Amber Archive Jan 2014 by thread
- [AMBER] how to calculate diffusion coefficient ? Sohag Biswas (Tue Dec 31 2013 - 19:31:06 PST)
- Re: [AMBER] RMSD vs RMSF vs nofit-RMSD Nitin Sharma (Wed Jan 01 2014 - 02:51:27 PST)
- Re: [AMBER] AMBER Asfa Ali (Wed Jan 01 2014 - 06:23:35 PST)
- Re: [AMBER] SQM seems to run out of memory? Jonathan Saboury (Wed Jan 01 2014 - 12:51:57 PST)
- [AMBER] request for help in radial command Robin Jain (Thu Jan 02 2014 - 00:42:29 PST)
- [AMBER] binding free energy analysis Nitin Sharma (Thu Jan 02 2014 - 02:48:49 PST)
- [AMBER] Binding free energy for two small polymers? X Sun (Thu Jan 02 2014 - 11:21:05 PST)
- [AMBER] Langevin Dynamics on selected atoms? Jose Borreguero (Thu Jan 02 2014 - 12:21:41 PST)
- [AMBER] OSX Mavericks: Failure in parallel installation of Amber12 George Tzotzos (Fri Jan 03 2014 - 03:13:18 PST)
- [AMBER] atoms with non-standard hybridization Ivanov, Maxim (Fri Jan 03 2014 - 11:30:25 PST)
- [AMBER] cuda job not working Jio M (Fri Jan 03 2014 - 15:26:46 PST)
- [AMBER] antechamber charge method Zahra Khatti (Fri Jan 03 2014 - 22:44:52 PST)
- [AMBER] ANN: MDTraj 0.5.0 Release Robert (Fri Jan 03 2014 - 23:19:59 PST)
- [AMBER] antechamber charge method? Zahra Khatti (Sat Jan 04 2014 - 06:47:28 PST)
- [AMBER] antechamber charge method Zahra Khatti (Sat Jan 04 2014 - 06:53:53 PST)
- [AMBER] standard for atomic fluctioantion Nitin Sharma (Sat Jan 04 2014 - 09:09:42 PST)
- [AMBER] Dynamics with R_OF_GYRATION Nihal Korkmaz (Sat Jan 04 2014 - 20:42:09 PST)
- [AMBER] not reading a second dihedral term in frcmod Allen, Scott Edward (Sun Jan 05 2014 - 16:52:45 PST)
- [AMBER] Calculating the bending angle of a DNA sequence Yip Yew Mun (Mon Jan 06 2014 - 01:55:32 PST)
- [AMBER] bondbydistance Sourav Purohit (Mon Jan 06 2014 - 09:27:00 PST)
- [AMBER] bondbydiatance Sourav Purohit (Mon Jan 06 2014 - 09:42:57 PST)
- [AMBER] Error with cpptraj strip and MMGBSA.py Brian Radak (Mon Jan 06 2014 - 12:28:57 PST)
- [AMBER] PCA/ essential dynamics Andre C. Stiel (Tue Jan 07 2014 - 06:53:55 PST)
- [AMBER] parameters from frcmod not overwriting gaff.dat Allen, Scott Edward (Tue Jan 07 2014 - 09:11:24 PST)
- [AMBER] calculating MSD by correcting the center-of-mass-motion Vijay Manickam Achari (Tue Jan 07 2014 - 23:45:07 PST)
- [AMBER] Charge calculation methods for RED server Yip Yew Mun (Wed Jan 08 2014 - 01:56:04 PST)
- [AMBER] am1bcc method charge Zahra Khatti (Wed Jan 08 2014 - 02:44:33 PST)
- [AMBER] Visualisation of metal ions ligand after tleap Mahendra B Thapa (Wed Jan 08 2014 - 12:42:02 PST)
- [AMBER] Applying nmr restraints: Radius of gyration or COM distance for large groups of atoms Nihal Korkmaz (Wed Jan 08 2014 - 13:15:33 PST)
- [AMBER] Modelling stereochemical molecule with "R" and "S" type. Vijay Manickam Achari (Wed Jan 08 2014 - 19:48:28 PST)
- [AMBER] Is the RMSD using ptraj normalized with respect to residues ?? Himanshu Joshi (Wed Jan 08 2014 - 20:25:14 PST)
- [AMBER] Error Nmode entropy calculation Nitin Sharma (Wed Jan 08 2014 - 22:39:33 PST)
- [AMBER] "image" command with "familiar" option kurisaki (Thu Jan 09 2014 - 01:03:13 PST)
- [AMBER] R.E.D, alkene isostere, Gly-Pro, P9501 Cecilia Lindgren (Thu Jan 09 2014 - 02:28:40 PST)
- Re: [AMBER] Problem when calculating MMPBSA (Jason Swails) Jason Swails (Thu Jan 09 2014 - 11:47:28 PST)
- [AMBER] Utility to compute the auto-correlation function for a dihedral angle? Jose Borreguero (Thu Jan 09 2014 - 12:02:19 PST)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure filip fratev (Fri Jan 10 2014 - 01:48:49 PST)
- [AMBER] How to generate boron atom paramaters? Mengyuan Zhu (Fri Jan 10 2014 - 08:15:32 PST)
- [AMBER] restart for second time Saeed Nasiri (Fri Jan 10 2014 - 11:07:43 PST)
- [AMBER] request for help Robin Jain (Sat Jan 11 2014 - 00:54:36 PST)
- [AMBER] Building parameter files for a zinc finger Yip Yew Mun (Sat Jan 11 2014 - 02:47:41 PST)
- [AMBER] Creating an frcmod file for zinc finger Yip Yew Mun (Sat Jan 11 2014 - 04:08:26 PST)
- [AMBER] restart for second time Saeed Nasiri (Sat Jan 11 2014 - 21:26:46 PST)
- [AMBER] Problems on IRED analyses for order parameter Ye Wei (Sun Jan 12 2014 - 06:37:33 PST)
- [AMBER] ionic liquid simulation Saeed Nasiri (Sun Jan 12 2014 - 09:24:16 PST)
- [AMBER] restarting the MD Saeed Nasiri (Sun Jan 12 2014 - 22:54:07 PST)
- [AMBER] Antechamber Segmentation fault (core dumped) Arun Kumar Somavarapu (Sun Jan 12 2014 - 23:27:38 PST)
- [AMBER] request for help me in hydrogen bond analysis Robin Jain (Mon Jan 13 2014 - 00:28:37 PST)
- [AMBER] polymers interaction Zhuang, Yu (Mon Jan 13 2014 - 04:58:32 PST)
- Re: [AMBER] makeDIST command disfuntion Jan Zalesak (Mon Jan 13 2014 - 12:10:26 PST)
- [AMBER] Converting DL_POLY OPLS dihedral ff function to AMBER format Parker, Qamreen (Tue Jan 14 2014 - 02:06:37 PST)
- [AMBER] iwrap=1 or netcdf Jio M (Tue Jan 14 2014 - 05:10:13 PST)
- [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Kanin Wichapong (Tue Jan 14 2014 - 06:24:47 PST)
- [AMBER] Query about next amber release Kshatresh Dutta Dubey (Wed Jan 15 2014 - 03:20:47 PST)
- [AMBER] question for pre-treat protein model Zhuang, Yu (Wed Jan 15 2014 - 06:17:27 PST)
- [AMBER] cpptraj density routine Dickson, Callum J (Wed Jan 15 2014 - 07:01:14 PST)
- [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap 肖立 (Wed Jan 15 2014 - 11:24:36 PST)
- [AMBER] stfcdiffusion error Diego de paula (Wed Jan 15 2014 - 18:43:46 PST)
- [AMBER] IGB doubt Sushi Shilpa (Wed Jan 15 2014 - 20:06:00 PST)
- [AMBER] How to make a nonequilibrium molecular dynamics on an external force field like electromagnetic or microwave? 张明焜 (Thu Jan 16 2014 - 18:06:07 PST)
- [AMBER] order params Jio M (Fri Jan 17 2014 - 08:16:34 PST)
- [AMBER] Free energy workshop in May, 2014 David A Case (Fri Jan 17 2014 - 15:21:07 PST)
- [AMBER] error in naming list problem Sushi Shilpa (Sun Jan 19 2014 - 20:21:22 PST)
- [AMBER] output of radius of gyration Zhuang, Yu (Mon Jan 20 2014 - 03:13:00 PST)
- [AMBER] append more nucleotides to solution structure Asaminew Haile (Mon Jan 20 2014 - 09:09:09 PST)
- [AMBER] restart MD Saeed Nasiri (Mon Jan 20 2014 - 12:42:30 PST)
- [AMBER] rmsd with fit Jio M (Mon Jan 20 2014 - 15:46:46 PST)
- [AMBER] Creating a restart file from a trajectory file Ahmed Ayoub (Tue Jan 21 2014 - 00:45:49 PST)
- [AMBER] AMBER-cis-trans conversion Gözde YALÇIN (Tue Jan 21 2014 - 07:19:31 PST)
- [AMBER] Current system recommendations Jonathan Sheehan (Tue Jan 21 2014 - 14:06:23 PST)
- [AMBER] Question Eric Smoll (Tue Jan 21 2014 - 15:26:39 PST)
- [AMBER] Compiling Amber 12 using IBM XL compilers - fixed versus free format Fortran Ben Roberts (Tue Jan 21 2014 - 17:49:10 PST)
- Re: [AMBER] Problem when calculating MMPBSA dongying0512 (Tue Jan 21 2014 - 18:31:54 PST)
- [AMBER] fluctuation of pressure during MD Zhuang, Yu (Wed Jan 22 2014 - 00:53:45 PST)
- [AMBER] Oscillating electric fields Bernhard Reuter (Wed Jan 22 2014 - 04:10:32 PST)
- [AMBER] AmberTools vs. Amber: Installation practice subject to different licenses Sternberg, Michael G. (Wed Jan 22 2014 - 15:46:30 PST)
- [AMBER] simulation output Saeed Nasiri (Wed Jan 22 2014 - 22:56:06 PST)
- [AMBER] PIMD_pure_QM_EXTERN Jheng Wei Li (Wed Jan 22 2014 - 23:54:35 PST)
- [AMBER] Release of FESetup 1.0 Hannes Loeffler (Thu Jan 23 2014 - 03:03:17 PST)
- [AMBER] restart MD Saeed Nasiri (Thu Jan 23 2014 - 03:33:47 PST)
- [AMBER] input preparation esther nehu (Thu Jan 23 2014 - 04:49:13 PST)
- [AMBER] checkpoint on Amber within batch job Zhuang, Yu (Thu Jan 23 2014 - 05:33:53 PST)
- [AMBER] SPAM: A Simple Approach for Profiling Bound Water Molecules Sergey Samsonov (Thu Jan 23 2014 - 05:57:18 PST)
- [AMBER] correct way of imaging for rdf Jio M (Thu Jan 23 2014 - 08:06:19 PST)
- [AMBER] Can we solvate the box with ligand Ayesha Fatima (Thu Jan 23 2014 - 23:42:26 PST)
- [AMBER] mpi-pmemd Saeed Nasiri (Fri Jan 24 2014 - 01:00:07 PST)
- Re: [AMBER] status of the Amber lipid framework? Igor Marques (Fri Jan 24 2014 - 09:12:33 PST)
- [AMBER] MMPBSA bharat lakhani (Fri Jan 24 2014 - 11:24:29 PST)
- [AMBER] effect of born radii on the binding energies of a protein-ligand system Manikanthan Bhavaraju (Fri Jan 24 2014 - 12:58:06 PST)
- [AMBER] REMD on one GPU Milo Westler (Fri Jan 24 2014 - 13:28:17 PST)
- [AMBER] Error generating prmtop file for protein with NAD+ Prema Mallipeddi (Fri Jan 24 2014 - 13:43:16 PST)
- [AMBER] Ptraj's "NO ATOMS DETECTED" problem Yip Yew Mun (Fri Jan 24 2014 - 17:36:17 PST)
- [AMBER] enquiry regarding latest Amber Ved Prakash (Sat Jan 25 2014 - 08:14:48 PST)
- [AMBER] no output file when running espgen Kim TaeHwan (Sun Jan 26 2014 - 00:47:00 PST)
- [AMBER] How to make a nonequilibrium molecular dynamics on an external force field like electromagnetic or microwave? 张明焜 (Sun Jan 26 2014 - 01:18:18 PST)
- [AMBER] Unable to read coords from rst Yip Yew Mun (Sun Jan 26 2014 - 19:04:39 PST)
- [AMBER] Creating Non-canonical Structures in NAB Robyn Ayscue (Sun Jan 26 2014 - 20:07:24 PST)
- [AMBER] question . mirage (Mon Jan 27 2014 - 05:04:23 PST)
- [AMBER] tracking ions in protein channel Jio M (Mon Jan 27 2014 - 06:15:38 PST)
- [AMBER] internal energy in TI decomposition Schackert Nico (Mon Jan 27 2014 - 07:13:28 PST)
- [AMBER] Explicit solvent constant pH simulation Logan Ahlstrom (Mon Jan 27 2014 - 08:40:04 PST)
- [AMBER] Indentified the cause - Error generating prmtop file for protein with NAD+ Prema Mallipeddi (Mon Jan 27 2014 - 11:10:10 PST)
- [AMBER] internal energy in TI decomposition Schackert Nico (Tue Jan 28 2014 - 01:18:51 PST)
- [AMBER] Number of cores for a parallel job FyD (Tue Jan 28 2014 - 04:29:01 PST)
- [AMBER] fun with units? Brian Radak (Tue Jan 28 2014 - 06:43:19 PST)
- [AMBER] amber12 GPU performance degrades? Guanglei Cui (Tue Jan 28 2014 - 08:37:07 PST)
- [AMBER] optimise ligand geomatry before MD Nitin Sharma (Tue Jan 28 2014 - 10:44:53 PST)
- [AMBER] Prep file is empty DEBOSTUTI GHOSHDASTIDAR (Wed Jan 29 2014 - 06:07:14 PST)
- [AMBER] Has anyone tested to newer nvidia drivers for linux? Matthew Wampole (Wed Jan 29 2014 - 07:43:12 PST)
- [AMBER] Fwd: Re: Prep file is empty FyD (Wed Jan 29 2014 - 23:25:21 PST)
- [AMBER] GTX 780: 8 file comparisons failed de Waal, Parker (Thu Jan 30 2014 - 15:36:47 PST)
- [AMBER] Accuracy of solvation free energy calculated by 3D-RISM n.ricky0204.gmail.com (Fri Jan 31 2014 - 03:07:02 PST)
- [AMBER] Problems with MM_GBSA Joachim Stump (Fri Jan 31 2014 - 05:18:31 PST)
- [AMBER] continuing runs with latest patched AMBER Jio M (Fri Jan 31 2014 - 09:24:26 PST)
- [AMBER] ATOMIC NUMBER section in prmtop file - Sustiva example rohitarora10.gmail.com (Fri Jan 31 2014 - 10:29:01 PST)
- [AMBER] VMD lipid in AMBER Rejwan (Fri Jan 31 2014 - 11:40:21 PST)
- [AMBER] Fwd: amber Jorgen Simonsen (Fri Jan 31 2014 - 21:25:38 PST)
- Last message date: Fri Jan 31 2014 - 21:30:02 PST
- Archived on: Wed Oct 30 2024 - 05:54:54 PDT
