Amber Archive Mar 2013 by thread
- [AMBER] Softcore selection Fabrício Bracht (Thu Feb 28 2013 - 20:19:24 PST)
- [AMBER] March 5, 2013 Webinar: AMBER and Kepler GPUs mark94025.comcast.net (Thu Feb 28 2013 - 21:00:11 PST)
- Re: [AMBER] PCI-E 2.0 vs 3.0 (AMD vs INTEL?) Aron Broom (Thu Feb 28 2013 - 21:24:10 PST)
- Re: [AMBER] Modified amino acid parameter generation FyD (Thu Feb 28 2013 - 22:13:51 PST)
- Re: [AMBER] force field file FyD (Thu Feb 28 2013 - 22:32:25 PST)
- [AMBER] amber12 configure error Asmita Gupta (Fri Mar 01 2013 - 00:09:27 PST)
- [AMBER] Kepler and Amber11? Ismail, Mohd F. (Fri Mar 01 2013 - 00:16:16 PST)
- [AMBER] Build DNA structure based on squence Tong ZHU (Fri Mar 01 2013 - 01:48:25 PST)
- Re: [AMBER] Amber MD using NAMD Massimiliano Porrini (Fri Mar 01 2013 - 01:58:01 PST)
- [AMBER] Problem in Arsenite parameterisation Kshatresh Dutta Dubey (Fri Mar 01 2013 - 05:28:00 PST)
- [AMBER] restraint domains zhenquan hu (Fri Mar 01 2013 - 08:42:15 PST)
- [AMBER] Implicit membrane models Gustavo Seabra (Fri Mar 01 2013 - 10:32:02 PST)
- Re: [AMBER] Estimating time in AMD Thomas Evangelidis (Sat Mar 02 2013 - 05:48:07 PST)
- [AMBER] ptraj action command Sun (Sun Mar 03 2013 - 18:57:49 PST)
- [AMBER] problem in calculating electrostatic potential using PBSA N Nandi (Sun Mar 03 2013 - 21:52:11 PST)
- [AMBER] Problem parsing PB output using MMPBSA.py in AMBER11 and AmberTools 1.5 dbaogen (Mon Mar 04 2013 - 04:27:08 PST)
- [AMBER] temperature fluctuation amber ntp ensemble Neha Gandhi (Mon Mar 04 2013 - 06:50:53 PST)
- [AMBER] Segmentation fault with EVB calculations on multiple cores for a system with more than 60 atom types Elise Duboué-Dijon (Mon Mar 04 2013 - 15:19:05 PST)
- [AMBER] bug report: tinker_to_amber failed for systems containing counter ions Ye MEI (Mon Mar 04 2013 - 20:54:51 PST)
- [AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA kurisaki (Tue Mar 05 2013 - 01:38:00 PST)
- Re: [AMBER] Wrong Annotation of PREPIN generated by RESIDUEGEN kurisaki (Tue Mar 05 2013 - 01:42:02 PST)
- [AMBER] Query On Steered Molecular Dynamics siddharth kesharwani (Tue Mar 05 2013 - 05:01:34 PST)
- [AMBER] Charge relocation Amber 12 CHAMI F. (Tue Mar 05 2013 - 05:54:03 PST)
- [AMBER] how to restart a molecular dynamics simulation Emilio Angelina (Tue Mar 05 2013 - 11:46:52 PST)
- [AMBER] bug report: tinker_to_amber failed for systems containing counter ions Amber Amoeba (Tue Mar 05 2013 - 12:33:21 PST)
- [AMBER] test Amber Amoeba (Tue Mar 05 2013 - 14:27:01 PST)
- [AMBER] RMSD Fluctuation Theodosia Teo (Tue Mar 05 2013 - 19:28:40 PST)
- Re: [AMBER] bug report: tinker_to_amber failed for systems containingcounter ions Ye MEI (Wed Mar 06 2013 - 00:19:25 PST)
- [AMBER] Cross correlation calculation Indrajit Deb (Wed Mar 06 2013 - 01:33:12 PST)
- [AMBER] TIP5P water simulation 강현아 (Wed Mar 06 2013 - 03:31:48 PST)
- [AMBER] Amber 2013 workshop psu4.uic.edu (Wed Mar 06 2013 - 09:31:50 PST)
- [AMBER] xleap_the hydrogen atom in C-terminus of peptides Nan Li (Wed Mar 06 2013 - 11:02:14 PST)
- [AMBER] MMPBSA jobs on a cluster Calcerror: Vivek Shankar Bharadwaj (Wed Mar 06 2013 - 12:05:01 PST)
- [AMBER] Error in MMPBSA Saugata Hazra (Wed Mar 06 2013 - 12:30:00 PST)
- [AMBER] antechamber dCTP YZ Qin (Wed Mar 06 2013 - 17:56:44 PST)
- [AMBER] VLIMIT problem with Folic acid (gaff parm) HIMANSHU JOSHI (Wed Mar 06 2013 - 21:19:07 PST)
- Re: [AMBER] bug report: tinker_to_amber failed forsystemscontainingcounter ions Ye MEI (Thu Mar 07 2013 - 02:31:24 PST)
- [AMBER] Is there a way to keep ions fixed in a amber MD? Changqing Yan (Thu Mar 07 2013 - 05:39:51 PST)
- [AMBER] Number Excluded Atoms List Generation Browning, Nicholas (Thu Mar 07 2013 - 08:53:40 PST)
- [AMBER] tleap output of mol2 format with incorrect bond order Marko Wehle (Thu Mar 07 2013 - 09:08:23 PST)
- Re: [AMBER] igb=8 available for MMPBSA.py ? Hai Nguyen (Thu Mar 07 2013 - 11:00:15 PST)
- [AMBER] Fwd: failed to run sander .... Shashidhar Rao (Thu Mar 07 2013 - 11:13:58 PST)
- [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Tu Zhiping (Thu Mar 07 2013 - 19:12:38 PST)
- [AMBER] Can IMPOSE apply to improper angle? kurisaki (Thu Mar 07 2013 - 21:05:04 PST)
- [AMBER] problem to generate pbsa.phi file using PBSA N Nandi (Thu Mar 07 2013 - 23:38:13 PST)
- Re: [AMBER] impose for improper torsion: from I. Kurisaki FyD (Fri Mar 08 2013 - 03:36:35 PST)
- [AMBER] Regarding centering a tetrameric molecule dilrajl.bii.a-star.edu.sg (Fri Mar 08 2013 - 04:51:00 PST)
- [AMBER] disulfide bonds Urszula Uciechowska (Fri Mar 08 2013 - 06:03:42 PST)
- Re: [AMBER] bug report: tinker_to_amber failedforsystemscontainingcounter ions Ye MEI (Fri Mar 08 2013 - 07:35:35 PST)
- [AMBER] March 15 deadline for ACS COMP division awards for Fall 2013 Indianapolis national meeting Carlos Simmerling (Sat Mar 02 2013 - 05:04:05 PST)
- [AMBER] N-Carboxymethionine charges and parameters for AMBER ABEL Stephane 175950 (Sat Mar 09 2013 - 02:46:58 PST)
- Re: [AMBER] [AMBER: gauche effect in OS-CT-CT-F Steven M. Graham (Sat Mar 09 2013 - 13:42:14 PST)
- [AMBER] Imaging issues with ptraj Kira Armacost (Sat Mar 09 2013 - 17:55:06 PST)
- [AMBER] generate prepin from mol2 which has charges/atom types for Heme Vaibhav Dixit (Sun Mar 10 2013 - 03:23:17 PDT)
- [AMBER] Does MMPBSA.py actually make a file called _MMPBSA_nmode.in? Joel Dockray (Sun Mar 10 2013 - 05:33:20 PDT)
- [AMBER] ligand molecule problem tianchuan881 (Sun Mar 10 2013 - 20:08:09 PDT)
- [AMBER] GTX 460 ? John Gehman (Sun Mar 10 2013 - 23:54:31 PDT)
- [AMBER] RESP charges for iron-sulfur cluster safwat abdel-azeim (Mon Mar 11 2013 - 02:42:45 PDT)
- [AMBER] Cyclic peptide Itamar Kass (Med) (Mon Mar 11 2013 - 03:34:59 PDT)
- [AMBER] mapping problem with makeDIST_RST Bayse, Craig A. (Mon Mar 11 2013 - 11:14:05 PDT)
- [AMBER] Amber 11 and Amber 12 David Winogradoff (Mon Mar 11 2013 - 15:34:31 PDT)
- [AMBER] Thermodynamic Integration Shruti Koulgi (Tue Mar 12 2013 - 05:25:47 PDT)
- [AMBER] frcmod file problem tianchuan881 (Tue Mar 12 2013 - 06:09:22 PDT)
- [AMBER] frcmod problem tianchuan881 (Tue Mar 12 2013 - 06:50:03 PDT)
- [AMBER] trajin: command not found uday spike (Tue Mar 12 2013 - 07:31:45 PDT)
- [AMBER] Restart SMD simulation Attilio Vittorio Vargiu (Tue Mar 12 2013 - 08:35:59 PDT)
- [AMBER] Problem in parallel installation of Amber 12 Kshatresh Dutta Dubey (Tue Mar 12 2013 - 08:41:49 PDT)
- [AMBER] Amber12 MPI OK on one node but not across nodes Jan Fredin (Tue Mar 12 2013 - 09:38:46 PDT)
- [AMBER] charge problem tianchuan881 (Wed Mar 13 2013 - 04:13:18 PDT)
- [AMBER] Query on Steered Molecular Dynamics siddharth kesharwani (Wed Mar 13 2013 - 04:29:51 PDT)
- Re: [AMBER] bug report: tinker_to_amberfailedforsystemscontainingcounter ions Ye MEI (Wed Mar 13 2013 - 07:48:07 PDT)
- [AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3 javacfish (Wed Mar 13 2013 - 10:54:21 PDT)
- [AMBER] MMPBSA ATP-Mg Chiara Pallara (Wed Mar 13 2013 - 10:54:38 PDT)
- [AMBER] Bad atom type: fe in MMPBSA calculations Cuiyl (Wed Mar 13 2013 - 22:03:59 PDT)
- [AMBER] problem tianchuan881 (Thu Mar 14 2013 - 00:13:54 PDT)
- [AMBER] Question about AM1BCC Ismail, Mohd F. (Thu Mar 14 2013 - 00:15:59 PDT)
- [AMBER] angle between two plan . mirage (Thu Mar 14 2013 - 02:10:50 PDT)
- [AMBER] QM/MM restart problem R. Xiong (Thu Mar 14 2013 - 07:42:56 PDT)
- [AMBER] PMEMD in amber12 Mary Varughese (Thu Mar 14 2013 - 08:04:05 PDT)
- [AMBER] ptraj skipping frames depending on the computer OS? Miguel Ortiz Lombardía (Thu Mar 14 2013 - 08:31:59 PDT)
- Re: [AMBER] GTX Titan was finally released filip fratev (Thu Mar 14 2013 - 09:33:40 PDT)
- [AMBER] REMD simulation sudipta (Thu Mar 14 2013 - 10:06:51 PDT)
- [AMBER] Cofactor GDP Atom Types Ahmed Ayoub (Thu Mar 14 2013 - 12:22:40 PDT)
- [AMBER] organic 纪晓峰 (Fri Mar 15 2013 - 00:37:47 PDT)
- [AMBER] the protein was crashed 纪晓峰 (Fri Mar 15 2013 - 00:44:55 PDT)
- [AMBER] modified dna Mary Varughese (Fri Mar 15 2013 - 02:45:49 PDT)
- [AMBER] Regarding MSD calculations in ptraj DEBOSTUTI GHOSHDASTIDAR (Fri Mar 15 2013 - 03:32:32 PDT)
- [AMBER] Hydration Free Enery by TI Kepa K. Burusco (Fri Mar 15 2013 - 10:06:25 PDT)
- [AMBER] Amber 9 pooja chahal (Fri Mar 15 2013 - 20:54:22 PDT)
- [AMBER] problem in generating pbsa.phi file using PBSA N Nandi (Sun Mar 17 2013 - 22:15:37 PDT)
- [AMBER] GPU job scheduling: looking for recommendations and experiences Jan-Philip Gehrcke (Mon Mar 18 2013 - 06:35:07 PDT)
- [AMBER] no restrains? Albert (Mon Mar 18 2013 - 06:43:30 PDT)
- [AMBER] ions (salt concentration) and deep energetics problem Neha Gandhi (Mon Mar 18 2013 - 07:04:24 PDT)
- [AMBER] NVT stacked at GPU running Albert (Mon Mar 18 2013 - 08:51:44 PDT)
- [AMBER] COM support with GPU Fabrício Bracht (Mon Mar 18 2013 - 12:04:27 PDT)
- [AMBER] can we specify mpi path in ./configure? Albert (Mon Mar 18 2013 - 13:30:28 PDT)
- [AMBER] Problem with Alanine Scanning using MMPBSA.py with Terminal Residues Yew Mun Yip (Mon Mar 18 2013 - 20:54:52 PDT)
- [AMBER] how to save a snapshot from the trajectory Sindrila Dutta banik (Mon Mar 18 2013 - 23:25:07 PDT)
- [AMBER] urea frcmod file gargi borgohai (Tue Mar 19 2013 - 00:17:29 PDT)
- [AMBER] problem combining trajectories with diff. number of residues Vaibhav Dixit (Tue Mar 19 2013 - 00:28:12 PDT)
- [AMBER] Antechamber: AM1-BCC charges from MOPAC output Miro Moman (Tue Mar 19 2013 - 02:05:03 PDT)
- [AMBER] Error while generating B factor Graph Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Tue Mar 19 2013 - 02:55:10 PDT)
- Re: [AMBER] leap insert missing atoms in aminoacids according to ... Marta Perez (Tue Mar 19 2013 - 03:25:51 PDT)
- [AMBER] tutorial on thermodynamic integration Shruti Koulgi (Tue Mar 19 2013 - 04:44:53 PDT)
- [AMBER] IED web link to essential dynamics is broken Vaibhav Dixit (Tue Mar 19 2013 - 05:20:49 PDT)
- [AMBER] Problem to save a particular snapshot from the trajectory Sindrila Dutta banik (Tue Mar 19 2013 - 05:56:01 PDT)
- [AMBER] why no periodic information? Albert (Tue Mar 19 2013 - 07:00:52 PDT)
- [AMBER] Meaning of electrostatic pairwise interaction in GB/PBSA Josep Maria Campanera Alsina (Tue Mar 19 2013 - 08:00:55 PDT)
- [AMBER] Ante-mmpbsa.py error Vivek Shankar Bharadwaj (Tue Mar 19 2013 - 10:22:57 PDT)
- [AMBER] Trouble with MM-PBSA calculations in large complex Amy Davenport (Tue Mar 19 2013 - 17:27:19 PDT)
- [AMBER] How protein-water electrostatic interaction can be turned off keeping protein-protein vdw, protein-protein (vdw+elect) and water-water (vdw+elect) intact somedatta pal (Wed Mar 20 2013 - 03:28:42 PDT)
- [AMBER] solvating and neutralizing a lipid bilayer John Gehman (Wed Mar 20 2013 - 07:16:11 PDT)
- [AMBER] mmpbsa calculations on a PROTEIN/DNA/LIGAND ternary complex Giulia Palermo (Wed Mar 20 2013 - 10:33:11 PDT)
- [AMBER] pmemd.cuda compilation problems on Ubuntu 12.4 Weinzierl, Robert O J (Wed Mar 20 2013 - 10:56:51 PDT)
- Re: [AMBER] AMBER Digest, Vol 457, Issue 1 Amy Davenport (Wed Mar 20 2013 - 12:48:36 PDT)
- [AMBER] How to use AMBER parameters for modified amino acids Symon Gathiaka (Wed Mar 20 2013 - 14:27:37 PDT)
- [AMBER] how can we plot energy profile for REMD? Albert (Thu Mar 21 2013 - 01:51:11 PDT)
- [AMBER] aMD simulations in AMBER 12 (GPU version) Neha Gandhi (Thu Mar 21 2013 - 03:26:44 PDT)
- [AMBER] GLYCAM-Web server disruptions Lachele Foley (Thu Mar 21 2013 - 07:17:38 PDT)
- [AMBER] mmpbsa calculations for a ternary protein/dna/ligand complex in presence of cocrystalized Mg ions Giulia (Thu Mar 21 2013 - 08:26:00 PDT)
- Re: [AMBER] Trouble with MM-PBSA calculations in large complex Amy Davenport (Thu Mar 21 2013 - 12:05:12 PDT)
- [AMBER] RXSGLD Simulation Error Mark Healey (Thu Mar 21 2013 - 12:53:27 PDT)
- Re: [AMBER] aMD simulations in AMBER 12 (GPU version) update Neha Gandhi (Thu Mar 21 2013 - 17:20:26 PDT)
- [AMBER] Which memory of GTX580 should I choose in 30, 000-50, 000 atoms system Mu Xia (Thu Mar 21 2013 - 20:24:55 PDT)
- [AMBER] amber12 remd problem and solution recompiling sander.MPI with AMBERBUILDFLAGS -DVERBOSE_REM Guillermo Mulliert Carlín (Fri Mar 22 2013 - 00:21:01 PDT)
- [AMBER] problem in generating pbsa.phi file using PBSA N Nandi (Fri Mar 22 2013 - 01:57:55 PDT)
- [AMBER] can we calculate them together? Albert (Fri Mar 22 2013 - 07:44:32 PDT)
- [AMBER] leap - removing terminals problem Ignacio J. General (Fri Mar 22 2013 - 08:59:32 PDT)
- [AMBER] Langevin Dynamics George Tzotzos (Fri Mar 22 2013 - 12:00:27 PDT)
- [AMBER] SMD centre of the restraint George Tzotzos (Sat Mar 23 2013 - 14:51:21 PDT)
- [AMBER] one sided connection warning HEM P450 MD input files Vaibhav Dixit (Sat Mar 23 2013 - 22:53:15 PDT)
- [AMBER] how can we calculate average dihedral for aMD? Albert (Sun Mar 24 2013 - 04:41:17 PDT)
- [AMBER] how to plot CA matrix? Albert (Sun Mar 24 2013 - 05:14:00 PDT)
- [AMBER] patching unsuccessful even after modifying patch_amber.py Vaibhav Dixit (Sun Mar 24 2013 - 05:17:50 PDT)
- [AMBER] Amber release time table Jonathan Gough (Sun Mar 24 2013 - 12:11:01 PDT)
- [AMBER] '.' follows exponent in NUMBER-like thing Yun Shi (Sun Mar 24 2013 - 12:15:15 PDT)
- [AMBER] membrane protein modeling Kong, Ren (Sun Mar 24 2013 - 16:55:38 PDT)
- [AMBER] the prpblem in constructing the close circular DNA llduan (Sun Mar 24 2013 - 18:02:42 PDT)
- Re: [AMBER] Amber Digest, Vol. 458, Issue 1, Topic 1 pmemd.cuda compilation problems on Ubuntu 12.4 (Daniel Roe) Weinzierl, Robert O J (Mon Mar 25 2013 - 04:01:10 PDT)
- [AMBER] Fwd: cudaMemcpy GpuBuffer::Download failed Alessandro Orro (Mon Mar 25 2013 - 05:06:13 PDT)
- [AMBER] problems in parameters calculated with AMBER Anna MARABOTTI (Mon Mar 25 2013 - 05:12:09 PDT)
- [AMBER] problem in running antechamber Anshuman Dixit (Tue Mar 26 2013 - 00:39:08 PDT)
- [AMBER] residue-wise SASA calculation in CPPTRAJ aneesh cna (Tue Mar 26 2013 - 03:08:48 PDT)
- [AMBER] cpptraj Ignacio J. General (Tue Mar 26 2013 - 07:25:58 PDT)
- [AMBER] Question about 'sequence' command Ismail, Mohd F. (Tue Mar 26 2013 - 22:47:34 PDT)
- [AMBER] aMD job failed Albert (Wed Mar 27 2013 - 00:21:05 PDT)
- [AMBER] minor development note: make symbolic link to pmemd.cuda relative instead of absolute Jan-Philip Gehrcke (Wed Mar 27 2013 - 05:26:40 PDT)
- [AMBER] MMPBSA calculations Chinthaka Ratnaweera (Wed Mar 27 2013 - 09:08:20 PDT)
- [AMBER] RMSD with ptraj fit vs unfit HIMANSHU JOSHI (Wed Mar 27 2013 - 10:17:38 PDT)
- [AMBER] Histidine problem Changqing Yan (Wed Mar 27 2013 - 20:18:15 PDT)
- [AMBER] Generating PDB files with atom radii information aneesh cna (Wed Mar 27 2013 - 22:01:18 PDT)
- [AMBER] How to implement QM/MM-PBSA method in Amber 11 with AmberTools 12 dbaogen (Wed Mar 27 2013 - 23:36:58 PDT)
- [AMBER] strange output information Albert (Thu Mar 28 2013 - 03:02:53 PDT)
- [AMBER] ff10 with ILDN + Best&Hummer modifications Vlad Cojocaru (Thu Mar 28 2013 - 03:56:59 PDT)
- [AMBER] MM PBSA tutorial rajith bhaskaran (Thu Mar 28 2013 - 05:42:42 PDT)
- [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 530 C5' CI Xioling Chuang (Thu Mar 28 2013 - 08:25:51 PDT)
- [AMBER] problem in generating pbsa.phi file using PBSA N Nandi (Thu Mar 28 2013 - 22:06:09 PDT)
- [AMBER] rotational diffusion via cpptraj Vijay Manickam Achari (Fri Mar 29 2013 - 04:11:12 PDT)
- [AMBER] Problem reading a psf file in cpptraj Ganesh Kamath (Fri Mar 29 2013 - 11:43:15 PDT)
- [AMBER] conformational sampling in non helical RNA structures Asmita Gupta (Sat Mar 30 2013 - 08:44:39 PDT)
- Last message date: Sat Mar 30 2013 - 12:30:02 PDT
- Archived on: Fri Dec 20 2024 - 05:54:47 PST
