Amber Archive Jan 2013 by thread
- [AMBER] not getting dipole moment values in pmemd.cuda Sanjib Paul (Tue Jan 01 2013 - 03:36:05 PST)
- Re: [AMBER] NPT and NVE Energy Ismail, Mohd F. (Tue Jan 01 2013 - 20:58:16 PST)
- [AMBER] Need assistance to generate forcefield for PYRIDOXAL-5'-PHOSPHATE BALA SUBRAMANI G L (Wed Jan 02 2013 - 05:27:21 PST)
- Re: [AMBER] Amber LES.MPI crash Kirill Nuzhdin (Wed Jan 02 2013 - 08:08:16 PST)
- [AMBER] MMPBSA error marawan hussain (Wed Jan 02 2013 - 21:11:59 PST)
- [AMBER] Thermodynamic integration with iwrap=1 in SANDER Miroslav Krepl (Thu Jan 03 2013 - 04:39:30 PST)
- [AMBER] Problems creating topology file for Dfrom Giri tomp (Thu Jan 03 2013 - 16:31:41 PST)
- [AMBER] Issue with creating topology file due to atom type not being recognised in frcmod Giri tomp (Thu Jan 03 2013 - 16:34:52 PST)
- [AMBER] bad atom type: f Date, Mihir (Fri Jan 04 2013 - 10:42:21 PST)
- [AMBER] Announcement: Release of DOCK 6.6 Scott Brozell (Fri Jan 04 2013 - 20:02:33 PST)
- [AMBER] REMD restart gargi borgohai (Fri Jan 04 2013 - 22:46:50 PST)
- [AMBER] positive DeltaEel and negative DeltaGsolv in MMPBSA Emilio Angelina (Sat Jan 05 2013 - 11:44:23 PST)
- [AMBER] rfree parsing error in group specification Joel Dockray (Sat Jan 05 2013 - 16:51:47 PST)
- [AMBER] GPUs and PBSPro Vijay Manickam Achari (Sun Jan 06 2013 - 20:05:45 PST)
- [AMBER] how to assign atom types. Salma Zahir (Mon Jan 07 2013 - 02:43:12 PST)
- [AMBER] AMBER parameter problem osalo.abo.fi (Mon Jan 07 2013 - 06:25:08 PST)
- [AMBER] Group specification for energy decomposition in thermodynamic integration (Corrected spacing) Joel Dockray (Mon Jan 07 2013 - 10:35:00 PST)
- [AMBER] bugfix.31 Norah Schlacter (Mon Jan 07 2013 - 12:50:11 PST)
- [AMBER] AMBER12 Installation failed Udaysankar Midya (Mon Jan 07 2013 - 22:39:31 PST)
- [AMBER] Error with TIP4P Chandrasekaran, Suryanarayanan (Tue Jan 08 2013 - 06:18:25 PST)
- [AMBER] Query regarding GB calculation on a protein with FE using MMPBSA.py Prajwal Nandekar (Tue Jan 08 2013 - 06:22:48 PST)
- [AMBER] GAFFlipid FF concern jfloresc.andrew.cmu.edu (Tue Jan 08 2013 - 13:54:28 PST)
- [AMBER] Is AM1-BCC charges ok for ligands with idodine atoms Shulin Zhuang (Tue Jan 08 2013 - 17:54:10 PST)
- [AMBER] hybrid imlicit/explicit system Алексей Раевский (Wed Jan 09 2013 - 02:44:16 PST)
- [AMBER] problem with identifying Zn ion in Amber11 Agnieszka Dybala-Defratyka (Wed Jan 09 2013 - 13:55:21 PST)
- [AMBER] cudaMemcpyToSymbol: SetSim copy to Sim failed for K20x using JAC and Cellulose benchmarks Mohammad Ashraf Bhuiyan (Wed Jan 09 2013 - 14:02:41 PST)
- [AMBER] bug in sander nmr.F90, amber12? Fabian Zeller (Thu Jan 10 2013 - 06:27:09 PST)
- [AMBER] Problems using NAB and GCC Roberto Vera (Thu Jan 10 2013 - 08:13:58 PST)
- [AMBER] AMBER bonded parameters Dr. Vitaly Chaban (Thu Jan 10 2013 - 14:50:34 PST)
- [AMBER] antechamber problem Changqing Yan (Thu Jan 10 2013 - 19:15:45 PST)
- [AMBER] amber12 Bio Learner (Thu Jan 10 2013 - 22:41:30 PST)
- [AMBER] Simulating Folic Acid JD John (Thu Jan 10 2013 - 22:53:10 PST)
- [AMBER] how to construct new molecule Bio Learner (Fri Jan 11 2013 - 00:00:50 PST)
- [AMBER] Glycam_06 in amber12 Subrata Paul (Fri Jan 11 2013 - 02:03:53 PST)
- [AMBER] AMD pooja chahal (Fri Jan 11 2013 - 02:28:31 PST)
- [AMBER] installation problem Tanmoy Paul (Fri Jan 11 2013 - 03:09:30 PST)
- [AMBER] dnaiontracker command in cpptraj Le,Huy Tuan (Fri Jan 11 2013 - 11:50:41 PST)
- [AMBER] question about force fields and external QM program Kirill Nuzhdin (Fri Jan 11 2013 - 11:59:53 PST)
- [AMBER] RMS2D Syed Tarique Moin (Sat Jan 12 2013 - 03:49:22 PST)
- [AMBER] Fwd: Query regarding umbrella sampling minhazul arfeen (Sat Jan 12 2013 - 08:07:30 PST)
- [AMBER] Software announcement: Release of PUPIL 2.0 Joan Torras (Sun Jan 13 2013 - 15:44:03 PST)
- [AMBER] command used to upload pdb Bio Learner (Mon Jan 14 2013 - 00:51:40 PST)
- [AMBER] installation error Bio Learner (Mon Jan 14 2013 - 01:58:27 PST)
- [AMBER] amber organic box 纪晓峰 (Mon Jan 14 2013 - 02:16:59 PST)
- [AMBER] Citrate ion (-3) parameters moitrayee.mbu.iisc.ernet.in (Mon Jan 14 2013 - 03:34:13 PST)
- [AMBER] Problem with Identification of bonds Volker Lesch (Mon Jan 14 2013 - 06:33:07 PST)
- [AMBER] density for PBC system; addles error Kirill Nuzhdin (Mon Jan 14 2013 - 14:17:53 PST)
- [AMBER] Getting AmberTools12 to work in Ubuntu 12.04? David Dubins (Mon Jan 14 2013 - 14:39:21 PST)
- [AMBER] vlimit exceeded and distorted bonds Chris Chris (Mon Jan 14 2013 - 15:02:33 PST)
- [AMBER] Membrane-protein simulation using amber12 Manikanthan Bhavaraju (Mon Jan 14 2013 - 20:38:11 PST)
- [AMBER] xlead aentrena (Tue Jan 15 2013 - 04:03:43 PST)
- [AMBER] Atom reordering for TI Thomas Exner (Tue Jan 15 2013 - 04:25:01 PST)
- [AMBER] umbrella sampling Elisa Frezza (Tue Jan 15 2013 - 06:12:16 PST)
- [AMBER] Getting total dipole moment of molecules in periodic box. 강현아 (Tue Jan 15 2013 - 06:47:00 PST)
- [AMBER] Is it possible to do TI calculations with pmemd? Anna Bauß (Tue Jan 15 2013 - 07:10:07 PST)
- [AMBER] atom type definition mm_pbsa Andrew Anighoro (Tue Jan 15 2013 - 08:01:13 PST)
- [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM (Tue Jan 15 2013 - 09:18:16 PST)
- [AMBER] using image command in cpptraj... Shashidhar Rao (Tue Jan 15 2013 - 10:34:52 PST)
- [AMBER] MMPBSA/Disulfide bond error Divi (Tue Jan 15 2013 - 11:22:34 PST)
- [AMBER] parameters for deoxyADP Jorgen Simonsen (Tue Jan 15 2013 - 11:30:04 PST)
- [AMBER] How to choose the boost for aMD when using restraints Thomas Evangelidis (Tue Jan 15 2013 - 12:32:35 PST)
- [AMBER] A link atoms between protein and sugar! john Kerk (Wed Jan 16 2013 - 00:33:52 PST)
- [AMBER] LJ parameters for Ho in GLYCAM06 changes ABEL Stephane 175950 (Wed Jan 16 2013 - 05:05:26 PST)
- [AMBER] Structure refinement protocol on the AMPS-NMR portal Baptiste Legrand (Wed Jan 16 2013 - 05:40:38 PST)
- [AMBER] xtc to mdcrd box coords Federica Chiappori (Wed Jan 16 2013 - 06:04:02 PST)
- [AMBER] Errors while reading a MOL2 file with "parm" in cpptraj... Shashidhar Rao (Wed Jan 16 2013 - 15:04:58 PST)
- [AMBER] generating restart file with velocity information Vijay Manickam Achari (Wed Jan 16 2013 - 22:53:31 PST)
- [AMBER] Simulating one molecule in the gas phase Volker Lesch (Wed Jan 16 2013 - 23:09:12 PST)
- [AMBER] H-bond analysis of backbone atoms HM (Thu Jan 17 2013 - 02:30:53 PST)
- [AMBER] SHAKE error with dt=0.002 DEBOSTUTI GHOSHDASTIDAR (Thu Jan 17 2013 - 02:52:22 PST)
- [AMBER] velocity information lost in traj files when select frames Vijay Manickam Achari (Thu Jan 17 2013 - 05:43:19 PST)
- [AMBER] Amoeba water model parameters Kirill Nuzhdin (Thu Jan 17 2013 - 08:25:01 PST)
- [AMBER] difficulty with basic tutorial 1 mhclewett.msn.com (Thu Jan 17 2013 - 10:50:22 PST)
- [AMBER] pmemd.amoeba.MPI run error 旭东 肖 (Thu Jan 17 2013 - 18:12:13 PST)
- [AMBER] Query regarding Amber atom type Shubhadip Das (Thu Jan 17 2013 - 23:13:21 PST)
- [AMBER] problem starting amber Ayesha Fatima (Fri Jan 18 2013 - 06:34:51 PST)
- [AMBER] Using multiple CPU cores with pmemd.cuda Filippo Pullara (Fri Jan 18 2013 - 09:02:15 PST)
- [AMBER] RRES and LRES card not recognized when using idecomp with sander WenJuan Huang (Fri Jan 18 2013 - 12:48:48 PST)
- Re: [AMBER] [AMBER: gauche effect in OS-CT-CT-F Steven M. Graham (Sat Jan 19 2013 - 15:00:44 PST)
- [AMBER] Minimum distance between the protein and membrane Manikanthan Bhavaraju (Sun Jan 20 2013 - 16:59:32 PST)
- [AMBER] amber11 installation test files Mary Varughese (Mon Jan 21 2013 - 02:28:40 PST)
- [AMBER] Bug in amber12, pmemd ch2int function Ake Sandgren (Mon Jan 21 2013 - 03:50:35 PST)
- [AMBER] Defining a dihedral torsional energy for non-serial atoms. Negar Ashari Astani (Mon Jan 21 2013 - 06:27:12 PST)
- [AMBER] Dihedral energy for non-serial atoms Negar Ashari Astani (Mon Jan 21 2013 - 07:32:25 PST)
- [AMBER] Query regarding rms2d with cpptraj HM (Mon Jan 21 2013 - 08:41:17 PST)
- [AMBER] Charge relocation CHAMI F. (Mon Jan 21 2013 - 08:52:48 PST)
- Re: [AMBER] solvent accessible volume vs Daniel Roe (Mon Jan 21 2013 - 09:41:36 PST)
- [AMBER] question on the latest manifestation of AMBER force field... Shashidhar Rao (Mon Jan 21 2013 - 20:48:21 PST)
- [AMBER] Amber ff03w/tip4p2005 Neha Gandhi (Tue Jan 22 2013 - 00:10:20 PST)
- [AMBER] mmpbsa-with and without entropy colvin (Tue Jan 22 2013 - 00:20:18 PST)
- [AMBER] Minimization failure of a ligand Sun (Tue Jan 22 2013 - 00:58:27 PST)
- [AMBER] multi pmemd and REMD Neha Gandhi (Tue Jan 22 2013 - 01:20:58 PST)
- [AMBER] 27th Molecular Modelling Workshop 2013 Feb., 25th-27th in Erlangen, Germany Harald Lanig (Tue Jan 22 2013 - 02:52:51 PST)
- [AMBER] Steered MD in Specific Direction Kyle Roberts (Tue Jan 22 2013 - 07:55:34 PST)
- [AMBER] Building a new structure! Ibrahim Said (Tue Jan 22 2013 - 08:39:33 PST)
- [AMBER] Amber12 Cuda installation issues Vivek Shankar Bharadwaj (Tue Jan 22 2013 - 10:05:43 PST)
- [AMBER] Theoretical explanation of adding ions to make the system neutral Mahendra B Thapa (Tue Jan 22 2013 - 14:41:57 PST)
- [AMBER] glibc detected in ptraj Jagur Lambix (Tue Jan 22 2013 - 15:55:50 PST)
- [AMBER] Analyzing AMBER10 trajectories using AmberTools1.4 Kamali Sripathi (Wed Jan 23 2013 - 04:52:18 PST)
- [AMBER] Problem compatibility pdb in tleap Stefan Knippenberg (Wed Jan 23 2013 - 10:22:35 PST)
- [AMBER] KCl crystals with Dang parameters ? Vlad Cojocaru (Wed Jan 23 2013 - 11:23:34 PST)
- [AMBER] error in running a minimization job.... Shashidhar Rao (Wed Jan 23 2013 - 12:16:32 PST)
- [AMBER] how to keep the previous restart file when saving the current one Thomas Evangelidis (Wed Jan 23 2013 - 14:17:35 PST)
- [AMBER] minimization problem Sanjib Paul (Wed Jan 23 2013 - 22:27:04 PST)
- [AMBER] Cpptraj: distance does not work with center of mass Vlastimil Zíma (Thu Jan 24 2013 - 00:47:05 PST)
- [AMBER] Dihedral angle PCA Sergey Samsonov (Thu Jan 24 2013 - 08:27:48 PST)
- [AMBER] TI alpha-beta glucose Glycam06h Kepa K. Burusco (Fri Jan 25 2013 - 05:42:45 PST)
- [AMBER] Mixing Small Organic + Water Ismail, Mohd F. (Sat Jan 26 2013 - 01:27:41 PST)
- [AMBER] Generating Electrostatic Potential Maps Kamali Sripathi (Sat Jan 26 2013 - 07:00:50 PST)
- [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file Jonathan Saboury (Sun Jan 27 2013 - 00:42:59 PST)
- [AMBER] about iwrap=1 and ntxo=2 Thomas Evangelidis (Sun Jan 27 2013 - 03:57:33 PST)
- [AMBER] distance restraints between the primary molecule and its periodic image Thomas Evangelidis (Sun Jan 27 2013 - 10:22:50 PST)
- [AMBER] cudaMemcpyToSymbol Lars Skjærven (Sun Jan 27 2013 - 13:01:02 PST)
- [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file (2) Jonathan Saboury (Sun Jan 27 2013 - 13:49:17 PST)
- [AMBER] installation of amber10 in cluster fails Jorgen Simonsen (Sun Jan 27 2013 - 23:16:44 PST)
- [AMBER] amber 12 patch for cuda-5.0 Asmita Gupta (Mon Jan 28 2013 - 00:50:55 PST)
- [AMBER] Explicit ions in GB solvent Debayan Chakraborty (Mon Jan 28 2013 - 06:04:31 PST)
- [AMBER] Sigmoidal dielectric functions in AMBER Debayan Chakraborty (Mon Jan 28 2013 - 15:50:15 PST)
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file(case) Jonathan Saboury (Mon Jan 28 2013 - 18:38:13 PST)
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file(jason) Jonathan Saboury (Mon Jan 28 2013 - 18:43:47 PST)
- [AMBER] patching problem amber12 Vaibhav Dixit (Mon Jan 28 2013 - 20:19:26 PST)
- [AMBER] How to calculate PMF using Jarzynski’s equality? Cuiyl (Tue Jan 29 2013 - 00:34:27 PST)
- [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters Sanjib Paul (Tue Jan 29 2013 - 04:22:28 PST)
- [AMBER] Fwd: Regarding the problem with ligand conformation aneesh cna (Tue Jan 29 2013 - 05:12:38 PST)
- [AMBER] Pocket Volume Calculation Soumya Lipsa Rath (Tue Jan 29 2013 - 06:29:40 PST)
- [AMBER] CPPTRAJ Parmstrip error HM (Tue Jan 29 2013 - 08:20:00 PST)
- [AMBER] coexisting nab and nab openmp Scott Brozell (Tue Jan 29 2013 - 15:19:14 PST)
- [AMBER] saving PDB with chain ID in leap aneesh cna (Wed Jan 30 2013 - 02:59:59 PST)
- [AMBER] error while running mmpbsa.py in amber12 Alessandro Contini (Wed Jan 30 2013 - 03:47:41 PST)
- [AMBER] How to save secondary structure gnuplot as image HM (Wed Jan 30 2013 - 06:13:27 PST)
- [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead Marko Wehle (Wed Jan 30 2013 - 07:29:20 PST)
- [AMBER] mmPBSA.py: mmGBSA and solute dielectric constant psu4.uic.edu (Wed Jan 30 2013 - 18:01:26 PST)
- [AMBER] two fold difference between MMPBSA.py and NAMDenergy plugin in vmd 1.9.1 dbaogen (Wed Jan 30 2013 - 22:10:55 PST)
- [AMBER] does iwrap=1 work with dodecahedra ? Thomas Evangelidis (Thu Jan 31 2013 - 04:24:13 PST)
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Alessandro Contini (Thu Jan 31 2013 - 08:45:40 PST)
- [AMBER] Sampling of a point by a molecule while keeping the relative position of the molecule unchanged in TMD Sajeewa Pemasinghe (Thu Jan 31 2013 - 10:03:37 PST)
- [AMBER] pmemd.cuda compilation with amber12 Vivek Shankar Bharadwaj (Thu Jan 31 2013 - 14:41:34 PST)
- [AMBER] mmPBSA and restraint energy decreasing psu4.uic.edu (Thu Jan 31 2013 - 15:37:29 PST)
- Re: [AMBER] Problem using solvatebox for large, linear peptide David A Case (Thu Jan 31 2013 - 18:44:38 PST)
- Re: [AMBER] scaling problem in RADIAL of CPPTRAJ Daniel Roe (Thu Jan 31 2013 - 20:37:30 PST)
- Last message date: Thu Jan 31 2013 - 21:00:02 PST
- Archived on: Fri Nov 15 2024 - 05:54:46 PST
