Amber Archive Sep 2014 by thread
- [AMBER] mmpbsa amber error while running decomp Sucharita Dey (Sun Aug 31 2014 - 22:52:26 PDT)
- [AMBER] Reading Error Soumendranath Bhakat (Mon Sep 01 2014 - 02:39:14 PDT)
- [AMBER] Bridging Sodium ions using hbond DEBOSTUTI GHOSHDASTIDAR (Mon Sep 01 2014 - 03:36:28 PDT)
- [AMBER] time scales for running MD Asmita Gupta (Mon Sep 01 2014 - 03:42:21 PDT)
- Re: [AMBER] antechamber error message 전선희 (Mon Sep 01 2014 - 23:17:25 PDT)
- [AMBER] Reaction profile calculation in Amber by QM/MM method MOHD HOMAIDUR RAHMAN (Tue Sep 02 2014 - 00:24:31 PDT)
- [AMBER] atom types for QM region in QM/MM Spelnikov Dmitriy (Tue Sep 02 2014 - 00:29:00 PDT)
- [AMBER] meeting a problem when using ptraj to extract the replica exchanging self-guided MD trajectory wliu (Tue Sep 02 2014 - 06:05:15 PDT)
- [AMBER] PHI Intel Compilation Jacopo Sgrignani (Tue Sep 02 2014 - 06:40:39 PDT)
- [AMBER] protein-peptide alanine scaning Renato Freitas (Tue Sep 02 2014 - 10:12:21 PDT)
- [AMBER] cuda versions advice Scott Brozell (Tue Sep 02 2014 - 12:50:13 PDT)
- Re: [AMBER] system size more than 1000 residues Pengzhi Zhang (Tue Sep 02 2014 - 14:32:59 PDT)
- [AMBER] ncsu_abmd qm/mm Fekete Attila (Wed Sep 03 2014 - 01:35:58 PDT)
- [AMBER] many initial systems for a two molecules system Fabian Glaser (Wed Sep 03 2014 - 04:26:10 PDT)
- [AMBER] amber force field 王珍 (Wed Sep 03 2014 - 06:50:11 PDT)
- Re: [AMBER] Distance command Daniel Roe (Wed Sep 03 2014 - 08:39:09 PDT)
- [AMBER] Ambertools14 sander_pbsa_decres test failure Shan-ho Tsai (Wed Sep 03 2014 - 12:31:53 PDT)
- [AMBER] parallel cuda test errors Gard Nelson (Wed Sep 03 2014 - 12:49:38 PDT)
- [AMBER] No hybrid REMD for cuda? Hugo Azurmendi (Wed Sep 03 2014 - 12:53:25 PDT)
- Re: [AMBER] On combining different force-fields and charge-derivation methods Mohammad Salem (Wed Sep 03 2014 - 15:26:27 PDT)
- [AMBER] iwrap on very long simulation Setyanto Md (Wed Sep 03 2014 - 18:12:31 PDT)
- [AMBER] building AmberTools14 to use with Amber12 i iordanov (Wed Sep 03 2014 - 19:34:53 PDT)
- [AMBER] decomposition output file Nadia Li (Wed Sep 03 2014 - 21:47:06 PDT)
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Wed Sep 03 2014 - 23:17:05 PDT)
- [AMBER] Which atomtype in Amber99sb FF correspond to the Nitro atomtype of GAFF bipin singh (Thu Sep 04 2014 - 00:28:45 PDT)
- [AMBER] dihedral in parmtop: negative third index vs ICP(H) Hannes Loeffler (Thu Sep 04 2014 - 01:57:53 PDT)
- [AMBER] DMPG lipid bilayer simulations? Smith, Jarrod A (Thu Sep 04 2014 - 13:28:34 PDT)
- [AMBER] extract energies from trajectory Milo Westler (Thu Sep 04 2014 - 15:55:31 PDT)
- [AMBER] Can (cp)ptraj calculate the diffusion of the center of mass? Jose Borreguero (Thu Sep 04 2014 - 15:59:21 PDT)
- [AMBER] One third of Amber 14's test.cuda tests are failing for me Jan-Philip Gehrcke (Fri Sep 05 2014 - 03:18:27 PDT)
- [AMBER] diffusion in octahedron box newamber list (Fri Sep 05 2014 - 04:55:43 PDT)
- [AMBER] Equilibration of the membrane protein with the restrains James Starlight (Fri Sep 05 2014 - 05:30:45 PDT)
- [AMBER] Lennard-Jones Parameters for Each Atom Uday Midya (Fri Sep 05 2014 - 06:46:54 PDT)
- [AMBER] Calculation of Urea_Urea Interaction energy MOHD HOMAIDUR RAHMAN (Fri Sep 05 2014 - 08:06:51 PDT)
- [AMBER] MMGBSA giving to high VDW energies Ahmed Ayoub (Fri Sep 05 2014 - 12:12:00 PDT)
- [AMBER] Solvation of the membrane bilayer using tleap James Starlight (Sun Sep 07 2014 - 00:34:14 PDT)
- [AMBER] amber-Gaussian find the transition 王珍 (Sun Sep 07 2014 - 02:04:25 PDT)
- [AMBER] QM/MM optimization error 王珍 (Sun Sep 07 2014 - 19:46:32 PDT)
- [AMBER] Enquiring about RMSD of small and large proteins Yip Yew Mun (Sun Sep 07 2014 - 19:52:54 PDT)
- [AMBER] Trajectory analysis using ptraj James Starlight (Mon Sep 08 2014 - 01:45:44 PDT)
- [AMBER] mismatch pdb files when created using ambpdb and savepdb sunita.tifrh.res.in (Mon Sep 08 2014 - 06:13:05 PDT)
- [AMBER] HID or HIE which one to consider? sunita.tifrh.res.in (Mon Sep 08 2014 - 06:34:07 PDT)
- [AMBER] amber course Fabian Glaser (Mon Sep 08 2014 - 06:35:04 PDT)
- [AMBER] PBSA in AT14: invalid test case, estatic potential values are written in wrong units to DX files. Jan-Philip Gehrcke (Mon Sep 08 2014 - 06:57:00 PDT)
- [AMBER] Rewrapping restart file Geoffrey Gray (Mon Sep 08 2014 - 09:08:21 PDT)
- [AMBER] ligand shift Nadia Li (Mon Sep 08 2014 - 12:03:00 PDT)
- Re: [AMBER] bash scripting for MD tasks James Starlight (Mon Sep 08 2014 - 12:24:42 PDT)
- [AMBER] Slow dissociation of ligand from binding pocket of protein George Tzotzos (Mon Sep 08 2014 - 13:11:36 PDT)
- [AMBER] [ANN] MDTraj 1.0: Trajectory Analysis in Python Robert McGibbon (Mon Sep 08 2014 - 13:17:02 PDT)
- [AMBER] Postdoc Position Available Dirar Homouz (Tue Sep 09 2014 - 03:20:51 PDT)
- [AMBER] Amber/ Orca problem Aixiao Li (Tue Sep 09 2014 - 04:11:12 PDT)
- [AMBER] mm_pbsa vertex atom mismatch Fengxue Li (Tue Sep 09 2014 - 05:36:15 PDT)
- [AMBER] distance restraint Mary Varughese (Tue Sep 09 2014 - 13:08:31 PDT)
- [AMBER] frcmod format file Maria Osorios (Tue Sep 09 2014 - 18:57:53 PDT)
- [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol Scott Brozell (Tue Sep 09 2014 - 23:23:18 PDT)
- [AMBER] Query for Hbond lifetime analysis with AmberTools14 Indrajit Deb (Wed Sep 10 2014 - 03:00:33 PDT)
- [AMBER] Not getting solute-solvent hbond by cpptraj (AmberTools14) Indrajit Deb (Wed Sep 10 2014 - 04:27:44 PDT)
- [AMBER] the out file of qm/mm in amber 王珍 (Wed Sep 10 2014 - 05:09:22 PDT)
- [AMBER] mm_pbsa vertex atom mismatch Fengxue Li (Wed Sep 10 2014 - 07:03:21 PDT)
- [AMBER] FW: about trajectory unwrap Kong, Ren (Wed Sep 10 2014 - 08:06:34 PDT)
- [AMBER] Problem running multiple GPU's jon.maguire.louisville.edu (Wed Sep 10 2014 - 08:53:26 PDT)
- [AMBER] Problem running pmemd.cuda.mpi REMD with different number of replicas Thiago Lipinski Paes (Wed Sep 10 2014 - 09:21:40 PDT)
- [AMBER] Total vs per-residue MMGBSA energies Ahmed Ayoub (Wed Sep 10 2014 - 11:54:20 PDT)
- [AMBER] hbond lifetime George Tzotzos (Wed Sep 10 2014 - 13:13:13 PDT)
- [AMBER] Equilibration phase and RMSD Ibrahim Said (Wed Sep 10 2014 - 13:22:17 PDT)
- [AMBER] mmpbsa: PB Bomb in pb_aaradi() Wei Chen (Wed Sep 10 2014 - 14:18:53 PDT)
- [AMBER] Problems to minimize with Sander Maria Osorios (Wed Sep 10 2014 - 14:54:18 PDT)
- [AMBER] cuda version not working Fabian Glaser (Thu Sep 11 2014 - 02:39:07 PDT)
- [AMBER] setting up topology file using GLYCAM Vijyan Achari (Thu Sep 11 2014 - 06:59:53 PDT)
- [AMBER] Solvation and processing of lipid bilayers using tleap James Starlight (Thu Sep 11 2014 - 14:02:08 PDT)
- [AMBER] Compiling Amber14 using --with-netcdf Lawrenz, Morgan (Thu Sep 11 2014 - 16:20:48 PDT)
- [AMBER] Force field ff99SB*-ILDN request sunita.tifrh.res.in (Fri Sep 12 2014 - 06:18:22 PDT)
- [AMBER] ACS COMP Division travel awards for Spring 2015 National Meeting in Denver Carlos Simmerling (Fri Sep 12 2014 - 07:41:21 PDT)
- [AMBER] Building Amber14 with -nofftw3 Lawrenz, Morgan (Fri Sep 12 2014 - 09:45:26 PDT)
- [AMBER] Amber12 serial test failure Samaneh Ghassabi Kondalaji (Fri Sep 12 2014 - 11:01:07 PDT)
- [AMBER] generate amoeba parameters for amber Jorgen Simonsen (Sat Sep 13 2014 - 21:34:19 PDT)
- [AMBER] tleap neutralization bug? Gulsevin,Alican (Sun Sep 14 2014 - 11:28:53 PDT)
- [AMBER] about dihedral type Arun Srikanth (Sun Sep 14 2014 - 11:47:20 PDT)
- [AMBER] ESP fitting centers exist, but the fitting values are missing 张冬冬 (Mon Sep 15 2014 - 05:29:08 PDT)
- [AMBER] cpptraj - atomicfluct George Tzotzos (Mon Sep 15 2014 - 11:57:57 PDT)
- [AMBER] CHAMBER: problem with water and swissparam generated ligand Eric Lang (Mon Sep 15 2014 - 13:59:53 PDT)
- [AMBER] Replica Exchange Jacopo Sgrignani (Tue Sep 16 2014 - 01:39:34 PDT)
- [AMBER] Antechamber ligand parametrization James Starlight (Tue Sep 16 2014 - 04:14:59 PDT)
- [AMBER] MMPBSA.py: PrmtopError: Residue mismatch while mapping. Incompatible topology files or bad mask definitions Thomas Evangelidis (Tue Sep 16 2014 - 07:05:34 PDT)
- [AMBER] how to simulate a polyester? 张冬冬 (Tue Sep 16 2014 - 07:52:19 PDT)
- [AMBER] Tetrazole: parameters Esra Bozkurt (Tue Sep 16 2014 - 08:23:11 PDT)
- [AMBER] For Amber14 TI, how to perform only the discharge/recharge steps? Lawrenz, Morgan (Tue Sep 16 2014 - 18:01:04 PDT)
- [AMBER] Simulating Silver Salt Soumendranath Bhakat (Wed Sep 17 2014 - 03:56:31 PDT)
- [AMBER] h-bond erik.laurini.di3.units.it (Wed Sep 17 2014 - 04:38:33 PDT)
- [AMBER] Clustering problem Alessandro Mariani (Wed Sep 17 2014 - 04:43:00 PDT)
- [AMBER] Aligning a trajectory Jonathan Gough (Wed Sep 17 2014 - 05:20:27 PDT)
- [AMBER] average structure with RMSF or RMSD? newamber list (Wed Sep 17 2014 - 07:17:29 PDT)
- [AMBER] Cpptraj hbond function - solvent bridge Miroslav Krepl (Wed Sep 17 2014 - 08:36:49 PDT)
- [AMBER] MMPBSA: Default inp warnings George Tzotzos (Wed Sep 17 2014 - 10:39:25 PDT)
- Re: [AMBER] Question for residues.py to parameterize a nonstandard residue for constant pH MD M Olivia Kim (Wed Sep 17 2014 - 11:11:32 PDT)
- [AMBER] Problems to minimize with Sander Investigador Química (Wed Sep 17 2014 - 11:19:58 PDT)
- [AMBER] MMPBSA Sourav Purohit (Wed Sep 17 2014 - 15:46:32 PDT)
- [AMBER] Two questions about Net charge and write frcmod in parmed.py Arun Srikanth (Wed Sep 17 2014 - 18:36:39 PDT)
- [AMBER] Preparing a system of 7.4 PH ammarah.ghaffar.comsats.edu.pk (Wed Sep 17 2014 - 23:12:02 PDT)
- [AMBER] MMPBSA Sourav Purohit (Thu Sep 18 2014 - 01:00:51 PDT)
- [AMBER] CUDA version still not working Fabian Glaser (Thu Sep 18 2014 - 01:39:32 PDT)
- [AMBER] GTX 780SC error "cudaMempcpy GpuBuffer :: Download failed unspecified launch failure" Dieter Buyst (Thu Sep 18 2014 - 01:51:19 PDT)
- [AMBER] Error: cannot run Vishal Nemaysh (Thu Sep 18 2014 - 02:50:12 PDT)
- [AMBER] pmemd cuda error Kshatresh Dutta Dubey (Thu Sep 18 2014 - 04:47:41 PDT)
- [AMBER] Distance restraint John Smith (Thu Sep 18 2014 - 04:50:04 PDT)
- [AMBER] MMPBSA Asfa Ali (Thu Sep 18 2014 - 07:10:13 PDT)
- [AMBER] GTX780 versus K40? Carlos Sosa (Thu Sep 18 2014 - 10:33:11 PDT)
- [AMBER] ask for help m13654940810 (Thu Sep 18 2014 - 18:18:52 PDT)
- [AMBER] Any other way ? Arun Srikanth (Thu Sep 18 2014 - 19:13:16 PDT)
- Re: [AMBER] sander QM/MM with terachem using MPI Andreas Goetz (Thu Sep 18 2014 - 22:52:20 PDT)
- [AMBER] lipids14 pdb format Sergio Decherchi (Fri Sep 19 2014 - 04:31:45 PDT)
- [AMBER] CUDA 5.0 versus 5.5/6.0 Carlos Sosa (Fri Sep 19 2014 - 05:31:40 PDT)
- [AMBER] cpptraj Error: Atom was assigned a lower molecule # than previous atom Oliver Grant (Fri Sep 19 2014 - 06:12:20 PDT)
- [AMBER] PMEMD Distance Restraints Parker de Waal (Sat Sep 20 2014 - 13:55:44 PDT)
- [AMBER] Suitability of MMPBSA to intercalator binding. 3-trajectory no improvement over 1-trajectory? Keiran Rowell (Sun Sep 21 2014 - 02:51:16 PDT)
- [AMBER] Hbond Difference For Ambertools 12 and 14, or bug leexa.intern.bii.a-star.edu.sg (Sun Sep 21 2014 - 23:37:41 PDT)
- [AMBER] RMSD on two slightly different structures Guillaume Roellinger (Mon Sep 22 2014 - 00:18:47 PDT)
- [AMBER] restart file Jacopo Sgrignani (Mon Sep 22 2014 - 02:26:31 PDT)
- [AMBER] Sudden change of energies in min.out files maryam azimzadehirani (Mon Sep 22 2014 - 03:15:40 PDT)
- [AMBER] questions about Amber to run MD of Amoeba m13654940810 (Mon Sep 22 2014 - 05:12:40 PDT)
- [AMBER] How can I run Production MD for lipid in Amber12 using Lipid11-ff? Bikash Ranjan Sahoo (Tue Sep 23 2014 - 01:06:31 PDT)
- [AMBER] metalloproteins modeling Spelnikov Dmitriy (Tue Sep 23 2014 - 02:22:58 PDT)
- [AMBER] trajout frames that statisfy hbond criteria George Green (Tue Sep 23 2014 - 04:57:01 PDT)
- [AMBER] file contains 2 atoms not in residue templates Vishal Nemaysh (Tue Sep 23 2014 - 06:22:57 PDT)
- [AMBER] restrainr problem with PMEMD: using nmropt=1 and NTR=1 simultaneously George Green (Tue Sep 23 2014 - 06:39:58 PDT)
- [AMBER] why the same structure and same topology have different energies using CHARMM and AMBER ? wliu (Tue Sep 23 2014 - 07:52:11 PDT)
- [AMBER] negative values for the dihedral height barrier in GLYCAM ABEL Stephane 175950 (Tue Sep 23 2014 - 08:09:30 PDT)
- [AMBER] Charmmlipid2amber.py failure Julio Dominguez (Tue Sep 23 2014 - 13:20:05 PDT)
- [AMBER] Minimizing Size of Membrane Simulation Box Parker de Waal (Tue Sep 23 2014 - 18:05:57 PDT)
- [AMBER] Zn CCCH Fonti Giulia (Wed Sep 24 2014 - 00:49:55 PDT)
- [AMBER] Patches Installation Failure 张后今 (Wed Sep 24 2014 - 01:42:12 PDT)
- [AMBER] Using nvt production run after npt equilibration James Starlight (Wed Sep 24 2014 - 03:28:01 PDT)
- [AMBER] problem on minimization ZHAO Ruisheng (Wed Sep 24 2014 - 05:18:48 PDT)
- [AMBER] Parameter bond and angle file could not find Vishal Nemaysh (Wed Sep 24 2014 - 06:39:27 PDT)
- [AMBER] Xparmed.py Arun Srikanth (Wed Sep 24 2014 - 06:43:42 PDT)
- [AMBER] Removing periodicity from the restart file James Starlight (Wed Sep 24 2014 - 07:38:07 PDT)
- [AMBER] failure to run MMPBSA job... Shashidhar Rao (Wed Sep 24 2014 - 08:13:17 PDT)
- [AMBER] neutralizing systems for AMBER TI Lawrenz, Morgan (Wed Sep 24 2014 - 16:02:09 PDT)
- [AMBER] entropy Asfa Ali (Thu Sep 25 2014 - 00:31:48 PDT)
- [AMBER] Strip pdb from the hydrogens James Starlight (Thu Sep 25 2014 - 01:25:05 PDT)
- [AMBER] Combined cartesian and NMR restraints Parker de Waal (Thu Sep 25 2014 - 18:43:54 PDT)
- [AMBER] US AMBER Workshop - Save the date Ross Walker (Thu Sep 25 2014 - 21:27:26 PDT)
- [AMBER] cpptraj/parmbox amirhossein taghavi (Fri Sep 26 2014 - 00:13:59 PDT)
- [AMBER] Fw: Welcome to Beijing for the 15th International Congress of Quantum Chemistry 石文 (Fri Sep 26 2014 - 05:49:17 PDT)
- [AMBER] FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type Soumendranath Bhakat (Fri Sep 26 2014 - 08:21:04 PDT)
- [AMBER] about MD m13654940810 (Fri Sep 26 2014 - 19:47:18 PDT)
- [AMBER] Wrong atom type in the JCTC paper of lipid 14 ? ABEL Stephane 175950 (Sat Sep 27 2014 - 11:45:16 PDT)
- [AMBER] Wrong atom type in the JCTC paper of lipid 14 ? - update ABEL Stephane 175950 (Sat Sep 27 2014 - 12:09:50 PDT)
- [AMBER] MD simulation at 1M or 2M salt concentration 张后今 (Sat Sep 27 2014 - 18:59:03 PDT)
- [AMBER] Entropy calculation using nmode fails Neha Rana (Sun Sep 28 2014 - 07:35:27 PDT)
- Re: [AMBER] AMBER Digest, Vol 989, Issue 1 amirhossein taghavi (Mon Sep 29 2014 - 00:42:41 PDT)
- [AMBER] some problems when using pmemd.cuda xueqiaoup.gmail.com (Mon Sep 29 2014 - 01:05:22 PDT)
- [AMBER] Parameter file was not saved. Vishal Nemaysh (Mon Sep 29 2014 - 06:38:05 PDT)
- [AMBER] key word to pull out eigenvalues Nicole Ippolito (Mon Sep 29 2014 - 21:37:15 PDT)
- [AMBER] about amoeba m13654940810 (Tue Sep 30 2014 - 01:04:40 PDT)
- [AMBER] learn more about cpptraj amirhossein taghavi (Tue Sep 30 2014 - 02:53:48 PDT)
- [AMBER] writing trr trajectory newamber list (Tue Sep 30 2014 - 15:50:43 PDT)
- Last message date: Tue Sep 30 2014 - 16:00:02 PDT
- Archived on: Sun Nov 24 2024 - 05:55:13 PST
