Amber Archive Mar 2009 by thread
- Re: [AMBER] binding free energy Barbault Florent (Sun Mar 01 2009 - 04:20:39 PST)
- Re: [AMBER] Question about NAB module David A. Case (Sun Mar 01 2009 - 05:52:19 PST)
- [AMBER] Pseudoatoms waleed zalloum (Mon Mar 02 2009 - 04:12:33 PST)
- [AMBER] calculate shear viscosity oguz gurbulak (Mon Mar 02 2009 - 05:35:06 PST)
- Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? David A. Case (Mon Mar 02 2009 - 06:56:54 PST)
- [AMBER] Re: using Gromacs for analysis oguz gurbulak (Mon Mar 02 2009 - 08:17:45 PST)
- [AMBER] assigning velocities to each atom without heating the system Parimal Kar (Mon Mar 02 2009 - 08:44:26 PST)
- [AMBER] specification of antechamber AC file format? Nicholas Musolino (Mon Mar 02 2009 - 23:53:23 PST)
- [AMBER] inpcrd and prmtop m m (Tue Mar 03 2009 - 01:27:06 PST)
- [AMBER] Fail to allocate ff Madhurima Jana (Tue Mar 03 2009 - 03:17:57 PST)
- [AMBER] A good way to use an Amber force field with NAMD? Sasha Buzko (Tue Mar 03 2009 - 13:37:29 PST)
- [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory Jeff Schwinefus (Tue Mar 03 2009 - 14:18:25 PST)
- [AMBER] angle between ligand ring plane and axis Jia Xu (Wed Mar 04 2009 - 03:00:08 PST)
- [AMBER] hydrogen bond . .. (Wed Mar 04 2009 - 03:12:33 PST)
- [AMBER] Regarding leap aneesh cna (Wed Mar 04 2009 - 03:43:52 PST)
- [AMBER] unning MMPBSA in CHCl3 environment SAFAK OZHAN (Wed Mar 04 2009 - 03:55:52 PST)
- [AMBER] Thermodynamic Intergration problem Xiaohui Jiang [Contractor] (Wed Mar 04 2009 - 07:36:14 PST)
- [AMBER] Compilation and qmmm_div Benjamin Roberts (Wed Mar 04 2009 - 07:48:16 PST)
- [AMBER] radial distribution function mask iccy liu (Wed Mar 04 2009 - 10:57:08 PST)
- Re: [AMBER] H-Bonds Thomas Cheatham III (Wed Mar 04 2009 - 13:00:30 PST)
- [AMBER] Segmentation faults Benjamin Roberts (Wed Mar 04 2009 - 16:17:50 PST)
- Re: [AMBER] solvent and counter ions Bill Ross (Wed Mar 04 2009 - 16:20:45 PST)
- [AMBER] DNA simulation: Problem with RMSD BERGY (Wed Mar 04 2009 - 19:44:26 PST)
- [AMBER] Fwd: please help me out bharat lakhani (Wed Mar 04 2009 - 20:42:06 PST)
- [AMBER] Re: Fw:How to creat .frcmod file FyD (Wed Mar 04 2009 - 22:22:56 PST)
- [AMBER] please help me out bharat lakhani (Thu Mar 05 2009 - 00:35:44 PST)
- [AMBER] chemical shift penalty Jacopo Sgrignani (Thu Mar 05 2009 - 01:47:03 PST)
- [AMBER] divcon error during antechamber run, convergence problem drugdesign (Thu Mar 05 2009 - 05:53:59 PST)
- [AMBER] secstruct Beale, John (Thu Mar 05 2009 - 05:54:20 PST)
- [AMBER] MM-PBSA decomp by residue and snapshot? Bradshaw, Richard (Thu Mar 05 2009 - 09:55:05 PST)
- [AMBER] Warning: name change in pdb file residue Donald Keidel (Thu Mar 05 2009 - 11:25:38 PST)
- [AMBER] GBSA: dielectric symmetry Giacomo Bastianelli (Thu Mar 05 2009 - 15:29:50 PST)
- [AMBER] High RMSD for DNA: A to B transition study BERGY (Thu Mar 05 2009 - 23:26:57 PST)
- [AMBER] Quality/size of HDD for Amber Francesco Pietra (Fri Mar 06 2009 - 01:26:03 PST)
- [AMBER] Solvate Box od amoeba water Hemant Gangwar (Fri Mar 06 2009 - 01:50:01 PST)
- [AMBER] catenan simulation problems Cristina Sisu (Fri Mar 06 2009 - 05:16:08 PST)
- [AMBER] Help with torsions in parm99.dat file Gregersen, Brent (Fri Mar 06 2009 - 14:44:17 PST)
- [AMBER] Problem with particle-mesh Ewald method Yunjie Zhao (Fri Mar 06 2009 - 19:29:02 PST)
- [AMBER] analysis on Amber oguz gurbulak (Sat Mar 07 2009 - 10:04:19 PST)
- [AMBER] Fw:how to select force field Nancy (Sun Mar 08 2009 - 07:07:48 PDT)
- [AMBER] nmoldyn2 with Amber Adrien Delmont (Sun Mar 08 2009 - 07:37:40 PDT)
- [AMBER] PMEMD error message neville forlemu (Sun Mar 08 2009 - 13:37:09 PDT)
- [AMBER] addles segmentation fault gmail (Mon Mar 09 2009 - 01:28:56 PDT)
- [AMBER] Particle-mesh Ewald method Yunjie Zhao (Mon Mar 09 2009 - 02:46:15 PDT)
- [AMBER] 8Mureabox anna berteotti (Mon Mar 09 2009 - 03:07:52 PDT)
- [AMBER] Restraint Mask length restriction !! Sampath Koppole (Mon Mar 09 2009 - 06:32:35 PDT)
- [AMBER] generalized distance restraint Rausch, Felix (Mon Mar 09 2009 - 06:48:01 PDT)
- [AMBER] Free Energy Decomposition Problem ozlem ulucan (Mon Mar 09 2009 - 06:55:45 PDT)
- [AMBER] Changing Force Fields in "Midstream" Hopkins, Robert (Mon Mar 09 2009 - 17:12:27 PDT)
- [AMBER] problem in rmsd Parimal Kar (Mon Mar 09 2009 - 20:18:48 PDT)
- [AMBER] PB Bomb from MM-PBSA of Amber 10 Zhu, Yong-Liang (Mon Mar 09 2009 - 21:30:33 PDT)
- [AMBER] sulfotyrosine parameters Ryan Pavlovicz (Tue Mar 10 2009 - 08:05:59 PDT)
- [AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero (Tue Mar 10 2009 - 09:09:48 PDT)
- [AMBER] about MD simulation 廖青华 (Wed Mar 11 2009 - 02:19:28 PDT)
- [AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman (Wed Mar 11 2009 - 05:44:17 PDT)
- 回复： [AMBER] about MD simulation 廖青华 (Wed Mar 11 2009 - 09:25:05 PDT)
- [AMBER] installing AmberTools on Windows machines David A. Case (Wed Mar 11 2009 - 13:27:07 PDT)
- [AMBER] polarizable force field and solvent zeinab bagheri (Wed Mar 11 2009 - 15:02:06 PDT)
- [AMBER] Understanding the all.out file in the MM-PBSA output gmail (Wed Mar 11 2009 - 18:39:10 PDT)
- [AMBER] polarizable force field and solvent zeinab bagheri (Wed Mar 11 2009 - 22:40:33 PDT)
- [AMBER] Problem with REMD parul sharma (Thu Mar 12 2009 - 00:45:09 PDT)
- [AMBER] Problems with MM-PBSA Calculation after MD German Erlenkamp (Thu Mar 12 2009 - 02:28:23 PDT)
- [AMBER] SMD in Amber10 Dmitri Nilov (Thu Mar 12 2009 - 11:12:13 PDT)
- Re: [AMBER] NAB md function prints strange output Scott Brozell (Thu Mar 12 2009 - 14:04:15 PDT)
- [AMBER] Thermodynamic Integration at higher values of clambda using AMBER 9 PRADEEP VENKATARAMAN (Thu Mar 12 2009 - 14:56:59 PDT)
- [AMBER] Problem running test.pmemd.AMOEBA mloureiro.cesga.es (Fri Mar 13 2009 - 04:45:30 PDT)
- [AMBER] to understand multiplicity in antechamber Alan (Fri Mar 13 2009 - 05:06:45 PDT)
- [AMBER] to understand multiplicity in antechamber Alan (Fri Mar 13 2009 - 07:43:45 PDT)
- [AMBER] doubt-reg_ Targeted molecular dynamics balaji nagarajan (Fri Mar 13 2009 - 09:20:41 PDT)
- [AMBER] problems compiling ambertool Per Jr. Greisen (Fri Mar 13 2009 - 12:08:36 PDT)
- [AMBER] suggestions for PB simulation Bala subramanian (Sat Mar 14 2009 - 09:41:19 PDT)
- [AMBER] sander.MPI and pmemd.MPI in Fedora 8 John Bennett (Sun Mar 15 2009 - 14:23:16 PDT)
- [AMBER] Unit 5 Error on OPEN: nan.in Nancy (Mon Mar 16 2009 - 05:49:31 PDT)
- [AMBER] about mm-pbsa 廖青华 (Mon Mar 16 2009 - 07:59:40 PDT)
- [AMBER] about mm-pbsa 廖青华 (Mon Mar 16 2009 - 08:02:49 PDT)
- [AMBER] minimisation with igb=10 Bala subramanian (Mon Mar 16 2009 - 08:43:10 PDT)
- [AMBER] Actual force constant in SMD Dmitri Nilov (Mon Mar 16 2009 - 11:07:09 PDT)
- [AMBER] Re: join two units in amber9 or amber10 Taufik Al-Sarraj (Mon Mar 16 2009 - 14:11:30 PDT)
- Re: [AMBER] Re: join two units in amber9 or amber10 Bill Ross (Mon Mar 16 2009 - 15:56:01 PDT)
- [AMBER] Unit 5 Error on OPEN: nan.in Nancy (Mon Mar 16 2009 - 18:02:09 PDT)
- [AMBER] Input file of the second stage RESP fitting Cen Gao (Mon Mar 16 2009 - 21:29:17 PDT)
- [AMBER] regarding tutorial on united atom force field jani sahil (Mon Mar 16 2009 - 21:51:16 PDT)
- [AMBER] Unit 5 Error on OPEN: nan.in Nancy (Tue Mar 17 2009 - 02:11:10 PDT)
- [AMBER] removing center of mass Bala subramanian (Tue Mar 17 2009 - 08:21:28 PDT)
- [AMBER] convert .mol2 file to .pdb with atomtype definitions Pansy Patel (Tue Mar 17 2009 - 08:50:57 PDT)
- [AMBER] temperature rises with igb=1 Bala subramanian (Tue Mar 17 2009 - 09:35:41 PDT)
- Re: [AMBER] Unit 5 Error on OPEN: nan.in Bill Ross (Tue Mar 17 2009 - 10:12:07 PDT)
- [AMBER] CCL4 simulation sudipta (Tue Mar 17 2009 - 11:18:07 PDT)
- [AMBER] error in constructing DNA from nucgen Pansy Patel (Tue Mar 17 2009 - 11:43:49 PDT)
- [AMBER] About error of "vertex atom mismatch" 廖青华 (Wed Mar 18 2009 - 01:30:29 PDT)
- [AMBER] errors about install amber9 on MAC OS zgong.hust (Wed Mar 18 2009 - 01:41:19 PDT)
- [AMBER] protein protrudes from unit cell Jeffrey (Wed Mar 18 2009 - 01:59:06 PDT)
- Re: [AMBER] TMD Carlos Simmerling (Wed Mar 18 2009 - 03:32:14 PDT)
- [AMBER] sleap and check Alan (Wed Mar 18 2009 - 04:18:27 PDT)
- Re: [AMBER] problem in running sander Carlos Simmerling (Wed Mar 18 2009 - 07:58:04 PDT)
- Re: [AMBER] IG not change at each restart of NPT simulation Hopkins, Robert (Wed Mar 18 2009 - 15:55:33 PDT)
- RE: [AMBER] IG not change at each restart of NPT simulation Ross Walker (Wed Mar 18 2009 - 16:07:07 PDT)
- [AMBER] Mass of LP PRADEEP VENKATARAMAN (Wed Mar 18 2009 - 20:27:24 PDT)
- [AMBER] simulation in water-oil (or water/hydrophobic-solvent) box ranga nath (Wed Mar 18 2009 - 21:27:54 PDT)
- [AMBER] Metal in MD simulation priya priya (Wed Mar 18 2009 - 23:25:09 PDT)
- [AMBER] About mm-pbsa 廖青华 (Wed Mar 18 2009 - 23:48:21 PDT)
- [AMBER] [about advanced tutorial 1] How could I get conformations for gaussian that have minimum energy? Youn Kyeung Lee (Thu Mar 19 2009 - 00:31:16 PDT)
- [AMBER] error for nmode Dechang Li (Thu Mar 19 2009 - 04:00:09 PDT)
- [AMBER] pmemd compile error.... Giorgos Lamprinidis (Thu Mar 19 2009 - 08:06:04 PDT)
- [AMBER] Parametrisation of Silicon based molecules for Amber simulations ? Marek Malý (Thu Mar 19 2009 - 16:49:21 PDT)
- [AMBER] Help needed in amber parallel installation sushobhan.iiar.res.in (Thu Mar 19 2009 - 23:39:36 PDT)
- Re: [AMBER] analysing DNA trajectory Bala subramanian (Fri Mar 20 2009 - 01:06:08 PDT)
- [AMBER] QM/MM charges Jacopo Sgrignani (Fri Mar 20 2009 - 02:38:30 PDT)
- [AMBER] Announcement of Model(l)ing'09 - The annual 2009 MGMS Meeting in Erlangen, Germany Harald Lanig (Fri Mar 20 2009 - 04:25:09 PDT)
- [AMBER] MMGBSA IG Value Rajesh Raju (Fri Mar 20 2009 - 10:20:52 PDT)
- [AMBER] xmgrace Nancy (Fri Mar 20 2009 - 21:41:33 PDT)
- [AMBER] adding chain id to ptraj pdb output Paul Brandt (Sat Mar 21 2009 - 19:09:59 PDT)
- [AMBER] about mm-pbsa 廖青华 (Mon Mar 23 2009 - 02:10:29 PDT)
- [AMBER] leap and chirality Karl Kirschner (Mon Mar 23 2009 - 02:54:29 PDT)
- [AMBER] problem in installing AMBER10 Dr. Debaprasad Giri (Mon Mar 23 2009 - 03:31:26 PDT)
- [AMBER] Regarding use of PME along with Implict solvation jani sahil (Mon Mar 23 2009 - 03:38:39 PDT)
- Re: [AMBER] helical parameters Bala subramanian (Mon Mar 23 2009 - 11:14:29 PDT)
- [AMBER] pmemd compile error Giorgos Lamprinidis (Mon Mar 23 2009 - 13:54:37 PDT)
- [AMBER] errors on reading time series file in WHAM calculation gmail (Mon Mar 23 2009 - 17:35:02 PDT)
- [AMBER] validation of parameters and request of suggestions Jeffrey (Mon Mar 23 2009 - 19:16:35 PDT)
- [AMBER] continuam water Mannan (Mon Mar 23 2009 - 21:11:50 PDT)
- [AMBER] change in protein ligand order Hannes Wallnoefer (Tue Mar 24 2009 - 04:05:36 PDT)
- [AMBER] validation of parameters and request suggestions Jeffrey (Tue Mar 24 2009 - 04:52:19 PDT)
- Re: [AMBER] problem with amber installation nicholus bhattacharjee (Tue Mar 24 2009 - 10:14:10 PDT)
- [AMBER] POLARIZABLE WATER MODEL CHAMI F. (Tue Mar 24 2009 - 11:03:25 PDT)
- [AMBER] create new crd files from transformed coordinates Donald Keidel (Tue Mar 24 2009 - 18:49:03 PDT)
- [AMBER] question about pair wise per-residue energy decomposition; idecomp=3 wfli.biophy.nju.edu.cn (Wed Mar 25 2009 - 02:48:29 PDT)
- [AMBER] About Free energy decomposition Rajesh Raju (Wed Mar 25 2009 - 07:08:00 PDT)
- [AMBER] Rosetta Academic Training Webinar Nir London (Wed Mar 25 2009 - 09:14:21 PDT)
- [AMBER] How to reproduce a parallel PMEMD run? Siang Yip (Wed Mar 25 2009 - 15:33:56 PDT)
- [AMBER] Amber 10 and core i7 Supat Jiranusornkul (Thu Mar 26 2009 - 02:13:10 PDT)
- [AMBER] To find radial distribution curve nicholus bhattacharjee (Thu Mar 26 2009 - 10:16:07 PDT)
- [AMBER] installing resp on linux 64bit aditya chhikara (Thu Mar 26 2009 - 10:24:27 PDT)
- [AMBER] Problem with "Atom does not have a type" Richard Tseng (Thu Mar 26 2009 - 16:17:19 PDT)
- [AMBER] Fwd: AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Thu Mar 26 2009 - 16:44:59 PDT)
- [AMBER] Problem reading PDB file into XLEAP Hopkins, Robert (Thu Mar 26 2009 - 17:01:26 PDT)
- [AMBER] Antechamber problem 欧阳德方 (Thu Mar 26 2009 - 21:44:24 PDT)
- [AMBER] problem using amoeba Hemant Gangwar (Fri Mar 27 2009 - 03:41:26 PDT)
- [AMBER] Question Kshatresh Dutta Dubey (Fri Mar 27 2009 - 06:06:09 PDT)
- [AMBER] PMEMD 9 on MVAPICH / Infiniband problem Nick Holway (Fri Mar 27 2009 - 08:55:38 PDT)
- [AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Fri Mar 27 2009 - 19:30:04 PDT)
- RE: [AMBER] Problem reading PDB file into XLEAP - SLEAP Hopkins, Robert (Sat Mar 28 2009 - 16:12:06 PDT)
- [AMBER] .rst file generation problem. Aravind S (Sun Mar 29 2009 - 22:48:55 PDT)
- [AMBER] "rfree: End of file on unit 5" Remya S R (Sun Mar 29 2009 - 23:21:53 PDT)
- [AMBER] mm_pbsa problem Giorgos Lamprinidis (Mon Mar 30 2009 - 03:02:07 PDT)
- [AMBER] Creating conditions for biased MD Francesco Pietra (Mon Mar 30 2009 - 03:16:54 PDT)
- [AMBER] amber tools installation Jayalakshmi Sridhar (Mon Mar 30 2009 - 08:44:57 PDT)
- [AMBER] Announcing NMR validation web interface iCing Alan (Mon Mar 30 2009 - 09:55:00 PDT)
- [AMBER] problem with the results in the .out file! Aravind S (Mon Mar 30 2009 - 22:30:57 PDT)
- [AMBER] how to convert secstruct output file into plot or pictorial representation Siddharth Rastogi (Tue Mar 31 2009 - 03:56:37 PDT)
- [AMBER] modifying LYN Marius Retegan (Tue Mar 31 2009 - 06:36:21 PDT)
- [AMBER] combine many coord files into trajectory file Peter Gannett (Tue Mar 31 2009 - 06:51:16 PDT)
- Last message date: Wed Apr 01 2009 - 01:18:02 PDT
- Archived on: Mon Dec 23 2024 - 05:53:43 PST
