 - 01:39:33 PDT)
- [AMBER] Question about Charge derivation for GLYCAM force field Casalini Tommaso (Mon Jul 04 2016 - 07:03:00 PDT)
- [AMBER] Potential on each atom Elisa Pieri (Mon Jul 04 2016 - 07:43:20 PDT)
- [AMBER] SMD at constant force Ming Tang (Mon Jul 04 2016 - 19:06:25 PDT)
- [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng (Mon Jul 04 2016 - 20:00:11 PDT)
- [AMBER] iwrap=0 Ming Tang (Tue Jul 05 2016 - 04:25:13 PDT)
- Re: [AMBER] Error during amber 12 installation bharat gupta (Tue Jul 05 2016 - 06:07:37 PDT)
- Re: [AMBER] Help with Umbrella Sampling bharat gupta (Tue Jul 05 2016 - 22:31:57 PDT)
- [AMBER] Amber12 or lated on POWER8 platform Sanman Sabane (Wed Jul 06 2016 - 03:22:40 PDT)
- [AMBER] Problem to extending Simulation ATUL KUMAR (Wed Jul 06 2016 - 04:38:16 PDT)
- [AMBER] Multiplicity in antechamber Fabrício Bracht (Wed Jul 06 2016 - 11:22:44 PDT)
- [AMBER] Amber16 tutorials Corum, Katharine W (Wed Jul 06 2016 - 14:07:01 PDT)
- [AMBER] DPPC simulation temperature gsottile.unq.edu.ar (Wed Jul 06 2016 - 14:15:35 PDT)
- [AMBER] Question on SMD Ming Tang (Wed Jul 06 2016 - 14:46:02 PDT)
- [AMBER] Query on SMD Ming Tang (Wed Jul 06 2016 - 14:49:02 PDT)
- [AMBER] A question on SMD simulations Ming Tang (Wed Jul 06 2016 - 14:59:42 PDT)
- [AMBER] Stuck somewhere using antechamber Xiaoyu Wang (Wed Jul 06 2016 - 16:00:37 PDT)
- Re: [AMBER] Defining reaction coordinate for US bharat gupta (Thu Jul 07 2016 - 01:38:33 PDT)
- [AMBER] Gunning GIST in parallel ATUL KUMAR (Thu Jul 07 2016 - 03:05:07 PDT)
- [AMBER] An attempt for TI with QM/MM Hamiltonian Xiangyu Jia (Thu Jul 07 2016 - 06:13:51 PDT)
- Re: [AMBER] re-imaging bilayer Sally Pias (Thu Jul 07 2016 - 06:41:17 PDT)
- [AMBER] VMD Thakur, Abhishek (Thu Jul 07 2016 - 09:44:53 PDT)
- [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice (Thu Jul 07 2016 - 10:49:07 PDT)
- [AMBER] GLYCAM naming Fabrício Bracht (Thu Jul 07 2016 - 11:56:05 PDT)
- [AMBER] QM/MM issue Morteza Chehel Amirani (Thu Jul 07 2016 - 14:13:10 PDT)
- [AMBER] QM/MM simulations with Amber/deMon2k Morteza Chehel Amirani (Thu Jul 07 2016 - 14:19:53 PDT)
- Re: [AMBER] Patching Plumed 1.3 with Amber12 bharat gupta (Thu Jul 07 2016 - 18:04:39 PDT)
- [AMBER] rmsd plot error Saman Yousuf ali (Fri Jul 08 2016 - 03:55:51 PDT)
- [AMBER] how to fix COM of a group of atoms? Ming Tang (Fri Jul 08 2016 - 06:01:05 PDT)
- Re: [AMBER] Library errors while using NAB on Amber16 Slava Chushak (Fri Jul 08 2016 - 07:15:55 PDT)
- [AMBER] MMPBSA Thakur, Abhishek (Fri Jul 08 2016 - 09:57:16 PDT)
- [AMBER] ligand bond distortion during MD run. Saman Yousuf ali (Fri Jul 08 2016 - 10:48:21 PDT)
- [AMBER] MD of an elongated active site protein. Saman Yousuf ali (Sat Jul 09 2016 - 07:58:02 PDT)
- [AMBER] adding non-standard residue to RNA strand Martina Devi (Sat Jul 09 2016 - 10:21:28 PDT)
- [AMBER] Restrain COM of a group of atoms Ming Tang (Sat Jul 09 2016 - 18:18:11 PDT)
- [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. 朱 婧涵 (Mon Jul 11 2016 - 02:19:28 PDT)
- [AMBER] predicting RDCs for un-restrained bonds Thomas Pochapsky (Mon Jul 11 2016 - 06:23:03 PDT)
- [AMBER] Steered Molecular Dynamics Fair, Ryan (Mon Jul 11 2016 - 09:05:38 PDT)
- [AMBER] MMPBSA Thakur, Abhishek (Mon Jul 11 2016 - 13:31:32 PDT)
- [AMBER] rism1d convergence for solvent mixtures Shijie Sheng (Mon Jul 11 2016 - 16:30:42 PDT)
- Re: [AMBER] Help with SMD bharat gupta (Tue Jul 12 2016 - 01:02:31 PDT)
- [AMBER] QM/MM problems with Amber/Gaussian Allen Zou (Tue Jul 12 2016 - 08:11:25 PDT)
- [AMBER] Born Mayer Potential Vivien Ramothe (Tue Jul 12 2016 - 08:36:22 PDT)
- [AMBER] Decomposition in minimization step Atila Petrosian (Tue Jul 12 2016 - 23:14:57 PDT)
- [AMBER] strategies to speed up MM/GBSA screening Thomas Evangelidis (Wed Jul 13 2016 - 04:08:31 PDT)
- [AMBER] a question about resp restraints strength Bahaa Mostafa (Wed Jul 13 2016 - 05:40:44 PDT)
- [AMBER] WHAM-2D analysis Alessandra Lacetera (Wed Jul 13 2016 - 09:55:20 PDT)
- [AMBER] Compute SASA through molsurf Francesco Gentile (Wed Jul 13 2016 - 15:02:21 PDT)
- [AMBER] carbon nanotube Neha Gandhi (Wed Jul 13 2016 - 18:18:31 PDT)
- [AMBER] Generating a HETATM database to use with reduce Kucharski Jr., Amir N (Wed Jul 13 2016 - 21:01:37 PDT)
- [AMBER] ff99SB*-ildn again Neha Gandhi (Wed Jul 13 2016 - 23:47:07 PDT)
- [AMBER] Is the surf or the molsurf calculate the protein surface? windy (Thu Jul 14 2016 - 01:44:08 PDT)
- [AMBER] NEW parameters with AMBER Anna Cebrian Prats (Thu Jul 14 2016 - 02:55:16 PDT)
- [AMBER] a question about resp restraints strength Bahaa Mostafa (Thu Jul 14 2016 - 04:04:13 PDT)
- [AMBER] a question about resp restraints strength Bahaa Mostafa (Thu Jul 14 2016 - 04:10:27 PDT)
- [AMBER] Problem with Gaussian09 with B97D/def2TZVPPD basis set from EMSL Indrajit Deb (Thu Jul 14 2016 - 05:55:07 PDT)
- [AMBER] RMSD plot query esther nehu (Thu Jul 14 2016 - 07:29:41 PDT)
- [AMBER] Is the surf or the molsurf calculate the protein surface? windy (Thu Jul 14 2016 - 19:08:02 PDT)
- [AMBER] REMD Reg Annie Ancy (Fri Jul 15 2016 - 04:23:18 PDT)
- [AMBER] MMPBSA.py for complex or receptor or ligand only Bruno Falcone (Fri Jul 15 2016 - 07:10:17 PDT)
- [AMBER] MMPBSA (inp=1 or inp=2)?? Thakur, Abhishek (Fri Jul 15 2016 - 08:53:44 PDT)
- [AMBER] HMR 4fs failure? Gerald Monard (Fri Jul 15 2016 - 12:54:29 PDT)
- [AMBER] ff14SB compatible with Glycam_06j-1? yunshi11 . (Sat Jul 16 2016 - 03:06:13 PDT)
- [AMBER] Cpptraj Dd H (Sun Jul 17 2016 - 05:57:55 PDT)
- [AMBER] Regarding Parameter file not saved Vishal Nemaysh (Sun Jul 17 2016 - 10:52:32 PDT)
- [AMBER] Discrepancy between mdcrd and output files for MD run jandre17 (Sun Jul 17 2016 - 13:21:31 PDT)
- [AMBER] Amber 16 Installation Beale, John (Mon Jul 18 2016 - 00:17:35 PDT)
- [AMBER] Ligand RMSD anu chandra (Mon Jul 18 2016 - 10:27:26 PDT)
- [AMBER] RDF Mahmood Jasim (Mon Jul 18 2016 - 10:32:45 PDT)
- [AMBER] phosphorylated residues Neha Gandhi (Mon Jul 18 2016 - 23:40:36 PDT)
- [AMBER] Proton wanders away from tryptophan and histadine sidechain carbon Ross Cheloha (Tue Jul 19 2016 - 07:50:53 PDT)
- [AMBER] aMD with chloroform Stephan Schott (Tue Jul 19 2016 - 08:19:24 PDT)
- [AMBER] Multiple Replicas on a Single GPU Bin Sun (Tue Jul 19 2016 - 18:12:32 PDT)
- [AMBER] Is the surf or the molsurf calculate the protein surface? Windy CC (Tue Jul 19 2016 - 19:46:15 PDT)
- [AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d Shijie Sheng (Tue Jul 19 2016 - 23:14:25 PDT)
- [AMBER] sander QM/MM MD Masoud Kazemi (Wed Jul 20 2016 - 05:26:50 PDT)
- [AMBER] MCPB.py - coordinate sphere FE Anna Cebrian Prats (Wed Jul 20 2016 - 05:44:01 PDT)
- [AMBER] NMR restraint Ming Tang (Wed Jul 20 2016 - 06:18:07 PDT)
- [AMBER] MCPB.py Anna Cebrian Prats (Wed Jul 20 2016 - 06:44:08 PDT)
- [AMBER] Binding deltaG in ligand pose selction anu chandra (Wed Jul 20 2016 - 09:14:03 PDT)
- [AMBER] Remove rotation in postoprocess Fabrício Bracht (Wed Jul 20 2016 - 13:15:31 PDT)
- [AMBER] Amber16 Parallel CUDA Tests Steven Ford (Wed Jul 20 2016 - 13:19:16 PDT)
- [AMBER] Difference of two trajectories C.D. Okafor (Wed Jul 20 2016 - 14:25:54 PDT)
- [AMBER] CPPTRAJ Anna Cebrian Prats (Thu Jul 21 2016 - 03:30:20 PDT)
- [AMBER] MD simulation can not proceed normally 乔艳 (Thu Jul 21 2016 - 04:31:22 PDT)
- [AMBER] Save individual PDBs from MD trajectory Iqbal, Muhammad Sajid (Thu Jul 21 2016 - 06:52:50 PDT)
- Re: [AMBER] SMD and free energy value bharat gupta (Thu Jul 21 2016 - 07:20:47 PDT)
- [AMBER] Amber with Amoeba force field Xiaoliu Zhang (Thu Jul 21 2016 - 08:26:38 PDT)
- [AMBER] Minimization of a small molecule in gas phase Tiffani Rovira (Thu Jul 21 2016 - 08:31:38 PDT)
- [AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?) Stephan Schott (Thu Jul 21 2016 - 10:25:49 PDT)
- [AMBER] Wierd line in amber-TI output Files Khabiri, Morteza (Thu Jul 21 2016 - 10:52:53 PDT)
- [AMBER] selecting frames with distribution Neha Gandhi (Thu Jul 21 2016 - 22:02:45 PDT)
- [AMBER] Gaussian error with MCPB ion modeling calculation Bilal Nizami (Fri Jul 22 2016 - 01:19:36 PDT)
- [AMBER] MDCRD nida baig (Fri Jul 22 2016 - 04:19:49 PDT)
- [AMBER] parmed chamber Neha Gandhi (Fri Jul 22 2016 - 04:58:50 PDT)
- [AMBER] Cpptraj - Stat bug? Markus Schneider (Fri Jul 22 2016 - 05:22:44 PDT)
- [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Wesley Michael Botello-Smith (Fri Jul 22 2016 - 16:01:12 PDT)
- [AMBER] NMode binding entropy Error -- Line minimizer aborted 康宁 (Sat Jul 23 2016 - 03:16:24 PDT)
- [AMBER] NAB ABHIJEET CHOWDHURY (Sat Jul 23 2016 - 05:02:06 PDT)
- [AMBER] Create x.out and x.rst from x.mdcrd Mijiddorj Batsaikhan (Sat Jul 23 2016 - 06:27:54 PDT)
- [AMBER] SMD simulation protocols Ibrahim Said (Sun Jul 24 2016 - 09:25:47 PDT)
- [AMBER] restraintmask: select residues around the coordinates of a point Thomas Evangelidis (Sun Jul 24 2016 - 16:51:43 PDT)
- [AMBER] NMR restraint Ming Tang (Sun Jul 24 2016 - 17:51:17 PDT)
- [AMBER] Implicit solvent with Glycam force field yunshi11 . (Sun Jul 24 2016 - 17:58:48 PDT)
- [AMBER] charmmlipid2amber not found Kshatresh Dutta Dubey (Mon Jul 25 2016 - 01:08:23 PDT)
- [AMBER] ibelly to fix protein. Saman Yousuf ali (Mon Jul 25 2016 - 05:21:49 PDT)
- [AMBER] Applying different restraints to different sets of atoms Dmitry Suplatov (Mon Jul 25 2016 - 05:38:52 PDT)
- [AMBER] Creating topology file in MMPBSA Anwesha Sarkar (Mon Jul 25 2016 - 05:51:35 PDT)
- [AMBER] Error MCPB when send the input Tiffani Rovira (Mon Jul 25 2016 - 10:05:23 PDT)
- [AMBER] average pdb distorted Thakur, Abhishek (Mon Jul 25 2016 - 12:20:34 PDT)
- [AMBER] MDGX tutorial? Dickson, Callum J (Mon Jul 25 2016 - 13:20:01 PDT)
- Re: [AMBER] AMBER Digest, Vol 1646, Issue 1 bharat gupta (Mon Jul 25 2016 - 22:21:49 PDT)
- [AMBER] ntr vs ibelly. Saman Yousuf ali (Tue Jul 26 2016 - 02:38:42 PDT)
- [AMBER] ntr vs ibelly. Saman Yousuf ali (Tue Jul 26 2016 - 03:45:06 PDT)
- [AMBER] Failed to solvate the molecule during the TUTORIAL A8 Nikolay N. Kuzmich (Tue Jul 26 2016 - 04:18:49 PDT)
- [AMBER] Error cuda Anna Cebrian Prats (Tue Jul 26 2016 - 07:33:39 PDT)
- [AMBER] cpptraj grid command multiple trajectories Sarah Graham (Tue Jul 26 2016 - 10:17:47 PDT)
- [AMBER] How to modify forcefield to use TIP4P-D water model Suguru ASAI (Wed Jul 27 2016 - 03:24:29 PDT)
- [AMBER] paramfit Igor Marques (Wed Jul 27 2016 - 09:34:45 PDT)
- [AMBER] make test.cuda failed Nikolay N. Kuzmich (Thu Jul 28 2016 - 06:50:52 PDT)
- [AMBER] EEL become ****** in minimization Suguru ASAI (Thu Jul 28 2016 - 07:04:56 PDT)
- [AMBER] Sander bomb: how to create a larger box Ruth Helena Tichauer (Thu Jul 28 2016 - 07:48:43 PDT)
- [AMBER] NMR restraint Ming Tang (Thu Jul 28 2016 - 17:36:35 PDT)
- [AMBER] InVacuoWithDielc JAIME RUBIO MARTINEZ (Thu Jul 28 2016 - 23:38:17 PDT)
- [AMBER] can amber14 be run with gtx1060 xjq (Fri Jul 29 2016 - 02:43:08 PDT)
- [AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar (Fri Jul 29 2016 - 05:26:54 PDT)
- [AMBER] Question about QM/MM Anna Cebrian Prats (Fri Jul 29 2016 - 06:45:19 PDT)
- [AMBER] modified potentials Irem Altan (Fri Jul 29 2016 - 06:52:07 PDT)
- [AMBER] Problem setting AMBERHOME as environment variable Ambertools 16 Linux Elissa Fink (Fri Jul 29 2016 - 09:15:59 PDT)
- [AMBER] MMPBSA (MD or aMD) Thakur, Abhishek (Fri Jul 29 2016 - 12:27:21 PDT)
- [AMBER] figure legend problem in the tutorial? Albert (Fri Jul 29 2016 - 12:50:53 PDT)
- [AMBER] Exposed hydrophobic surface area anu chandra (Fri Jul 29 2016 - 16:50:43 PDT)
- [AMBER] where is amber.jupyter? Albert (Sat Jul 30 2016 - 00:17:08 PDT)
- [AMBER] Calculating Salt bridge interactions- Protein and RNA Muthukumaran R (Sat Jul 30 2016 - 00:27:51 PDT)
- [AMBER] dssp xlabel conversion. Saman Yousuf ali (Sat Jul 30 2016 - 00:38:04 PDT)
- [AMBER] hydrogen bond occupancy plot cpptraj Saman Yousuf ali (Sat Jul 30 2016 - 15:15:59 PDT)
- [AMBER] Hii ankita mehta (Sun Jul 31 2016 - 06:22:34 PDT)
- Last message date: Sun Jul 31 2016 - 07:00:03 PDT
- Archived on: Wed Dec 25 2024 - 05:55:24 PST
