Amber Archive Dec 2012 by thread
- [AMBER] Atom rename after RESP fitting by antechamber Liu Denis (Fri Nov 30 2012 - 19:17:16 PST)
- [AMBER] forcefield for PLP Bala Subramani (Sat Dec 01 2012 - 01:07:49 PST)
- Re: [AMBER] problem in loading pdb in xleap Jason Swails (Sat Dec 01 2012 - 06:35:14 PST)
- [AMBER] problem with cpptraj hbond action Marek Maly (Sat Dec 01 2012 - 17:12:22 PST)
- Re: [AMBER] sander.MPI Fabian Glaser (Sun Dec 02 2012 - 04:59:58 PST)
- [AMBER] using D-amino acids Thomas Evangelidis (Sun Dec 02 2012 - 14:59:25 PST)
- Re: [AMBER] Porcupine_Plots_Script monica.imtech.res.in (Sun Dec 02 2012 - 20:30:13 PST)
- [AMBER] Density in QM/MM marawan hussain (Mon Dec 03 2012 - 01:02:48 PST)
- [AMBER] rmsd of trajectories with different no. of residues in same protein? Vaibhav Dixit (Mon Dec 03 2012 - 03:16:28 PST)
- [AMBER] need assistance to generate forcefield for Pyridoxal phosphate BALA SUBRAMANI G L (Mon Dec 03 2012 - 04:03:31 PST)
- [AMBER] pbsa forces printout from sander (amber12) Dr. Holger Kruse (Mon Dec 03 2012 - 07:08:34 PST)
- [AMBER] Accelerated MD Shafinaz Chowdhury (Mon Dec 03 2012 - 10:43:03 PST)
- [AMBER] What are Inner Sp2 carbons and non-pure aromatic systems? Yun Shi (Mon Dec 03 2012 - 10:53:17 PST)
- [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 14 CB 2C Rahul Banerjee (Mon Dec 03 2012 - 11:40:52 PST)
- [AMBER] Questions regarding mmpbsa... Jonathan Gough (Mon Dec 03 2012 - 12:29:15 PST)
- Re: [AMBER] The differences of MMPBSA calculations between AT1.5and AT12, especially in PBSA solvation model. Ray Luo, Ph.D. (Mon Dec 03 2012 - 12:34:43 PST)
- [AMBER] Problem while running MMPBSA - stuck Jonathan Gough (Mon Dec 03 2012 - 15:13:08 PST)
- [AMBER] Lys-bound retinal parameters? Scarlett Dong (Mon Dec 03 2012 - 15:31:07 PST)
- [AMBER] iapbs installation Miguel Ortiz Lombardía (Tue Dec 04 2012 - 01:52:17 PST)
- [AMBER] ptraj centering problem Fabian Glaser (Tue Dec 04 2012 - 07:56:59 PST)
- [AMBER] EGB discrepancy between sander and pmemd Eng H Yap (Tue Dec 04 2012 - 08:02:18 PST)
- [AMBER] problem in solvation of binding pocket Zhenquan Hu (Tue Dec 04 2012 - 08:42:31 PST)
- [AMBER] amber on intel Xeon 5680 Marcela Madrid (Tue Dec 04 2012 - 15:48:48 PST)
- [AMBER] 回复： Re: problem in solvation of binding pocket zhenquan hu (Tue Dec 04 2012 - 15:58:35 PST)
- [AMBER] Patching Error occurred while Bugfixing Anogna (Tue Dec 04 2012 - 23:23:14 PST)
- [AMBER] Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module file Thomas Evangelidis (Wed Dec 05 2012 - 03:52:03 PST)
- [AMBER] NMR Order Parameter Restraints Brown, Kyle (Wed Dec 05 2012 - 08:52:22 PST)
- [AMBER] FW: EGB discrepancy between sander and pmemd Eng H Yap (Wed Dec 05 2012 - 08:56:30 PST)
- Re: [AMBER] problem with closest in cpptraj: trajout still writes all solvent molecules Marc van der Kamp (Wed Dec 05 2012 - 12:22:16 PST)
- Re: [AMBER] imaging issues during RMSF Daniel Roe (Wed Dec 05 2012 - 13:48:58 PST)
- [AMBER] How to Run MD of Glycol Nucleic Acid (GNA) Mu Xia (Thu Dec 06 2012 - 01:02:07 PST)
- [AMBER] ERROR: Regenerate prmtop file with bondi radii Thomas Evangelidis (Thu Dec 06 2012 - 07:55:31 PST)
- [AMBER] Call for paper Siavoush Dastmalchi (Thu Dec 06 2012 - 12:53:21 PST)
- [AMBER] nvidia driver installation problem Sanjib Paul (Thu Dec 06 2012 - 22:30:54 PST)
- [AMBER] Error in MM-PBSA execution Anogna (Thu Dec 06 2012 - 22:32:14 PST)
- [AMBER] developing parameters for HID-CU osalo.abo.fi (Fri Dec 07 2012 - 00:05:03 PST)
- [AMBER] Error of restraint of atom using "pmemd" program in Amber 11 dbaogen (Fri Dec 07 2012 - 02:42:35 PST)
- [AMBER] Getting error messages during testing the installation. Sanjib Paul (Fri Dec 07 2012 - 05:00:08 PST)
- [AMBER] problem with imposing planarity to a N3P3 ring Giovanni Pavan (Fri Dec 07 2012 - 10:36:08 PST)
- [AMBER] FATAL: Atom does not have a type. Jonathan Gough (Fri Dec 07 2012 - 12:47:36 PST)
- [AMBER] how to speed up implicit solvent simulation with infinite cutoff Thomas Evangelidis (Sat Dec 08 2012 - 08:17:40 PST)
- [AMBER] compare Delphi result using MMPBSA.py.MPI psu4.uic.edu (Sat Dec 08 2012 - 11:02:22 PST)
- [AMBER] For TI do corresponding same atoms in ligand pairs need to have the same charge Yulin Huang (Sat Dec 08 2012 - 12:15:34 PST)
- [AMBER] DNA planarity constraints in AMBER 丁鹏飞 (Sat Dec 08 2012 - 19:14:10 PST)
- [AMBER] Pairwise interaction energy between resiudes using MMPBSA.py in Amber 11 dbaogen (Sat Dec 08 2012 - 22:08:39 PST)
- [AMBER] where is .in file for AMBER GAFF lipids? Albert (Sun Dec 09 2012 - 06:18:06 PST)
- [AMBER] solvent accessible volume vs Nihal Korkmaz (Sun Dec 09 2012 - 20:08:14 PST)
- [AMBER] Any possibility of scripting in tleap? Sajeewa Pemasinghe (Sun Dec 09 2012 - 23:03:08 PST)
- [AMBER] enthalpy and sum of per residue energy decomposition not euqal Sangita Kachhap (Mon Dec 10 2012 - 01:09:21 PST)
- [AMBER] Should I optimize the structure before obtaining the RESP charges? Mu Xia (Mon Dec 10 2012 - 01:13:43 PST)
- [AMBER] Force calculation during SMD (jar=1): I'm looking for insights Jan-Philip Gehrcke (Mon Dec 10 2012 - 02:31:13 PST)
- [AMBER] Amber12 with Plumed Rajeswari A. (Mon Dec 10 2012 - 02:32:00 PST)
- [AMBER] Problem with molecule containing sulfonic acid substitution Bernhard Poll (Mon Dec 10 2012 - 02:32:27 PST)
- [AMBER] prmtop file Chandrasekaran, Suryanarayanan (Mon Dec 10 2012 - 04:04:46 PST)
- [AMBER] Problem in Nmode entropy calculation Mu Xia (Mon Dec 10 2012 - 08:02:52 PST)
- [AMBER] GAFF atom types for the headgroup of the LDAO surfactant ABEL Stephane 175950 (Mon Dec 10 2012 - 08:43:17 PST)
- [AMBER] NAB nmode memory requirements Ryan Pavlovicz (Mon Dec 10 2012 - 09:43:19 PST)
- [AMBER] Antechamber with jaguar outputs eneas.usal.es (Mon Dec 10 2012 - 14:53:26 PST)
- [AMBER] ptraj vs cpptraj: optimal clusters number choice adarm.nencki.gov.pl (Mon Dec 10 2012 - 16:03:48 PST)
- [AMBER] amber workshop question psu4.uic.edu (Mon Dec 10 2012 - 16:57:19 PST)
- [AMBER] prmtop file Chandrasekaran, Suryanarayanan (Mon Dec 10 2012 - 16:35:56 PST)
- [AMBER] conditional restraints Thomas Evangelidis (Tue Dec 11 2012 - 00:31:18 PST)
- [AMBER] MMGBSA result difference from whether use &decomp or not Liu Denis (Tue Dec 11 2012 - 00:49:06 PST)
- [AMBER] prmtop file Chandrasekaran, Suryanarayanan (Tue Dec 11 2012 - 02:01:51 PST)
- [AMBER] calculating single side-chain RMSF with ptraj / cpptraj Marc van der Kamp (Tue Dec 11 2012 - 07:00:57 PST)
- Re: [AMBER] RMSD reported in lmod output Wong, Sergio E. (Tue Dec 11 2012 - 11:37:43 PST)
- [AMBER] Starting Coordinates Switched? Ismail, Mohd F. (Tue Dec 11 2012 - 14:42:05 PST)
- [AMBER] MMPBSA.py.MPI import error marawan hussain (Wed Dec 12 2012 - 00:14:23 PST)
- [AMBER] About restraint on GPU 王军 (Wed Dec 12 2012 - 00:37:35 PST)
- [AMBER] If scee is no longer in Amber11, can I simply remove it? Amparo Garcia Lopez (Wed Dec 12 2012 - 03:19:38 PST)
- [AMBER] Brookhaven National Labs Jonathan Gough (Wed Dec 12 2012 - 04:53:45 PST)
- [AMBER] Antechamber with jaguar outputs eneas.usal.es (Wed Dec 12 2012 - 06:35:49 PST)
- [AMBER] MMPBSA.py.MPI: multiple trajectory mmPBSA question psu4.uic.edu (Wed Dec 12 2012 - 10:00:14 PST)
- [AMBER] cpptraj rmsd, 'perrescenter' clarification Marcus Arieno (Wed Dec 12 2012 - 12:22:09 PST)
- [AMBER] MMPBSA.py.MPI import error marawan hussain (Wed Dec 12 2012 - 18:08:42 PST)
- [AMBER] QM/MM AMBER-ORCA repulsion marawan hussain (Wed Dec 12 2012 - 22:07:31 PST)
- [AMBER] extract velocity from traj files Vijay Manickam Achari (Thu Dec 13 2012 - 01:08:20 PST)
- [AMBER] Steered Molecular Dynamics: Question George Tzotzos (Thu Dec 13 2012 - 03:35:31 PST)
- [AMBER] Ligand parameterization in AMOEBA to use in AMBER Jagur Lambix (Thu Dec 13 2012 - 14:29:04 PST)
- [AMBER] QM/MM AMBER-ORCA repulsion marawan hussain (Thu Dec 13 2012 - 19:47:45 PST)
- [AMBER] FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Thu Dec 13 2012 - 23:38:11 PST)
- [AMBER] Building peptides in a random conformation in AMBER.... Shashidhar Rao (Fri Dec 14 2012 - 11:20:56 PST)
- [AMBER] how to define solvated box dimensions Thomas Evangelidis (Fri Dec 14 2012 - 15:02:00 PST)
- [AMBER] Extraction of Box dimensions from MD Trajectories Jagur Lambix (Fri Dec 14 2012 - 15:20:10 PST)
- [AMBER] Higher values for polar contribution RANAJIT SHINDE (Sat Dec 15 2012 - 04:23:01 PST)
- [AMBER] branched disaccharide in leap Krisztina Feher (Sat Dec 15 2012 - 12:25:15 PST)
- [AMBER] Theoretical question about mmpbsa/docking energy values Chris Chris (Sat Dec 15 2012 - 13:21:44 PST)
- [AMBER] H-REMD, pmemd fails to calculate potential energy of neighbor coordinates Jiri Wiesner (Sat Dec 15 2012 - 20:26:41 PST)
- [AMBER] QM/MM AMBER-ORCA repulsion marawan hussain (Sat Dec 15 2012 - 21:16:14 PST)
- [AMBER] cannot use more than one node Fabian Glaser (Sun Dec 16 2012 - 00:26:13 PST)
- [AMBER] Problems with restart file - coordinates values are too high tommaso.casalini.mail.polimi.it (Sun Dec 16 2012 - 04:53:51 PST)
- [AMBER] Ethanol as solvent Chinthaka Ratnaweera (Sun Dec 16 2012 - 21:14:01 PST)
- [AMBER] why removal of terminal phosphate group is required? Asmita Gupta (Sun Dec 16 2012 - 22:22:39 PST)
- [AMBER] some problems in getting the parameters of GLYCAM in Leap deathsnake1991 (Sun Dec 16 2012 - 22:48:21 PST)
- [AMBER] AMBER to TINKER style trajectory Indrajit Deb (Mon Dec 17 2012 - 01:58:34 PST)
- [AMBER] problem to install amber9 in a cluster. Sindrila Dutta banik (Mon Dec 17 2012 - 03:39:35 PST)
- [AMBER] problem related to the amber9 installation Sindrila Dutta banik (Mon Dec 17 2012 - 04:06:57 PST)
- [AMBER] problem related to the amber9 installation Sindrila Dutta banik (Mon Dec 17 2012 - 04:11:11 PST)
- [AMBER] calculating velocity auto-correlation function Vijay Manickam Achari (Mon Dec 17 2012 - 04:27:25 PST)
- Re: [AMBER] Fwd: FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Mon Dec 17 2012 - 12:32:21 PST)
- [AMBER] alanine scanning Jonathan Gough (Mon Dec 17 2012 - 14:01:52 PST)
- Re: [AMBER] lmod error with large number of degrees of freedom Wong, Sergio E. (Mon Dec 17 2012 - 16:04:17 PST)
- [AMBER] Antechamber with jaguar outputs eneas.usal.es (Tue Dec 18 2012 - 02:24:41 PST)
- [AMBER] How to disable Coulomb interactions between two group of atoms Shenglong Wang (Tue Dec 18 2012 - 06:43:04 PST)
- [AMBER] getting warning when loading PDB created in amber9 in amber12 .. Vijay Manickam Achari (Tue Dec 18 2012 - 08:47:23 PST)
- [AMBER] deprotonation with SHAKE Antonija Tomić (Wed Dec 19 2012 - 05:32:11 PST)
- [AMBER] MMPBSA - GB is negative, but PB is positive? what am I missing? Jonathan Gough (Wed Dec 19 2012 - 08:20:32 PST)
- [AMBER] water box of specific dimensions Manikanthan Bhavaraju (Wed Dec 19 2012 - 18:58:01 PST)
- [AMBER] cluster analysis groups conformers without doing alignment Sun (Thu Dec 20 2012 - 00:38:33 PST)
- [AMBER] how to define head and tail for several residues? osalo.abo.fi (Thu Dec 20 2012 - 01:58:36 PST)
- [AMBER] problem in applying patches in AMBER12 and AMBERTools12 Prabu Manoharan (Thu Dec 20 2012 - 03:02:06 PST)
- [AMBER] how to use cpptraj in AMBER10 or 11 to generate new topology file HM (Thu Dec 20 2012 - 06:36:07 PST)
- [AMBER] analyzing DESMOND MD trajectories in cpptraj... Shashidhar Rao (Thu Dec 20 2012 - 11:01:44 PST)
- [AMBER] stripping water molecules except few ones (384-408) HM (Fri Dec 21 2012 - 02:19:37 PST)
- [AMBER] MD Average pdb edu troche (Fri Dec 21 2012 - 04:26:11 PST)
- [AMBER] voltage for membrane? Albert (Sun Dec 23 2012 - 01:30:46 PST)
- [AMBER] atom type john Kerk (Sun Dec 23 2012 - 01:47:49 PST)
- [AMBER] PBC value become small at Z direction Vijay Manickam Achari (Sun Dec 23 2012 - 21:29:02 PST)
- [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Vijay Manickam Achari (Sun Dec 23 2012 - 22:23:42 PST)
- [AMBER] problem with parallel installation of amber12 - MPI_COMM_WORLD Amparo Garcia Lopez (Mon Dec 24 2012 - 05:50:32 PST)
- [AMBER] query regarding two different restrain on protein residues HM (Mon Dec 24 2012 - 13:57:14 PST)
- [AMBER] restart file ERROR: I could not understand line 71821 Thomas Evangelidis (Tue Dec 25 2012 - 03:00:04 PST)
- [AMBER] calcium ion in AMBER HM (Tue Dec 25 2012 - 12:04:32 PST)
- [AMBER] movement of PBC Vijay Manickam Achari (Tue Dec 25 2012 - 22:12:02 PST)
- [AMBER] N-Methylacetamide-molecule-force field Subrata Paul (Wed Dec 26 2012 - 04:51:01 PST)
- [AMBER] Fwd: difference between GLYCAM_06 and GLYCAM_06h Subrata Paul (Wed Dec 26 2012 - 05:01:15 PST)
- [AMBER] Amber LES.MPI crash Kirill Nuzhdin (Wed Dec 26 2012 - 10:25:09 PST)
- [AMBER] GLYCAM_06 & GLYCAM_06h Subrata Paul (Wed Dec 26 2012 - 22:10:41 PST)
- [AMBER] MMPBSA Alanine Scanning AttrubuteError BERGY (Thu Dec 27 2012 - 04:12:31 PST)
- [AMBER] Is GTX580/GTX680 compatible with the sever motherboards? Mu Xia (Thu Dec 27 2012 - 22:54:11 PST)
- [AMBER] Question in umbrella sampling Sajeewa Pemasinghe (Fri Dec 28 2012 - 06:08:39 PST)
- [AMBER] MD simulation Jeremy AHHH (Fri Dec 28 2012 - 10:28:10 PST)
- [AMBER] NPT and NVE Energy Ismail, Mohd F. (Fri Dec 28 2012 - 13:06:43 PST)
- [AMBER] TI-charge removal step Nihal Korkmaz (Fri Dec 28 2012 - 15:46:46 PST)
- [AMBER] question about adaptive QM/MM yeqing2.ustc.edu.cn (Sat Dec 29 2012 - 00:29:47 PST)
- Last message date: Mon Dec 31 2012 - 15:00:03 PST
- Archived on: Mon Apr 22 2024 - 05:54:35 PDT
