Amber Archive Oct 2011 by thread
- Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Marek Maly (Fri Sep 30 2011 - 20:13:21 PDT)
- [AMBER] Amber10 Shesh Nath (Fri Sep 30 2011 - 23:09:06 PDT)
- [AMBER] building topology for a big DNA/protein complex with tleap and sleap Giulia Palermo (Sat Oct 01 2011 - 03:05:49 PDT)
- [AMBER] Add extra force in sander.MPI Chicago Ji (Sat Oct 01 2011 - 11:23:39 PDT)
- [AMBER] PLUMED for PATH COLLECTIVE VARIABLES Giulia Palermo (Sat Oct 01 2011 - 11:46:22 PDT)
- [AMBER] Problem in compilng AmberTools1.5 on Mac OSX 10.7.1 Wei Huang (Sat Oct 01 2011 - 14:02:55 PDT)
- [AMBER] bond lengths Aparna P (Sun Oct 02 2011 - 22:52:48 PDT)
- [AMBER] problem with sulphur pancham lal gupta (Mon Oct 03 2011 - 03:39:57 PDT)
- [AMBER] PDB file modification Asmita Gupta (Mon Oct 03 2011 - 07:26:53 PDT)
- [AMBER] MMPBSA.MPI: Entropy George Tzotzos (Mon Oct 03 2011 - 11:01:10 PDT)
- Re: [AMBER] MMPBSA: how to include only some residues Victor Ma (Mon Oct 03 2011 - 12:30:22 PDT)
- [AMBER] Solvent accessible area kirtana S (Mon Oct 03 2011 - 14:03:50 PDT)
- Re: [AMBER] ambertool question !!! Алексей Раевский (Mon Oct 03 2011 - 14:20:10 PDT)
- [AMBER] Error with 99SBnmr force field Peter Eastman (Mon Oct 03 2011 - 16:18:27 PDT)
- [AMBER] Illegal atomic numbers in nucleic10.lib Peter Eastman (Mon Oct 03 2011 - 16:57:17 PDT)
- Re: [AMBER] PNEB on GPUs William Cantara (Mon Oct 03 2011 - 17:33:21 PDT)
- [AMBER] TMD for a large conformation change William Cantara (Mon Oct 03 2011 - 17:52:39 PDT)
- [AMBER] MMPBSA input error for INP Niel Henriksen (Mon Oct 03 2011 - 19:33:20 PDT)
- [AMBER] A Gentle Reminder: Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021) Ross Walker (Mon Oct 03 2011 - 19:39:22 PDT)
- [AMBER] Calculating the force applied to a restrained point Ali M. Naserian-Nik (Tue Oct 04 2011 - 00:49:01 PDT)
- Re: [AMBER] AMOEBA potentials Neha Gandhi (Tue Oct 04 2011 - 02:41:08 PDT)
- [AMBER] Small inquiry regarding MMPBSA.py code Jan-Philip Gehrcke (Tue Oct 04 2011 - 10:00:55 PDT)
- [AMBER] Ordering of torsion definitions Peter Eastman (Tue Oct 04 2011 - 10:06:20 PDT)
- [AMBER] MMPBSA calculation Sangita Kachhap (Tue Oct 04 2011 - 10:14:20 PDT)
- [AMBER] pmemd.cuda and nonzero gbsa E. Nihal Korkmaz (Tue Oct 04 2011 - 11:25:32 PDT)
- [AMBER] Self assembled surface. ros (Tue Oct 04 2011 - 15:41:22 PDT)
- [AMBER] Using ff10 with ildn or nmr Peter Eastman (Tue Oct 04 2011 - 15:49:52 PDT)
- [AMBER] message during pbsa energy calculation Jorge Iulek (Tue Oct 04 2011 - 16:17:17 PDT)
- [AMBER] How to Calculate SASA with Amber? qiao xue (Wed Oct 05 2011 - 03:53:54 PDT)
- [AMBER] MMPBSA.py.MPI problems: L-J-parameters, bad file descriptors, MMPBSA hangup due to sander failure Jan-Philip Gehrcke (Wed Oct 05 2011 - 03:54:16 PDT)
- [AMBER] MMPBSA.py: no value inserted for "Residues to print": left as "RES EDIT" Jan-Philip Gehrcke (Wed Oct 05 2011 - 07:32:45 PDT)
- [AMBER] AMBER parameters for the acetylated lysine Gorka lasso (Wed Oct 05 2011 - 08:19:35 PDT)
- [AMBER] HO atom type van der Waals (GLYCAM) Matthew Tessier (Wed Oct 05 2011 - 10:44:58 PDT)
- [AMBER] not too many MD simulations of protein-ligand system? Yun Shi (Wed Oct 05 2011 - 12:50:54 PDT)
- [AMBER] QMMMMD Tutorial Question Yao Yao (Wed Oct 05 2011 - 14:52:09 PDT)
- Re: [AMBER] MMPBSA.py 3DRISM error Jesper Soerensen (Wed Oct 05 2011 - 17:18:40 PDT)
- [AMBER] Total Energy Autocorrelation Function Yao Yao (Wed Oct 05 2011 - 19:40:37 PDT)
- [AMBER] Radial distribution function tommaso.casalini.mail.polimi.it (Thu Oct 06 2011 - 02:31:48 PDT)
- [AMBER] MMPBSA error Soumya Lipsa Rath (Thu Oct 06 2011 - 03:03:31 PDT)
- [AMBER] iron sulphur cluster parameters francesco oteri (Thu Oct 06 2011 - 06:10:39 PDT)
- [AMBER] Reg:QM region + cutoff larger than box dimension kaustubh joshi (Thu Oct 06 2011 - 07:46:29 PDT)
- [AMBER] Parallel Amber11 Installation Error David Cantu (Thu Oct 06 2011 - 15:26:28 PDT)
- [AMBER] MMPBSA.MPI: IOError: [Errno 9] Bad file descriptor George Tzotzos (Thu Oct 06 2011 - 15:45:32 PDT)
- [AMBER] Problem installing on a mac Lion 10.7 using gcc 4.2 Gamal Akabani (Thu Oct 06 2011 - 16:01:44 PDT)
- [AMBER] MMPBSA on a protein-protein complex when protein contains non-protein Irene Newhouse (Thu Oct 06 2011 - 16:09:53 PDT)
- [AMBER] Amber 11, AmberTools 1.5 installation problem #MAZIAR SOLEYMANI ARDEJANI# (Fri Oct 07 2011 - 03:29:18 PDT)
- Re: [AMBER] bug in respgen ? thomas.fox.boehringer-ingelheim.com (Fri Oct 07 2011 - 05:15:08 PDT)
- [AMBER] oct or cubic box? Yun Shi (Fri Oct 07 2011 - 11:15:18 PDT)
- [AMBER] ptraj clustering error Rajesh Raju (Fri Oct 07 2011 - 12:08:59 PDT)
- [AMBER] Interaction Energy in QMMMMD Yao Yao (Fri Oct 07 2011 - 12:27:30 PDT)
- [AMBER] Gromacs Make Index in AMBER Yao Yao (Fri Oct 07 2011 - 15:56:47 PDT)
- [AMBER] Fw: Gromacs Make Index in AMBER Yao Yao (Fri Oct 07 2011 - 17:13:29 PDT)
- [AMBER] FEP E. Nihal Korkmaz (Sun Oct 09 2011 - 15:35:36 PDT)
- Re: [AMBER] sander mpi error when unfolding the protein Chinh Su Tran To (Sun Oct 09 2011 - 19:45:31 PDT)
- [AMBER] residue stripping in ptraj Praapti Jayaswal (Sun Oct 09 2011 - 22:11:15 PDT)
- [AMBER] "Frontiers in Biomolecular Simulation" - Heraeus conference in Germany, Jan. 22.-25. 2012 steinbrt.rci.rutgers.edu (Mon Oct 10 2011 - 07:34:54 PDT)
- [AMBER] Turning off non-bonded interactions for specific atomtype pairs Marc van der Kamp (Tue Oct 11 2011 - 01:42:49 PDT)
- [AMBER] ff99-ildn frcmod validation question D.G. Sprous, PhD (Tue Oct 11 2011 - 05:12:01 PDT)
- [AMBER] regarding qmmm simulation jani vinod (Tue Oct 11 2011 - 05:30:16 PDT)
- [AMBER] mmtsb problem Sel Ercan (Tue Oct 11 2011 - 06:03:19 PDT)
- [AMBER] MMPBSA.py: error during parsing of _MMPBSA_complex_gb.mdout Jan-Philip Gehrcke (Tue Oct 11 2011 - 06:20:14 PDT)
- [AMBER] Antechamber/SQM Chidambar Kulkarni (Tue Oct 11 2011 - 09:13:07 PDT)
- [AMBER] 3D-RISM bugfix for polar/apolar decomposition Tyler Luchko (Tue Oct 11 2011 - 11:49:36 PDT)
- [AMBER] LMOD error and questions Sarah Edwards (Tue Oct 11 2011 - 11:54:41 PDT)
- [AMBER] Question regarding HAS_10_12 flag in PMEMD (LINMIN Failure) brian_jo.berkeley.edu (Tue Oct 11 2011 - 17:30:21 PDT)
- [AMBER] please help me pancham lal gupta (Wed Oct 12 2011 - 06:04:25 PDT)
- [AMBER] extract trajectory and average structure najmul arfin (Wed Oct 12 2011 - 07:13:13 PDT)
- [AMBER] extract trajectory and average structure najmul arfin (Wed Oct 12 2011 - 07:17:00 PDT)
- [AMBER] proteins with Ff10 + igb=7 Abhishek Singh (Wed Oct 12 2011 - 08:15:03 PDT)
- [AMBER] chiral restraints kirtana S (Wed Oct 12 2011 - 11:05:35 PDT)
- [AMBER] New to AMBER, installation issues Matthew D Antalek (Wed Oct 12 2011 - 12:06:02 PDT)
- [AMBER] About SMD simulation restart file Mo Chen (Wed Oct 12 2011 - 13:26:29 PDT)
- [AMBER] Can we avoid output the distance between closed atoms in the same residue: question for usage of checkoverlap in PTRAJ. kurisaki (Wed Oct 12 2011 - 23:31:15 PDT)
- [AMBER] PMEMD command Chinh Su Tran To (Thu Oct 13 2011 - 00:18:24 PDT)
- Re: [AMBER] Turning off non-bonded interactions for specificatomtype pairs CHAMI F. (Thu Oct 13 2011 - 04:03:45 PDT)
- [AMBER] SASA calculate Tong Zhu (Thu Oct 13 2011 - 06:36:19 PDT)
- [AMBER] One more Gentle Reminder: Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021) Ross Walker (Thu Oct 13 2011 - 10:33:34 PDT)
- [AMBER] About pmemd and pmemd.MPI Mo Chen (Thu Oct 13 2011 - 12:27:34 PDT)
- [AMBER] safemem.o error while compiling Ambertools 1.5 Josmar R. da Rocha (Thu Oct 13 2011 - 15:35:25 PDT)
- [AMBER] sander pb focusing error Niel Henriksen (Thu Oct 13 2011 - 20:17:06 PDT)
- [AMBER] Inquiry about Amber installation Mo Chen (Thu Oct 13 2011 - 20:21:09 PDT)
- [AMBER] Poisson-Boltzmann/GB Solvents with FF02 Neha Gandhi (Thu Oct 13 2011 - 22:50:32 PDT)
- Re: [AMBER] From amber to gromacs madhumita das (Fri Oct 14 2011 - 00:48:33 PDT)
- [AMBER] changes in secstruct command Antje Wolf (Fri Oct 14 2011 - 03:42:34 PDT)
- [AMBER] GB simulation on GPU freezes E. Nihal Korkmaz (Fri Oct 14 2011 - 10:55:24 PDT)
- [AMBER] QMMMMD blowup Yao Yao (Fri Oct 14 2011 - 12:58:35 PDT)
- [AMBER] sander bug? Yao Yao (Fri Oct 14 2011 - 15:24:16 PDT)
- [AMBER] converting Amber trajectories to Gromacs XTC mish (Sat Oct 15 2011 - 03:52:40 PDT)
- [AMBER] xleap problem souvik sur (Sat Oct 15 2011 - 04:16:34 PDT)
- [AMBER] How to make the library of PNA-DNA duplex souvik sur (Sat Oct 15 2011 - 04:57:10 PDT)
- [AMBER] relative binding free energy calculation leila karami (Sat Oct 15 2011 - 07:00:59 PDT)
- [AMBER] problem in interpreting RMSDs Sajeewa Pemasinghe (Sat Oct 15 2011 - 09:15:21 PDT)
- [AMBER] SASA calculation: removing water and ion problem. Ouaray Z. (Sun Oct 16 2011 - 06:14:36 PDT)
- [AMBER] Self-assembled monolayers ros (Sun Oct 16 2011 - 09:19:53 PDT)
- [AMBER] Solvent accessible area kirtana S (Sun Oct 16 2011 - 09:38:58 PDT)
- [AMBER] subscription! Dr. Alaa El-Din A. Gawad (Fri Oct 14 2011 - 13:09:22 PDT)
- [AMBER] AmberTools-1.5 installation Dr. Alaa El-Din A. Gawad (Fri Oct 14 2011 - 13:07:04 PDT)
- [AMBER] Judje error Алексей Раевский (Sun Oct 16 2011 - 15:19:37 PDT)
- [AMBER] Energy calculateion from MD trajectory: can we skip the minimization? kurisaki (Sun Oct 16 2011 - 23:58:17 PDT)
- Re: [AMBER] Trouble with Installation of AmberTools 1.5 Ben Ahmady (Mon Oct 17 2011 - 09:11:53 PDT)
- [AMBER] Help on self-assembled mono layer ros (Mon Oct 17 2011 - 11:58:02 PDT)
- [AMBER] solvents in AMBER Yao Yao (Mon Oct 17 2011 - 13:36:02 PDT)
- Re: [AMBER] vmd-l: AMBER prmtop and traj to pqr - radii error Jesper Soerensen (Mon Oct 17 2011 - 16:58:53 PDT)
- [AMBER] Force field parameters for polyethene 陶晓芳 (Mon Oct 17 2011 - 20:18:20 PDT)
- [AMBER] sander pbsa and imin = 5 problem Niel Henriksen (Mon Oct 17 2011 - 20:27:18 PDT)
- [AMBER] error "reset fillratio to a larger number 2.000" in mm_pbsa calculation Prajwal Nandekar (Mon Oct 17 2011 - 23:14:54 PDT)
- [AMBER] Amber 10 compile error Kijeong Kwac (Tue Oct 18 2011 - 08:25:11 PDT)
- [AMBER] Is Amber a 32-bit or 64-bit program? Jiaqi Jin (Tue Oct 18 2011 - 14:58:57 PDT)
- [AMBER] Material including Boron, "ATTN need revision" Hoshin Kim (Tue Oct 18 2011 - 16:51:14 PDT)
- [AMBER] Amber Tools 1.5 installation Matthew D Antalek (Tue Oct 18 2011 - 17:10:50 PDT)
- [AMBER] AMBER10 Shesh Nath (Tue Oct 18 2011 - 23:26:41 PDT)
- [AMBER] Applying Bugfixes Amber11 Matthew D Antalek (Wed Oct 19 2011 - 15:46:07 PDT)
- [AMBER] Inquiry about the cutoff (cut, vdw_cutoff, es_cutoff) settings of PMEMD Mo Chen (Wed Oct 19 2011 - 19:18:46 PDT)
- [AMBER] Failure minimizing pamr7 files from A1 tutorial with NAMD=CUDA Francesco Pietra (Wed Oct 19 2011 - 23:32:13 PDT)
- [AMBER] please help me pancham lal gupta (Thu Oct 20 2011 - 02:59:57 PDT)
- [AMBER] Sander.MPI parallel run Lianhu Wei (Thu Oct 20 2011 - 09:04:26 PDT)
- [AMBER] Error using set default PBradii bondi in tleap with pmemd.cuda or sander Fabrício Bracht (Thu Oct 20 2011 - 21:05:04 PDT)
- [AMBER] crash due to ewald Jorgen Simonsen (Fri Oct 21 2011 - 05:17:42 PDT)
- [AMBER] errors when add Zn ions Yunjie Zhao (Fri Oct 21 2011 - 05:37:15 PDT)
- [AMBER] PB parameters: SURFTEN/SURFOFF Qiong Zhang (Sat Oct 22 2011 - 13:56:33 PDT)
- [AMBER] how to get tetramer coordinate of Melittin Form PDB ID:2MLT. hai wei (Sat Oct 22 2011 - 18:36:27 PDT)
- [AMBER] for mm_pbsa.pl, when MS=0, PB does not work, GB works Qiong Zhang (Sat Oct 22 2011 - 22:46:27 PDT)
- [AMBER] AMBER, haris p has invited you to open a Gmail account haris p (Sun Oct 23 2011 - 00:58:40 PDT)
- [AMBER] Polarization term in Energy Anglea A. (Sun Oct 23 2011 - 06:55:38 PDT)
- [AMBER] ATP+Mg Алексей Раевский (Mon Oct 24 2011 - 00:59:38 PDT)
- [AMBER] How to use "impose" command in ptraj to rotate dihedral angle mish (Mon Oct 24 2011 - 02:49:49 PDT)
- [AMBER] Minor RNA bases gunajyoti das (Mon Oct 24 2011 - 05:04:47 PDT)
- [AMBER] does CHECKOVERLAP check image cell? kurisaki (Mon Oct 24 2011 - 05:14:44 PDT)
- [AMBER] Final chance to win a C2070 - Survey ends at midnight PDT tonight Monday Oct 24th 2011. Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021) Ross Walker (Mon Oct 24 2011 - 09:24:57 PDT)
- Re: [AMBER] Final chance to win a C2070 - Survey ends at midnight PDT tonight Monday Oct 24th 2011. Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f peker milas (Mon Oct 24 2011 - 09:26:42 PDT)
- Re: [AMBER] GPU Survey link: http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021 Ross Walker (Mon Oct 24 2011 - 09:55:46 PDT)
- [AMBER] please help me pancham lal gupta (Mon Oct 24 2011 - 20:08:06 PDT)
- [AMBER] Ambertools1.5, mmpbsa.py. PB Bomb in pb_atmlist(): maxnba too short Qiong Zhang (Tue Oct 25 2011 - 02:07:55 PDT)
- [AMBER] REMD: mismatches in potential energy values Mariarosaria Ferraro (Tue Oct 25 2011 - 03:24:22 PDT)
- [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Ashutosh Shandilya (Tue Oct 25 2011 - 06:04:20 PDT)
- [AMBER] sander.MPI tsurma.umich.edu (Tue Oct 25 2011 - 08:06:42 PDT)
- [AMBER] reimage method and hbond analysis mirage . (Wed Oct 26 2011 - 00:02:47 PDT)
- [AMBER] quasi-harmonic analysis Neha Gandhi (Wed Oct 26 2011 - 01:50:48 PDT)
- [AMBER] Molecular velocity from molecular trajectories tommaso.casalini.mail.polimi.it (Wed Oct 26 2011 - 02:51:53 PDT)
- [AMBER] box information in .inpcrd and .rst files Giovanni Pavan (Wed Oct 26 2011 - 04:35:59 PDT)
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Wed Oct 26 2011 - 05:19:32 PDT)
- Re: [AMBER] How to avoid Zn parametrization? Andrew Voronkov (Wed Oct 26 2011 - 05:32:56 PDT)
- Re: [AMBER] How to avoid Zn parametrization? Andrew Voronkov (Wed Oct 26 2011 - 05:36:28 PDT)
- [AMBER] pseudorotation phase angle for RNA Charles Johnson (Wed Oct 26 2011 - 08:50:56 PDT)
- [AMBER] Amber on IBM Power7 or Opteron 6200 series? Gustavo Seabra (Wed Oct 26 2011 - 09:17:53 PDT)
- [AMBER] input conformations for RESP procedure for modified amino? jzintsma.nd.edu (Wed Oct 26 2011 - 10:04:20 PDT)
- [AMBER] pseudorotation phase angle for RNA Charles Johnson (Wed Oct 26 2011 - 13:57:28 PDT)
- [AMBER] About defining force direction in SMD simulation Mo Chen (Wed Oct 26 2011 - 15:25:02 PDT)
- [AMBER] prmtop details Yao Yao (Wed Oct 26 2011 - 17:10:10 PDT)
- [AMBER] molecule out box and correct hbond analysis mirage . (Thu Oct 27 2011 - 01:27:54 PDT)
- [AMBER] E-mail change Maciej Masłyk (Thu Oct 27 2011 - 05:47:39 PDT)
- [AMBER] distribution of selected water kirtana S (Thu Oct 27 2011 - 10:10:20 PDT)
- [AMBER] Query for using Curves+ from Amber trajectories souvik sur (Thu Oct 27 2011 - 23:19:49 PDT)
- [AMBER] Bug in nmode Ake Sandgren (Fri Oct 28 2011 - 01:15:51 PDT)
- [AMBER] compiling amber11 (sander) on Blue Gene/P piotr zarzycki (Fri Oct 28 2011 - 01:56:37 PDT)
- [AMBER] Salt in explicit water Beale, John (Fri Oct 28 2011 - 02:01:20 PDT)
- [AMBER] Specifying a gcc compiler for amber tools installation Sai Kumar Ramadugu (Fri Oct 28 2011 - 10:21:50 PDT)
- [AMBER] 1st DNA Tutorial Pressure Yao Yao (Fri Oct 28 2011 - 11:58:34 PDT)
- [AMBER] iron sulphur cluster parametrization Francesco Oteri (Sat Oct 29 2011 - 01:39:52 PDT)
- [AMBER] Problems with AmberTools compilation under Debian James Starlight (Sat Oct 29 2011 - 10:42:29 PDT)
- [AMBER] 1JFF Antechamber, LEaP problems Matthew D Antalek (Sat Oct 29 2011 - 14:51:07 PDT)
- [AMBER] position restraints on heavy atoms or all? Yun Shi (Sat Oct 29 2011 - 17:04:16 PDT)
- [AMBER] tutorial A6 leila karami (Sun Oct 30 2011 - 03:21:18 PDT)
- [AMBER] tutorial A6 leila karami (Sun Oct 30 2011 - 03:40:42 PDT)
- [AMBER] Periodic Box in igb mode Davood Norouzi (Sun Oct 30 2011 - 05:26:06 PDT)
- [AMBER] Atom ordering after LEAP Gonzalo Jimenez (Sun Oct 30 2011 - 06:47:58 PDT)
- [AMBER] parameters for anchor-modified glycopeptides Urszula Uciechowska (Sun Oct 30 2011 - 10:10:35 PDT)
- [AMBER] umbrella sampling amber11 Elisa Frezza (Sun Oct 30 2011 - 14:40:50 PDT)
- [AMBER] how to load atom type for divalent ions in leaprc.ff10? Victor Ma (Mon Oct 31 2011 - 08:56:49 PDT)
- [AMBER] Issue with running sander with SHAKE Breuer, Marian (Mon Oct 31 2011 - 11:07:37 PDT)
- Last message date: Mon Oct 31 2011 - 18:30:02 PDT
- Archived on: Wed Apr 17 2024 - 05:54:18 PDT
