Amber Archive Feb 2012 by thread
- Re: [AMBER] antechamber doesn't create mol2 file FyD (Tue Jan 31 2012 - 22:17:03 PST)
- [AMBER] MMPBSA problem Urszula Uciechowska (Tue Jan 31 2012 - 22:26:33 PST)
- [AMBER] about using MMPBSA Tan and Luo method in AMBER 11: discrepancy in ECAVITY values Therese Malliavin (Wed Feb 01 2012 - 00:48:36 PST)
- [AMBER] tLEaP Алексей Раевский (Wed Feb 01 2012 - 02:38:05 PST)
- [AMBER] Fw: rmsd input file Sel Ercan (Wed Feb 01 2012 - 02:47:36 PST)
- [AMBER] parm.frosst parameters thomas.fox.boehringer-ingelheim.com (Wed Feb 01 2012 - 07:32:24 PST)
- [AMBER] other makeDIST_RST issues Thomas Pochapsky (Wed Feb 01 2012 - 08:34:24 PST)
- [AMBER] Problems in ions in Amber11 TAEJIN KIM (Wed Feb 01 2012 - 11:11:30 PST)
- [AMBER] Multiple frcmod files in tleap: Do parameters come from the last frcmod file loaded? Joel Dockray (Wed Feb 01 2012 - 11:16:49 PST)
- [AMBER] need KDO prep file Camille Sultana (Wed Feb 01 2012 - 17:06:22 PST)
- Re: [AMBER] NMODE list index out of range error Sangeetha B (Wed Feb 01 2012 - 20:18:27 PST)
- [AMBER] [Fwd: Problems with ff99SB force field reading] vladanstefanovic.kg.ac.rs (Thu Feb 02 2012 - 08:05:59 PST)
- Re: [AMBER] makeDIST_RST command problem Olena Dobrovolska (Thu Feb 02 2012 - 08:13:42 PST)
- [AMBER] Ptraj - Multimodel PDB Segmentation Fault... Cihan Aydin (Thu Feb 02 2012 - 20:12:03 PST)
- [AMBER] AMBER11 installation Hirdesh Kumar (Thu Feb 02 2012 - 21:53:43 PST)
- [AMBER] regarding QM/MM simulation jani vinod (Fri Feb 03 2012 - 03:32:03 PST)
- [AMBER] error in .rst file creation abinayar.imsc.res.in (Fri Feb 03 2012 - 03:51:22 PST)
- [AMBER] PMEMD.CUDA.MPI PME tests/Benchmarks Martin Peters (Fri Feb 03 2012 - 07:08:46 PST)
- [AMBER] fail to compile Amber 9 with intel/10.1 + openmpi/1.2.4 Yubo Fan (Fri Feb 03 2012 - 08:03:51 PST)
- [AMBER] ptraj to make NMR structure ensemble Charles Johnson (Fri Feb 03 2012 - 11:26:55 PST)
- [AMBER] Amber11 Installation Error Hirdesh Kumar (Sat Feb 04 2012 - 00:35:26 PST)
- [AMBER] Fwd: Re: : about using MMPBSA Tan and Luo method in AMBER 11: discrepancy in ECAVITY values Holger Gohlke (Sat Feb 04 2012 - 01:34:53 PST)
- [AMBER] Deprotonated Tyrosine Thomas Exner (Sat Feb 04 2012 - 07:35:21 PST)
- [AMBER] RNA/Protein Interaction amir abbasi (Sat Feb 04 2012 - 13:53:39 PST)
- [AMBER] mmpbsa Sel Ercan (Sat Feb 04 2012 - 17:05:08 PST)
- [AMBER] GL4 at C-terminal kurisaki (Sun Feb 05 2012 - 04:56:36 PST)
- [AMBER] Fwd: [q4md-fft] Constraint during geometry optimization FyD (Sun Feb 05 2012 - 11:21:06 PST)
- [AMBER] MMPBSA entropy calculations ASSERTion ' ier == 0 ' failed in nmode.f at line 114. ? Urszula Uciechowska (Sun Feb 05 2012 - 12:50:54 PST)
- [AMBER] Error during extending the simulations... Rajendra Sharma (Sun Feb 05 2012 - 18:06:16 PST)
- [AMBER] cygwin-ambertools Алексей Раевский (Mon Feb 06 2012 - 00:08:39 PST)
- [AMBER] compilation of amber 11 + amber tools 1.5 with intel 12.1.2 Vlad Cojocaru (Mon Feb 06 2012 - 02:13:41 PST)
- [AMBER] Error in running energy minimization DEBOSTUTI GHOSHDASTIDAR (Mon Feb 06 2012 - 03:12:11 PST)
- [AMBER] NAB+fortran Daniel Hollas (Mon Feb 06 2012 - 03:20:09 PST)
- [AMBER] Charge calculation using RESP: MCPB kanika singal (Mon Feb 06 2012 - 04:06:04 PST)
- [AMBER] a general question about membrane simulation Albert (Mon Feb 06 2012 - 05:11:34 PST)
- [AMBER] loading of fullerene2160 gargi borgohai (Mon Feb 06 2012 - 05:15:50 PST)
- [AMBER] How to set the existing waters to be the cap molecules? liu junjun (Mon Feb 06 2012 - 06:22:49 PST)
- [AMBER] pmemd test failure when compiling with intel 12.1.2 Vlad Cojocaru (Mon Feb 06 2012 - 07:22:52 PST)
- [AMBER] TI: error in reading namelist cntrl leila karami (Mon Feb 06 2012 - 07:36:18 PST)
- [AMBER] HTML page explaining mm_pbsa.pl error messages available Nadine Homeyer (Mon Feb 06 2012 - 08:50:25 PST)
- [AMBER] force field Hydroxide ion iccy liu (Mon Feb 06 2012 - 10:59:25 PST)
- [AMBER] ante-MMPBSA error message:additional OXT atom Shuyi Cao (Mon Feb 06 2012 - 18:03:51 PST)
- [AMBER] Compile Amber 11 with IPP instead of OpenMPI Yubo Fan (Mon Feb 06 2012 - 19:37:57 PST)
- [AMBER] Does AMBER ignore CONECT information in pdb input? Chinh Su Tran To (Mon Feb 06 2012 - 20:05:04 PST)
- [AMBER] tleap: added ions are in close vicinity to protein Hirdesh Kumar (Mon Feb 06 2012 - 21:27:45 PST)
- [AMBER] Problems about dihedral restraint in umbrella sampling jylu (Mon Feb 06 2012 - 22:44:10 PST)
- [AMBER] query on .inpcrd file format abinayar.imsc.res.in (Tue Feb 07 2012 - 01:25:00 PST)
- [AMBER] Sander with NMROPT Rahul Banerjee (Tue Feb 07 2012 - 07:19:54 PST)
- [AMBER] Force Field Parameterization -- Torsion Potentials Ryan Pavlovicz (Tue Feb 07 2012 - 07:40:05 PST)
- [AMBER] AMBER minimization Olena Dobrovolska (Tue Feb 07 2012 - 08:19:43 PST)
- [AMBER] Charge calculation using RESP: MCPB kanika singal (Tue Feb 07 2012 - 08:45:54 PST)
- [AMBER] Stripping hydrogens etc. from the prmtop? Cihan Aydin (Tue Feb 07 2012 - 12:43:01 PST)
- [AMBER] error in tleap execution of loadpdb molguin.miners.utep.edu (Tue Feb 07 2012 - 22:09:48 PST)
- [AMBER] Problem with leaprc.ff99SB file sourcing vladanstefanovic.kg.ac.rs (Wed Feb 08 2012 - 02:11:57 PST)
- [AMBER] Error in running energy minimization DEBOSTUTI GHOSHDASTIDAR (Wed Feb 08 2012 - 02:18:47 PST)
- [AMBER] what do reprocessing steps do in md simulation? khaled bodoor (Wed Feb 08 2012 - 04:13:55 PST)
- [AMBER] about Ewald error estimate leila karami (Wed Feb 08 2012 - 04:19:55 PST)
- [AMBER] installation subrata paul (Wed Feb 08 2012 - 05:01:56 PST)
- Re: [AMBER] p2n file connectivity issue Steven M. Graham (Wed Feb 08 2012 - 08:00:48 PST)
- [AMBER] unit for SD in MMPBSa Urszula Uciechowska (Thu Feb 09 2012 - 00:33:22 PST)
- [AMBER] SD unit Urszula Uciechowska (Thu Feb 09 2012 - 02:49:55 PST)
- [AMBER] How to create a script to add two integers in bash shenna shearin (Thu Feb 09 2012 - 11:26:09 PST)
- [AMBER] Fwd: Residue Decomposition Sander Error Hirdesh Kumar (Thu Feb 09 2012 - 20:33:37 PST)
- [AMBER] Announcement: 2012 summer intern position at GSK Guanglei Cui (Fri Feb 10 2012 - 12:59:32 PST)
- [AMBER] a question about double bond in R.E.D Albert (Sat Feb 11 2012 - 21:52:02 PST)
- [AMBER] md stopping in TI calculation leila karami (Sun Feb 12 2012 - 04:11:06 PST)
- [AMBER] md stopping in TI calculation leila karami (Sun Feb 12 2012 - 06:07:46 PST)
- [AMBER] bond breaking amir abbasi (Sun Feb 12 2012 - 10:38:26 PST)
- [AMBER] Generating topology files for non standard amino acid residue Matthew D Antalek (Sun Feb 12 2012 - 18:41:19 PST)
- [AMBER] Amber 12 & Amoeba Ismail, Mohd F. (Sun Feb 12 2012 - 20:18:47 PST)
- [AMBER] AMBER QM/MM Coordinate resetting (SHAKE) cannot be accomplished tonghf (Sun Feb 12 2012 - 21:08:26 PST)
- [AMBER] use Restrain mask function in PMEMD Muhammad Khaled Tumbi (Mon Feb 13 2012 - 01:15:49 PST)
- [AMBER] dicrepancy of percentage nonbonded calculation between 2 and 1 node setyanto md (Mon Feb 13 2012 - 02:31:31 PST)
- [AMBER] MMPBSA query Soumya Lipsa Rath (Mon Feb 13 2012 - 04:20:31 PST)
- [AMBER] Water models in prmtop files Peter Eastman (Mon Feb 13 2012 - 11:33:09 PST)
- [AMBER] Problem with ampdb and ptraj Andrianopsyah Mas Jaya Putra (Mon Feb 13 2012 - 21:33:38 PST)
- [AMBER] using AMBER in GPU & MPI environment 홍종희 (Mon Feb 13 2012 - 23:45:46 PST)
- [AMBER] Query on Antechmaber Charge distribution Dilraj LAMA (Tue Feb 14 2012 - 00:13:53 PST)
- [AMBER] simulation without solvent Atila Petrosian (Tue Feb 14 2012 - 00:19:37 PST)
- [AMBER] MMPBSA results and huge SD Urszula Uciechowska (Tue Feb 14 2012 - 01:14:21 PST)
- [AMBER] ptraj analysis Giachetti Andrea - CERM (Tue Feb 14 2012 - 06:54:25 PST)
- Re: [AMBER] Restart file for pmemd not showing all information filip fratev (Tue Feb 14 2012 - 08:38:57 PST)
- [AMBER] Rupture of GlcNAc C-H bonds with AMBER8 Sebastian Enck (Tue Feb 14 2012 - 09:09:10 PST)
- [AMBER] energy decomposition for the surface term Junmei Wang (Tue Feb 14 2012 - 19:17:33 PST)
- [AMBER] iwrap concern Dilraj LAMA (Wed Feb 15 2012 - 01:14:29 PST)
- [AMBER] ff03.r1 issue Dmitry Mukha (Wed Feb 15 2012 - 01:31:55 PST)
- [AMBER] To account for the protonation states of amino acids at a constant pH abinayar.imsc.res.in (Wed Feb 15 2012 - 03:49:01 PST)
- [AMBER] Change the residue number in pdb file Olena Dobrovolska (Wed Feb 15 2012 - 05:46:27 PST)
- [AMBER] MD simulation of protein with Calcium ion in explicit solvent Quentin Delettre (Wed Feb 15 2012 - 07:02:27 PST)
- Re: [AMBER] Building Wrapped DNA in NAB David A Case (Wed Feb 15 2012 - 12:32:04 PST)
- Re: [AMBER] building wrapped DNA in NAB David A Case (Wed Feb 15 2012 - 13:31:42 PST)
- [AMBER] potential of mean force kirtana S (Wed Feb 15 2012 - 14:34:27 PST)
- [AMBER] GFP Chromophore 1EMB.pdb, Yasuo Kurita (Wed Feb 15 2012 - 22:59:17 PST)
- [AMBER] Amber 12 Artem Zhmurov (Wed Feb 15 2012 - 23:45:11 PST)
- [AMBER] Problem with rst file retrieval komal soni (Thu Feb 16 2012 - 03:01:01 PST)
- [AMBER] How to handle with two Zn2+ when calculates the free binding energy by mmpbsa.py in metalloprotein JiYuan Liu (Thu Feb 16 2012 - 05:56:11 PST)
- [AMBER] How to handle with two Zn2+ when calculates the free binding energy by mmpbsa.py in metalloprotein JiYuan Liu (Thu Feb 16 2012 - 06:16:51 PST)
- Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." David A Case (Thu Feb 16 2012 - 06:33:07 PST)
- Re: [AMBER] FW: calculation of spectral density Mahendra B Thapa (Thu Feb 16 2012 - 12:11:34 PST)
- [AMBER] format plotmtv and plotmtv for ubuntu 11.04 setyanto md (Thu Feb 16 2012 - 19:17:08 PST)
- [AMBER] Radii issue with mbondi2 + leaprc.parmCHI_YIL.bsc for RNA Hai Nguyen (Thu Feb 16 2012 - 20:38:56 PST)
- [AMBER] restraints in igb simulation Danny Xu (Thu Feb 16 2012 - 22:21:39 PST)
- [AMBER] GFP chromophore 1EMB.pdb(detail) Yasuo Kurita (Fri Feb 17 2012 - 03:25:16 PST)
- [AMBER] G09 incompatibility with ANTECHAMBER for RESP charges lfelberg.uchicago.edu (Fri Feb 17 2012 - 08:25:58 PST)
- [AMBER] Entropy analysis Amir Abbasi (Fri Feb 17 2012 - 12:56:46 PST)
- [AMBER] NVT and NPT simulation Atila Petrosian (Sat Feb 18 2012 - 03:02:31 PST)
- [AMBER] TI_All non-softcore atoms must be identical in both systems leila karami (Sun Feb 19 2012 - 03:52:18 PST)
- [AMBER] Ligands fly away from binding pocket tian zhu (Sun Feb 19 2012 - 15:30:35 PST)
- [AMBER] problem with atom type pancham lal gupta (Sun Feb 19 2012 - 23:50:58 PST)
- [AMBER] Antechamber Beale, John (Mon Feb 20 2012 - 02:04:32 PST)
- [AMBER] Calculating Binding Energy Ravleen, KAUR (Mon Feb 20 2012 - 03:06:02 PST)
- [AMBER] Protonated state of GLU, CYS Ngo Son Tung (Mon Feb 20 2012 - 07:11:45 PST)
- [AMBER] Problem building octahedral coordinated ligands in LEaP Cannon, John F. (Mon Feb 20 2012 - 08:27:38 PST)
- [AMBER] wrapping first molecule.. again Dmitry Mukha (Mon Feb 20 2012 - 09:46:36 PST)
- [AMBER] problem in getting required snapshots Mahendra B Thapa (Mon Feb 20 2012 - 13:05:28 PST)
- [AMBER] Mixing GAFF and OPLS force field Guoxiong Su (Mon Feb 20 2012 - 13:56:20 PST)
- [AMBER] ions Carlos Romero (Mon Feb 20 2012 - 18:21:31 PST)
- [AMBER] The charge of metal center is not integer which handled with MCPB JiYuan Liu (Mon Feb 20 2012 - 22:15:41 PST)
- [AMBER] partial atomic charges Mary Varughese (Tue Feb 21 2012 - 01:40:54 PST)
- [AMBER] mutation of the one base pair by leap leila karami (Tue Feb 21 2012 - 02:01:16 PST)
- [AMBER] [Fwd: Protonated state of GLU, CYS] Ngo Son Tung (Tue Feb 21 2012 - 02:11:43 PST)
- [AMBER] Charges Beale, John (Tue Feb 21 2012 - 02:11:32 PST)
- [AMBER] deletion of hydrogen atoms of pdb file Atila Petrosian (Tue Feb 21 2012 - 02:37:44 PST)
- [AMBER] Issue with mmpbsa Nick Rakowski (Tue Feb 21 2012 - 05:58:22 PST)
- [AMBER] Faking Vacuum Simulations with a GPU Aron Broom (Tue Feb 21 2012 - 06:56:03 PST)
- Re: [AMBER] R: Faking Vacuum Simulations with a GPU Aron Broom (Tue Feb 21 2012 - 07:55:58 PST)
- [AMBER] errors on testing pbsa Yubo Fan (Tue Feb 21 2012 - 08:26:17 PST)
- [AMBER] problem with vector principal fatima chami (Tue Feb 21 2012 - 14:34:21 PST)
- [AMBER] Problem with vector principal fatima chami (Tue Feb 21 2012 - 14:41:41 PST)
- [AMBER] Using Antechamber in order to make prmtop and inpcrd Aditya Setiajid (Tue Feb 21 2012 - 20:20:56 PST)
- [AMBER] Release of the R.E.D. III.5 tools FyD (Wed Feb 22 2012 - 02:46:40 PST)
- [AMBER] QM/MM atoms Fernando Martín García (Wed Feb 22 2012 - 07:55:34 PST)
- [AMBER] ATP minimization Sangita Kachhap (Wed Feb 22 2012 - 09:32:04 PST)
- [AMBER] restraining membrane diffusion Jose Borreguero (Wed Feb 22 2012 - 12:09:00 PST)
- [AMBER] Electrostatic calculation using Amber partial charge. SENTHIL KUMAR (Wed Feb 22 2012 - 23:56:01 PST)
- [AMBER] Polarization and normal Ewald Summation Volker Lesch (Thu Feb 23 2012 - 06:06:15 PST)
- [AMBER] problem in output file of the awk script in tutorial A6 shahab shariati (Thu Feb 23 2012 - 07:21:02 PST)
- [AMBER] MMPBSA.py troubleshooting Åge Skjevik (Thu Feb 23 2012 - 09:49:13 PST)
- [AMBER] CUDA version for Amber 11? Mettu, Ramgopal (Thu Feb 23 2012 - 14:09:35 PST)
- [AMBER] same simulation using different random seeds on GPU Oliver Kuhn (Fri Feb 24 2012 - 08:37:16 PST)
- Re: [AMBER] FW: problem in getting required snapshots Mahendra B Thapa (Fri Feb 24 2012 - 09:11:46 PST)
- [AMBER] Constant Temperature amir abbasi (Fri Feb 24 2012 - 11:35:22 PST)
- Re: [AMBER] [q4md-fft] How to show charge values using Jmol? FyD (Fri Feb 24 2012 - 23:09:44 PST)
- Re: [AMBER] [Contact q4md] HF/6-31++g(2d, 2p) option for anionic fragments in GLYCAM06 FyD (Sat Feb 25 2012 - 00:26:19 PST)
- [AMBER] Comaring energy values after restart Dilraj LAMA (Sat Feb 25 2012 - 00:32:33 PST)
- [AMBER] md sticking! amir abbasi (Sat Feb 25 2012 - 05:38:53 PST)
- [AMBER] Simulation set up John S (Sun Feb 26 2012 - 01:04:17 PST)
- [AMBER] Calculation of backbone torsion angles souvik sur (Mon Feb 27 2012 - 04:10:49 PST)
- [AMBER] Is there a membrane tutorial for Amber? Arthur Roberts (Mon Feb 27 2012 - 14:34:28 PST)
- [AMBER] Calculate the volume of a protein from the trajectory surasak chunsrivirot (Mon Feb 27 2012 - 23:41:08 PST)
- [AMBER] Cosine content of PCA analysis Catein Catherine (Tue Feb 28 2012 - 00:58:12 PST)
- [AMBER] How to calculate cosine content of PCA analysis? Catein Catherine (Tue Feb 28 2012 - 00:58:54 PST)
- [AMBER] when will Amber 12 be released? Albert (Tue Feb 28 2012 - 01:09:10 PST)
- Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW JiYuan Liu (Tue Feb 28 2012 - 01:16:04 PST)
- [AMBER] implicit and explicit amir abbasi (Tue Feb 28 2012 - 05:34:06 PST)
- [AMBER] PTRAJ H-bond analysis for protein and ligand Swati Adlakha (Tue Feb 28 2012 - 05:44:18 PST)
- [AMBER] 2D PMFs with multiple constraints Sampson C.M. (Tue Feb 28 2012 - 07:28:00 PST)
- [AMBER] Help with solvating organic molecule with input .prmtop file Andy Ballard (Tue Feb 28 2012 - 07:55:42 PST)
- [AMBER] Embed Shell Scripting in ptraj script Ismail, Mohd F. (Tue Feb 28 2012 - 09:48:13 PST)
- [AMBER] is there any tools that can convert Desmond .cms to Amber format? Albert (Tue Feb 28 2012 - 11:06:55 PST)
- [AMBER] strip and use of distance-based mask Nanna Holmgaard List (Tue Feb 28 2012 - 11:52:02 PST)
- [AMBER] bad atom type Osman, Roman (Tue Feb 28 2012 - 14:59:05 PST)
- [AMBER] About the source file regarding SMD calculations Mo Chen (Tue Feb 28 2012 - 15:08:57 PST)
- [AMBER] how to cite ambertool setyanto md (Tue Feb 28 2012 - 20:59:10 PST)
- [AMBER] simulation in lipid rukman kesh (Tue Feb 28 2012 - 21:38:44 PST)
- [AMBER] mm_pbsa error: Flag "RADII" not found in PARM file g t (Wed Feb 29 2012 - 04:32:06 PST)
- Last message date: Wed Feb 29 2012 - 14:30:02 PST
- Archived on: Wed Dec 25 2024 - 05:54:31 PST
