Amber Archive Jul 2014 by thread
- [AMBER] AmberTools parallel test experienced errors sunita.tifrh.res.in (Mon Jun 30 2014 - 21:01:27 PDT)
- [AMBER] RDF zahra khatti (Tue Jul 01 2014 - 03:04:24 PDT)
- Re: [AMBER] Setting up z-constraint Pierpaolo Cacciotto (Tue Jul 01 2014 - 03:22:17 PDT)
- [AMBER] support of "center of mass restraint" Takeshi Baba (Tue Jul 01 2014 - 05:53:02 PDT)
- [AMBER] sander error "Could not find cntrl namelist" Asmita Gupta (Tue Jul 01 2014 - 08:31:36 PDT)
- [AMBER] Cuda tests failure on GeForce GTX 780 Serzhan Sakipov (Tue Jul 01 2014 - 09:17:10 PDT)
- Re: [AMBER] cpptraj: arithmetic on data sets? Daniel Roe (Tue Jul 01 2014 - 09:24:47 PDT)
- [AMBER] about setting nscm kirtana S (Tue Jul 01 2014 - 09:27:58 PDT)
- Re: [AMBER] periodic box drifted during NVE run Quynh Vo (Tue Jul 01 2014 - 13:11:10 PDT)
- [AMBER] ZAFF-CCCH Histidine charge problem Christy Lee (Tue Jul 01 2014 - 14:00:09 PDT)
- [AMBER] Visualizing average solvent-oxygen density/occupancy from an MD trajectory Abhishek Mukhopadhyay (Tue Jul 01 2014 - 17:34:10 PDT)
- [AMBER] Understand the AMBER coordinate files Wujie Wang (Tue Jul 01 2014 - 18:52:13 PDT)
- [AMBER] grid analysis Mary Varughese (Tue Jul 01 2014 - 19:04:44 PDT)
- [AMBER] Fwd: error: unable to generate parameter file Harmeet Kaur (Wed Jul 02 2014 - 00:07:45 PDT)
- [AMBER] Extracting total energy and other enegy componenets of ligand Soumendranath Bhakat (Wed Jul 02 2014 - 02:51:27 PDT)
- [AMBER] How to Extract Energy Contribution of Ligand Only Soumendranath Bhakat (Wed Jul 02 2014 - 02:57:38 PDT)
- [AMBER] MM-PBSA Zeinab Tavasoli (Wed Jul 02 2014 - 03:08:44 PDT)
- [AMBER] No parameters for PGR in lipid14 Niels Geudens (Wed Jul 02 2014 - 03:41:19 PDT)
- [AMBER] NMR distance restrains Valentina Romano (Wed Jul 02 2014 - 06:28:55 PDT)
- [AMBER] Attempting to compile fresh version of Amber 11, bugfixes > 17 won't apply cleanly Bob Healey (Wed Jul 02 2014 - 08:22:11 PDT)
- [AMBER] high energy output kirtana S (Wed Jul 02 2014 - 11:52:58 PDT)
- [AMBER] Issues Compiling AmberTools13 Malachi Phillips (Wed Jul 02 2014 - 12:20:15 PDT)
- [AMBER] Debug amber energy parameters Ramuntcho Moretti (Thu Jul 03 2014 - 02:17:08 PDT)
- [AMBER] Wrong number of restrained atoms Valentina Romano (Thu Jul 03 2014 - 02:45:01 PDT)
- [AMBER] Failed to generate parameter file Vishal Nemaysh (Thu Jul 03 2014 - 02:45:46 PDT)
- [AMBER] ncsu_smd support in pmemd amber12 Asmita Gupta (Thu Jul 03 2014 - 06:31:56 PDT)
- [AMBER] neighbours around an atom Krisztina Feher (Thu Jul 03 2014 - 07:16:14 PDT)
- [AMBER] Time information lost. Domenico Marson (Thu Jul 03 2014 - 08:52:34 PDT)
- [AMBER] amoeba into ambertools Jorgen Simonsen (Thu Jul 03 2014 - 11:35:18 PDT)
- [AMBER] PMEMD running on Intel Xeon Phi Hai Long (Thu Jul 03 2014 - 12:22:29 PDT)
- [AMBER] MMPBSA Energy between system and its image Ahmed Ayoub (Thu Jul 03 2014 - 12:41:17 PDT)
- [AMBER] How to strip water from .mdcrd file? Wujie Wang (Thu Jul 03 2014 - 18:36:13 PDT)
- [AMBER] MMPBSA Sourav Purohit (Fri Jul 04 2014 - 02:10:46 PDT)
- [AMBER] Fwd: neighbours around an atom Krisztina Fehér (Fri Jul 04 2014 - 02:48:08 PDT)
- [AMBER] Fwd: neighbours around an atom Krisztina Fehér (Fri Jul 04 2014 - 04:49:44 PDT)
- [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Mele N. (Fri Jul 04 2014 - 06:19:41 PDT)
- [AMBER] imaging problem Jonathan Gough (Sun Jul 06 2014 - 14:41:48 PDT)
- [AMBER] Build Xleap Baptiste Legrand (Mon Jul 07 2014 - 01:24:32 PDT)
- [AMBER] errors in compiling AmberTools14 Alessandro Contini (Mon Jul 07 2014 - 02:21:40 PDT)
- [AMBER] Imaging issue Michael Criddle (Mon Jul 07 2014 - 02:24:49 PDT)
- [AMBER] questions on output files of hbond analysis zhangmk (Mon Jul 07 2014 - 03:01:23 PDT)
- [AMBER] inositol hexakisphosphate Hector A. Baldoni (Mon Jul 07 2014 - 14:12:39 PDT)
- [AMBER] cpptraj hbond Neha Gandhi (Mon Jul 07 2014 - 23:55:34 PDT)
- [AMBER] ATP and Mg2+ parameters Valentina Romano (Tue Jul 08 2014 - 03:41:26 PDT)
- [AMBER] RESP fitting with group restraint Niels Geudens (Tue Jul 08 2014 - 06:08:17 PDT)
- [AMBER] imin=5, maxcyc>1 stalls Allen, Scott Edward (Tue Jul 08 2014 - 06:59:59 PDT)
- [AMBER] Problem with MMPBSA.py Rajeswari A. (Tue Jul 08 2014 - 07:07:03 PDT)
- [AMBER] R: Re: ATP and Mg2+ parameters Alessandro Contini (Tue Jul 08 2014 - 08:21:14 PDT)
- [AMBER] Issues running RED ESP software Malachi Phillips (Tue Jul 08 2014 - 10:25:40 PDT)
- [AMBER] pmemdTI test failure Blake Mertz (Tue Jul 08 2014 - 10:32:49 PDT)
- [AMBER] Parameter file for polyethyleglycol PEG Iqbal, Muhammad Sajid (Tue Jul 08 2014 - 11:03:04 PDT)
- [AMBER] atomiccorr: glibc detected *** cpptraj: malloc(): memory corruption: Krisztina Feher (Tue Jul 08 2014 - 14:26:53 PDT)
- [AMBER] Orbital Hessian Not Positive Definite Error Malachi Phillips (Tue Jul 08 2014 - 14:49:17 PDT)
- [AMBER] how to quantify and visualize the flow of water into a protein Thomas Evangelidis (Tue Jul 08 2014 - 16:20:14 PDT)
- [AMBER] entropy Calculation Him Shweta (Tue Jul 08 2014 - 22:12:06 PDT)
- Re: [AMBER] Loop refirement James Starlight (Wed Jul 09 2014 - 03:01:15 PDT)
- [AMBER] Question Brittany Boykin (Wed Jul 09 2014 - 09:51:19 PDT)
- [AMBER] Finding a good REMD temperature ladder Eugene Yedvabny (Wed Jul 09 2014 - 11:01:39 PDT)
- [AMBER] autoimage doesn't work 肖立 (Wed Jul 09 2014 - 12:03:25 PDT)
- [AMBER] tinker to amber format Jorgen Simonsen (Wed Jul 09 2014 - 21:44:14 PDT)
- [AMBER] Switch function in Amber Ramuntcho Moretti (Thu Jul 10 2014 - 01:04:43 PDT)
- [AMBER] Ag+ ion parameters Rebeca García Fandiño (Thu Jul 10 2014 - 01:35:03 PDT)
- [AMBER] DCCP analysis Soumendranath Bhakat (Thu Jul 10 2014 - 02:04:18 PDT)
- [AMBER] Fwd: Re: [q4md-fft] Issues Running, missing Ante_RED 2 FyD (Thu Jul 10 2014 - 02:43:55 PDT)
- [AMBER] Fwd: Re: [q4md-fft] URGENT:Orbital Hessian Not Positive Definite FyD (Thu Jul 10 2014 - 02:57:12 PDT)
- [AMBER] Free Binding Energy Calculation Him Shweta (Thu Jul 10 2014 - 05:58:01 PDT)
- [AMBER] Sander of Amber11, Amber12 and AmberTools14 Massimiliano Porrini (Thu Jul 10 2014 - 10:59:30 PDT)
- [AMBER] cpptraj rotdif parameters Alegrete, Matthew (Thu Jul 10 2014 - 12:34:29 PDT)
- [AMBER] How is temperature in Amber MD simulations calculated? Arthur Roberts (Thu Jul 10 2014 - 13:04:20 PDT)
- [AMBER] Question Brittany Boykin (Thu Jul 10 2014 - 14:01:53 PDT)
- [AMBER] evaluating hydrogen bond using ptraj Vijay Manickam Achari (Thu Jul 10 2014 - 23:31:05 PDT)
- [AMBER] cholesterol with lipid14 Thomas Evangelidis (Fri Jul 11 2014 - 00:44:33 PDT)
- Re: [AMBER] parmchk2 segfaults Sushil Mishra (Fri Jul 11 2014 - 01:41:28 PDT)
- [AMBER] Thermodynamic Integration by using pmemd Sun (Fri Jul 11 2014 - 02:33:21 PDT)
- [AMBER] graph energy check after minimization amor san juan (Fri Jul 11 2014 - 11:59:47 PDT)
- [AMBER] diffusion path length newamber list (Fri Jul 11 2014 - 12:11:03 PDT)
- [AMBER] cuda.test errors Jonathan Gough (Fri Jul 11 2014 - 14:53:28 PDT)
- [AMBER] pressure tensor kirtana S (Sat Jul 12 2014 - 10:45:23 PDT)
- [AMBER] Query about QM/MM scanning using amber Kshatresh Dutta Dubey (Sun Jul 13 2014 - 04:24:50 PDT)
- [AMBER] hydrogen bond evaluation Vijay Manickam Achari (Mon Jul 14 2014 - 02:28:26 PDT)
- [AMBER] cpptraj help Saikat Dutta chowdhury (Mon Jul 14 2014 - 04:40:16 PDT)
- [AMBER] update amber12 zahra khatti (Mon Jul 14 2014 - 14:05:56 PDT)
- [AMBER] coordinate and topology files using tleap from RED server output files Iqbal, Muhammad Sajid (Mon Jul 14 2014 - 14:17:40 PDT)
- [AMBER] Downloading old versions of AMBERTools Marawan Hussien (Mon Jul 14 2014 - 14:55:19 PDT)
- [AMBER] gpu and cpu runs Mary Varughese (Tue Jul 15 2014 - 00:23:24 PDT)
- [AMBER] Error output file Faez Iqbal khan (Tue Jul 15 2014 - 01:17:49 PDT)
- [AMBER] Error while running tleap Suchetana Gupta (Tue Jul 15 2014 - 02:13:20 PDT)
- [AMBER] nativecontacts by amber14 cpptraj Rajeswari A. (Tue Jul 15 2014 - 04:36:00 PDT)
- [AMBER] Could not find cntrl namelist Fengxue Li (Tue Jul 15 2014 - 06:19:27 PDT)
- [AMBER] To get resp charges of a modified central residue (not an integer). Baptiste Legrand (Tue Jul 15 2014 - 08:24:52 PDT)
- [AMBER] installation of AMBER 12 in MAC 10.7 lion Vishal Nemaysh (Wed Jul 16 2014 - 00:14:42 PDT)
- [AMBER] RNA covalent bond angles Blatter Markus (Wed Jul 16 2014 - 02:33:35 PDT)
- Re: [AMBER] problem in "re-image" and "unwarp" Him Shweta (Wed Jul 16 2014 - 04:13:42 PDT)
- [AMBER] Tool in PTRAJ/CPPTRAJ to analyse residue movement anu chandra (Wed Jul 16 2014 - 05:00:25 PDT)
- [AMBER] Problem with atommap in cpptraj Rajeswari A. (Wed Jul 16 2014 - 07:04:15 PDT)
- [AMBER] ATP parameters: tleap error Valentina Romano (Wed Jul 16 2014 - 09:41:55 PDT)
- [AMBER] How do I apply cpptraj.timecorr to the output dataset of cpptraj.dihedral? Jose Borreguero (Wed Jul 16 2014 - 16:40:48 PDT)
- [AMBER] Implicit solvent and membrane protein James Starlight (Thu Jul 17 2014 - 00:21:29 PDT)
- [AMBER] Error installing Ambertools on Centos 6.3 and open suse 12.3 Charu Suri (Thu Jul 17 2014 - 05:45:58 PDT)
- [AMBER] imin=5 Lara rajam (Thu Jul 17 2014 - 08:12:13 PDT)
- [AMBER] iwrap Sourav Purohit (Thu Jul 17 2014 - 10:03:43 PDT)
- [AMBER] parameterizing a connected moiety Mohammad Salem (Thu Jul 17 2014 - 14:31:15 PDT)
- [AMBER] ScaledMD for proline dipeptide Niels Geudens (Thu Jul 17 2014 - 23:02:37 PDT)
- [AMBER] Fwd: problem in installation of ambertools14 Vidushi Sharma (Fri Jul 18 2014 - 04:13:12 PDT)
- [AMBER] Electrostatic energy calculated by MD in MM/GBSA menwer momo (Fri Jul 18 2014 - 13:06:08 PDT)
- [AMBER] memory allocation error for *bond Vishal Nemaysh (Sat Jul 19 2014 - 03:18:57 PDT)
- [AMBER] Hydrogen bond analysis menwer momo (Sat Jul 19 2014 - 03:56:41 PDT)
- [AMBER] mailing list problem Vidushi Sharma (Sat Jul 19 2014 - 04:04:34 PDT)
- [AMBER] X11 error Vidushi Sharma (Sat Jul 19 2014 - 07:00:53 PDT)
- [AMBER] memory allocation error for *bond Vishal Nemaysh (Sun Jul 20 2014 - 02:38:17 PDT)
- [AMBER] Lipid and protein - error reading group during heat Jonathan Gough (Sun Jul 20 2014 - 20:50:39 PDT)
- [AMBER] NVT and NPT ensemble Sangita Kachhap (Mon Jul 21 2014 - 01:17:41 PDT)
- [AMBER] Amber12 CUDA problems Lorenzo Gontrani (Mon Jul 21 2014 - 03:45:05 PDT)
- Re: [AMBER] bash scripting for MD tasks James Starlight (Mon Jul 21 2014 - 04:54:00 PDT)
- [AMBER] error in md simulation in pmemd.cuda.MPI Subrata Paul (Mon Jul 21 2014 - 07:07:05 PDT)
- [AMBER] Regarding LIE in cpptraj Kshatresh Dutta Dubey (Tue Jul 22 2014 - 00:23:50 PDT)
- [AMBER] AMP Parameters cye927.mail.ustc.edu.cn (Tue Jul 22 2014 - 01:40:26 PDT)
- [AMBER] sander.APBS: automatic grid adjustments in output? Brian Radak (Tue Jul 22 2014 - 09:55:47 PDT)
- [AMBER] Unable to compile cuda version of amber14 Manikanthan Bhavaraju (Tue Jul 22 2014 - 12:45:48 PDT)
- [AMBER] help Zeynep Topdemir (Tue Jul 22 2014 - 16:01:20 PDT)
- [AMBER] atom number same as line number for cpptraj newamber list (Tue Jul 22 2014 - 17:02:54 PDT)
- [AMBER] Hello SaeeD PourasaD (Tue Jul 22 2014 - 19:34:13 PDT)
- [AMBER] GIST - unusually high water-water energies Waldner, Birgit (Tue Jul 22 2014 - 23:13:33 PDT)
- [AMBER] On the values of boost potential for aMD based on amd.log James Starlight (Wed Jul 23 2014 - 02:08:40 PDT)
- [AMBER] Z-axis coordinates Him Shweta (Wed Jul 23 2014 - 02:34:25 PDT)
- [AMBER] Bug in tleap savemol2? David Minh (Wed Jul 23 2014 - 09:41:59 PDT)
- [AMBER] ptraj binary missing from AmberTools 13 install? Raik Grünberg (Wed Jul 23 2014 - 13:14:41 PDT)
- [AMBER] renumber all residues in prmtop Thomas Evangelidis (Wed Jul 23 2014 - 16:33:01 PDT)
- [AMBER] Hi SaeeD PourasaD (Thu Jul 24 2014 - 00:14:15 PDT)
- [AMBER] CYM charges in amino14ipq.lib wrong? Marc van der Kamp (Thu Jul 24 2014 - 05:27:11 PDT)
- Re: [AMBER] GPU error Attempting MC barostat change: Failed Raman Parkesh (Thu Jul 24 2014 - 07:10:07 PDT)
- [AMBER] Cpptraj clustering James Starlight (Thu Jul 24 2014 - 08:13:19 PDT)
- [AMBER] pbc problem Niloofar Nayebi (Thu Jul 24 2014 - 09:21:24 PDT)
- [AMBER] Not integer charge for glycoprotein Tommaso Casalini (Thu Jul 24 2014 - 09:28:52 PDT)
- [AMBER] cpptraj not processing all mdcrd files Kshatresh Dutta Dubey (Thu Jul 24 2014 - 14:50:24 PDT)
- [AMBER] problems with paramfit Marek Maly (Thu Jul 24 2014 - 14:56:00 PDT)
- [AMBER] Berendsen vs. Monte Carlo Parker de Waal (Thu Jul 24 2014 - 19:14:06 PDT)
- [AMBER] values of λ in Thermodynamic Integration Sun (Thu Jul 24 2014 - 19:25:16 PDT)
- [AMBER] element symbol error in tleap cq y (Fri Jul 25 2014 - 01:35:03 PDT)
- [AMBER] element symbol error in tleap Changqing Yan (Fri Jul 25 2014 - 01:52:40 PDT)
- [AMBER] Hi Him Shweta (Fri Jul 25 2014 - 02:19:46 PDT)
- [AMBER] Running PCA Nicole Ippolito (Fri Jul 25 2014 - 10:56:31 PDT)
- [AMBER] Fwd: AMBER Digest, Vol 926, Issue 1 Changqing Yan (Fri Jul 25 2014 - 19:22:45 PDT)
- [AMBER] On the ussage of the langevens thermostat with the gb models James Starlight (Sat Jul 26 2014 - 00:03:20 PDT)
- [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process Marek Maly (Sun Jul 27 2014 - 09:35:39 PDT)
- [AMBER] Problem on making inpcrd file 肖立 (Sun Jul 27 2014 - 13:06:34 PDT)
- [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Mon Jul 28 2014 - 06:04:14 PDT)
- [AMBER] PMF by WHAM Marta Wisniewska (Mon Jul 28 2014 - 06:22:46 PDT)
- [AMBER] Solvating the system with polyethylene glycol PEG Iqbal, Muhammad Sajid (Mon Jul 28 2014 - 10:07:35 PDT)
- [AMBER] NONBONDED_PARM_INDEX Him Shweta (Tue Jul 29 2014 - 00:37:39 PDT)
- [AMBER] !Help!: Normal Mode Analysis xy21hb (Tue Jul 29 2014 - 07:56:24 PDT)
- [AMBER] HELP Needed: AMBER12 cuda compilation ERROR Saikat Dutta chowdhury (Wed Jul 30 2014 - 04:18:19 PDT)
- [AMBER] Parameters for SulfoTyrosine Stephane Azoulay (Wed Jul 30 2014 - 07:52:19 PDT)
- [AMBER] AMBER renatoac.ufpa.br (Wed Jul 30 2014 - 12:15:24 PDT)
- [AMBER] erro na criação do complexo renatoac.ufpa.br (Wed Jul 30 2014 - 12:43:10 PDT)
- [AMBER] erro na criação do complexo renatoac.ufpa.br (Wed Jul 30 2014 - 12:50:07 PDT)
- [AMBER] Could not find vdW (or other) parameters for type Pedro Swagger (Wed Jul 30 2014 - 16:38:35 PDT)
- [AMBER] this a very green neophyte's question. J.W. Halley (Wed Jul 30 2014 - 17:56:49 PDT)
- [AMBER] How to calculate the parameters of metal ions? Jinfeng Huang (Thu Jul 31 2014 - 06:58:50 PDT)
- [AMBER] Zinc parameterization Nadia Li (Thu Jul 31 2014 - 09:55:01 PDT)
- [AMBER] Equilibirum/System convergence Parker de Waal (Thu Jul 31 2014 - 10:15:37 PDT)
- [AMBER] question about lipid tutorial Jonathan Gough (Thu Jul 31 2014 - 13:15:57 PDT)
- [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop Vivek Shankar Bharadwaj (Thu Jul 31 2014 - 18:23:43 PDT)
- Last message date: Thu Jul 31 2014 - 21:00:03 PDT
- Archived on: Fri Nov 15 2024 - 05:55:02 PST
