Amber Archive Jun 2009: by thread

[AMBER] sleap and delete FyD (Mon Jun 01 2009 - 00:35:32 PDT)
Re: [AMBER] Choice of force field Carlos Simmerling (Mon Jun 01 2009 - 04:14:09 PDT)
RE: [AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje) (Mon Jun 01 2009 - 04:21:19 PDT)
- RE: [AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje) (Fri Jun 12 2009 - 11:51:25 PDT)
  - Re: [AMBER] QQD psuedoatom restraints David A. Case (Mon Jun 15 2009 - 05:00:23 PDT)
[AMBER] converting vibrational frequency aneesh cna (Mon Jun 01 2009 - 04:22:01 PDT)
- Re: [AMBER] converting vibrational frequency David A. Case (Mon Jun 01 2009 - 04:39:32 PDT)
  - Re: [AMBER] converting vibrational frequency aneesh cna (Mon Jun 01 2009 - 09:53:22 PDT)
[AMBER] atom number exceeds the MAXATOM when running antechamber xueqin pang (Mon Jun 01 2009 - 05:53:23 PDT)
- Re: [AMBER] atom number exceeds the MAXATOM when running antechamber Gustavo Seabra (Tue Jun 02 2009 - 08:04:33 PDT)
Re: [AMBER] MM-PBSA nmode statistics Dmitry Osolodkin (Mon Jun 01 2009 - 06:12:15 PDT)
- RE: [AMBER] MM-PBSA nmode statistics Ray Luo (Mon Jun 01 2009 - 12:05:48 PDT)
[AMBER] different comformations to choose for RESP xueqin pang (Mon Jun 01 2009 - 06:47:30 PDT)
- Re: [AMBER] different comformations to choose for RESP FyD (Mon Jun 01 2009 - 07:32:21 PDT)
Re: [AMBER] makeDIST_RST: no map function for ambiguous restraint Peter Varnai (Mon Jun 01 2009 - 12:49:36 PDT)
Re: [AMBER] ask for parm99MOD Carlos Simmerling (Mon Jun 01 2009 - 13:12:47 PDT)
- RE: [AMBER] ask for parm99MOD xiaoqin huang (Mon Jun 01 2009 - 13:25:02 PDT)
[AMBER] minimization to reduce covalent deviation Peter Varnai (Mon Jun 01 2009 - 13:25:07 PDT)
- Re: [AMBER] minimization to reduce covalent deviation David A. Case (Tue Jun 02 2009 - 06:38:58 PDT)
[AMBER] how to choose different comformations for RESP xueqin pang (Mon Jun 01 2009 - 17:32:51 PDT)
- Re: [AMBER] how to choose different comformations for RESP cgji (Mon Jun 01 2009 - 22:14:02 PDT)
[AMBER] MMPBSA and mm_pbsa_statistics.pl error john smith (Mon Jun 01 2009 - 22:38:54 PDT)
- Re: [AMBER] MMPBSA and mm_pbsa_statistics.pl error Ray Luo (Tue Jun 02 2009 - 21:49:34 PDT)
[AMBER] how to add ions bharat lakhani (Tue Jun 02 2009 - 00:25:46 PDT)
[AMBER] Atom names Rose Tamil (Tue Jun 02 2009 - 03:53:50 PDT)
- Re: [AMBER] Atom names Carlos Simmerling (Tue Jun 02 2009 - 04:39:25 PDT)
- Re: [AMBER] Atom names David A. Case (Tue Jun 02 2009 - 04:44:39 PDT)
  - Re: [AMBER] Atom names Rose Tamil (Tue Jun 02 2009 - 04:50:47 PDT)
    - Re: [AMBER] Atom names Rose Tamil (Wed Jun 03 2009 - 07:53:51 PDT)
    - Re: [AMBER] Atom names David A. Case (Wed Jun 03 2009 - 09:00:15 PDT)
    - Re: [AMBER] Atom names Rose Tamil (Wed Jun 03 2009 - 13:43:56 PDT)
    - [AMBER] atom type Taufik Al-Sarraj (Thu Jun 04 2009 - 18:03:14 PDT)
    - Re: [AMBER] atom type David A. Case (Fri Jun 05 2009 - 05:32:45 PDT)
    - Re: [AMBER] atom type Taufik Al-Sarraj (Fri Jun 05 2009 - 06:58:50 PDT)
    - Re: [AMBER] atom type Taufik Al-Sarraj (Fri Jun 05 2009 - 09:07:14 PDT)
[AMBER] help with parameters for ions rebeca (Tue Jun 02 2009 - 05:46:14 PDT)
- Re: [AMBER] help with parameters for ions David A. Case (Tue Jun 02 2009 - 06:46:40 PDT)
  - Re: [AMBER] help with parameters for ions rebeca (Tue Jun 02 2009 - 08:10:17 PDT)
    - Re: [AMBER] help with parameters for ions InSuk Joung (Tue Jun 02 2009 - 08:28:55 PDT)
  - Re: [AMBER] help with parameters for ions rebeca (Tue Jun 02 2009 - 10:38:00 PDT)
    - Re: [AMBER] help with parameters for ions InSuk Joung (Tue Jun 02 2009 - 11:14:46 PDT)
[AMBER] Error in MM PBSA Vikas Sharma (Tue Jun 02 2009 - 06:42:16 PDT)
- Re: [AMBER] Error in MM PBSA David A. Case (Tue Jun 02 2009 - 07:05:09 PDT)
  - 回复： [AMBER] Error in MM PBSA 廖青华 (Tue Jun 02 2009 - 07:30:47 PDT)
    - Re: 回复： [AMBER] Error in MM PBSA David A. Case (Tue Jun 02 2009 - 07:36:39 PDT)
  - Re: [AMBER] Error in MM PBSA Vikas Sharma (Tue Jun 02 2009 - 23:45:35 PDT)
  - Re: [AMBER] Error in MM PBSA Vikas Sharma (Tue Jun 02 2009 - 23:46:03 PDT)
  - Re: [AMBER] Error in MM PBSA Vikas Sharma (Tue Jun 02 2009 - 23:46:06 PDT)
    - Re: [AMBER] Error in MM PBSA David A. Case (Wed Jun 03 2009 - 04:43:54 PDT)
    - Re: [AMBER] Error in MM PBSA Vikas Sharma (Wed Jun 03 2009 - 07:24:14 PDT)
Re: [AMBER] J coupling constant calculation Gustavo Seabra (Tue Jun 02 2009 - 07:18:08 PDT)
Re: [AMBER] Targeted MD and QM/MM Gustavo Seabra (Tue Jun 02 2009 - 07:43:35 PDT)
- Re: [AMBER] Targeted MD and QM/MM Gabriel Urquiza (Tue Jun 02 2009 - 15:08:11 PDT)
Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy Gustavo Seabra (Tue Jun 02 2009 - 07:53:19 PDT)
Re: [AMBER] Choice of force feild Gustavo Seabra (Tue Jun 02 2009 - 07:58:11 PDT)
Re: [AMBER] create a simulation box Gustavo Seabra (Tue Jun 02 2009 - 08:08:46 PDT)
Fwd: Re: [AMBER] help with parameters for ions rebeca (Tue Jun 02 2009 - 11:33:41 PDT)
Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy Marc Baaden (Tue Jun 02 2009 - 13:56:29 PDT)
- Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy jacky zhao (Wed Jun 03 2009 - 06:44:12 PDT)
[AMBER] PARMSCAN alegil.fq.uh.cu (Tue Jun 02 2009 - 15:26:42 PDT)
[AMBER] PARMSCAN alegil.fq.uh.cu (Tue Jun 02 2009 - 15:41:54 PDT)
[AMBER] preparation of two solutes of organic molecules in a simulation box Workalemhu Berhanu (Tue Jun 02 2009 - 16:09:04 PDT)
[AMBER] addions Shubhra Gupta (Tue Jun 02 2009 - 22:47:11 PDT)
- [AMBER] Re: addions Shubhra Gupta (Wed Jun 03 2009 - 04:12:32 PDT)
  - Re: [AMBER] Re: addions nicholus bhattacharjee (Wed Jun 03 2009 - 06:44:51 PDT)
  - [AMBER] Re: addions Peter Gannett (Wed Jun 03 2009 - 07:17:57 PDT)
    - Re: [AMBER] Re: addions Shubhra Gupta (Thu Jun 04 2009 - 21:38:20 PDT)
[AMBER] Distance restraints between groups of atoms Germain Vallverdu (Tue Jun 02 2009 - 23:58:57 PDT)
- Re: [AMBER] Distance restraints between groups of atoms David A. Case (Wed Jun 03 2009 - 05:27:04 PDT)
  - [AMBER] AMBER10: error message mdfil flag..... Catein Catherine (Wed Jun 03 2009 - 07:14:50 PDT)
    - Re: [AMBER] AMBER10: error message mdfil flag..... David A. Case (Wed Jun 03 2009 - 07:30:08 PDT)
  - Re: [AMBER] Distance restraints between groups of atoms Germain Vallverdu (Wed Jun 03 2009 - 07:43:37 PDT)
    - Re: [AMBER] Distance restraints between groups of atoms David A. Case (Wed Jun 03 2009 - 09:32:33 PDT)
    - Re: [AMBER] Distance restraints between groups of atoms Germain Vallverdu (Tue Jun 09 2009 - 01:39:45 PDT)
    - Re: [AMBER] Distance restraints between groups of atoms David A. Case (Tue Jun 09 2009 - 04:45:14 PDT)
[AMBER] use of random seed in multiple runs Andrew Voronkov (Wed Jun 03 2009 - 02:28:52 PDT)
- Re: [AMBER] use of random seed in multiple runs Carlos Simmerling (Wed Jun 03 2009 - 03:13:23 PDT)
  - Re: [AMBER] use of random seed in multiple runs Andrew Voronkov (Wed Jun 03 2009 - 10:00:32 PDT)
- Re: [AMBER] use of random seed in multiple runs Gustavo Seabra (Wed Jun 03 2009 - 06:55:24 PDT)
- Re: [AMBER] use of random seed in multiple runs Andrew Voronkov (Wed Jun 03 2009 - 12:26:48 PDT)
  - Re: [AMBER] use of random seed in multiple runs Gustavo Seabra (Wed Jun 03 2009 - 19:00:51 PDT)
- Re: [AMBER] use of random seed in multiple runs Robert Duke (Wed Jun 03 2009 - 20:59:48 PDT)
  - Re: [AMBER] use of random seed in multiple runs Jifeng Wang (Thu Jun 04 2009 - 07:10:50 PDT)
- Re: [AMBER] use of random seed in multiple runs Robert Duke (Thu Jun 04 2009 - 07:31:32 PDT)
  - Re: [AMBER] use of random seed in multiple runs Jifeng Wang (Thu Jun 04 2009 - 07:43:25 PDT)
  - Re: [AMBER] use of random seed in multiple runs Marek Maly (Thu Jun 04 2009 - 09:35:57 PDT)
  - Re: [AMBER] use of random seed in multiple runs Gustavo Seabra (Fri Jun 05 2009 - 06:28:03 PDT)
- Re: [AMBER] use of random seed in multiple runs Robert Duke (Thu Jun 04 2009 - 10:02:58 PDT)
  - Re: [AMBER] use of random seed in multiple runs Marek Maly (Thu Jun 04 2009 - 12:16:50 PDT)
    - Re: [AMBER] use of random seed in multiple runs Carlos Simmerling (Thu Jun 04 2009 - 12:20:59 PDT)
    - Re: [AMBER] use of random seed in multiple runs Marek Maly (Thu Jun 04 2009 - 13:01:54 PDT)
    - Re: [AMBER] use of random seed in multiple runs Gustavo Seabra (Fri Jun 05 2009 - 06:37:42 PDT)
    - Re: [AMBER] use of random seed in multiple runs Marek Maly (Fri Jun 05 2009 - 06:49:14 PDT)
    - Re: [AMBER] use of random seed in multiple runs Gustavo Seabra (Fri Jun 05 2009 - 12:18:35 PDT)
    - Re: [AMBER] use of random seed in multiple runs Marek Maly (Fri Jun 05 2009 - 12:40:13 PDT)
- Re: [AMBER] use of random seed in multiple runs Robert Duke (Fri Jun 05 2009 - 07:37:14 PDT)
  - Re: [AMBER] use of random seed in multiple runs Gustavo Seabra (Fri Jun 05 2009 - 08:16:00 PDT)
- Re: [AMBER] use of random seed in multiple runs Robert Duke (Fri Jun 05 2009 - 07:45:32 PDT)
  - Re: [AMBER] use of random seed in multiple runs Naser Alijabbari (Fri Jun 05 2009 - 08:30:55 PDT)
- Re: [AMBER] use of random seed in multiple runs Robert Duke (Fri Jun 05 2009 - 08:45:09 PDT)
[AMBER] only ff94 and ff99 for GBSA? Andrew Voronkov (Wed Jun 03 2009 - 03:28:15 PDT)
- Re: [AMBER] only ff94 and ff99 for GBSA? Carlos Simmerling (Wed Jun 03 2009 - 03:51:09 PDT)
- Re: [AMBER] only ff94 and ff99 for GBSA? Andrew Voronkov (Wed Jun 03 2009 - 04:52:13 PDT)
  - Re: [AMBER] only ff94 and ff99 for GBSA? David A. Case (Wed Jun 03 2009 - 05:24:56 PDT)
[AMBER] NO output when running espgen? xueqin pang (Wed Jun 03 2009 - 06:13:06 PDT)
[AMBER] Pentavalent Phosphorous and Antechamber Peterson, Matthew W. (Wed Jun 03 2009 - 07:12:44 PDT)
- Re: [AMBER] Pentavalent Phosphorous and Antechamber David A. Case (Wed Jun 03 2009 - 09:35:26 PDT)
- Re: [AMBER] Pentavalent Phosphorous and Antechamber Shubhra Gupta (Wed Jun 03 2009 - 21:37:08 PDT)
- Re: [AMBER] Pentavalent Phosphorous and Antechamber FyD (Wed Jun 03 2009 - 23:29:59 PDT)
[AMBER] spc.itp for the Amber force field rebeca (Wed Jun 03 2009 - 07:46:46 PDT)
- Re: [AMBER] spc.itp for the Amber force field Alan (Wed Jun 03 2009 - 08:38:56 PDT)
[AMBER] problems with EP of TIP4PEW rebeca (Wed Jun 03 2009 - 08:43:58 PDT)
- Re: [AMBER] problems with EP of TIP4PEW David A. Case (Wed Jun 03 2009 - 09:29:43 PDT)
  - Re: [AMBER] problems with EP of TIP4PEW rebeca (Wed Jun 03 2009 - 11:40:12 PDT)
Re: [AMBER] hbond_DNAtraj Jianyin Shao (Wed Jun 03 2009 - 09:52:41 PDT)
[AMBER] creating bond Jorgen Simonsen (Wed Jun 03 2009 - 10:04:11 PDT)
- Re: [AMBER] creating bond David A. Case (Wed Jun 03 2009 - 11:32:57 PDT)
- Re: [AMBER] creating bond Bill Ross (Wed Jun 03 2009 - 11:40:52 PDT)
  - Re: [AMBER] creating bond Jorgen Simonsen (Wed Jun 03 2009 - 12:56:29 PDT)
- Re: [AMBER] creating bond Bill Ross (Wed Jun 03 2009 - 14:40:09 PDT)
  - [AMBER] AMBER 10: sleap diff errors? Catein Catherine (Wed Jun 03 2009 - 22:37:35 PDT)
    - Re: [AMBER] AMBER 10: sleap diff errors? David A. Case (Thu Jun 04 2009 - 12:19:44 PDT)
[AMBER] ptraj image in non-orthorhombic cell Joanna Panecka (Wed Jun 03 2009 - 13:19:52 PDT)
[AMBER] no output when running Antechamber(espgen) xueqin pang (Wed Jun 03 2009 - 23:02:32 PDT)
[AMBER] how to add water for membrane, in Z direction only or xyz xueqin pang (Thu Jun 04 2009 - 01:13:07 PDT)
[AMBER] Binding Energy Vikas Sharma (Thu Jun 04 2009 - 04:25:01 PDT)
Re: [AMBER] ligand QM/semi-empirical coords optmisation Alan (Thu Jun 04 2009 - 07:19:28 PDT)
- Re: [AMBER] ligand QM/semi-empirical coords optmisation David A. Case (Thu Jun 04 2009 - 08:06:28 PDT)
  - Re: [AMBER] ligand QM/semi-empirical coords optmisation Alan (Thu Jun 04 2009 - 11:05:27 PDT)
- Re: [AMBER] ligand QM/semi-empirical coords optmisation Junmei Wang (Fri Jun 05 2009 - 08:01:32 PDT)
  - Re: [AMBER] ligand QM/semi-empirical coords optmisation Francesco Pietra (Fri Jun 05 2009 - 11:17:45 PDT)
[AMBER] Error in MM PBSA Vikas Sharma (Thu Jun 04 2009 - 07:58:43 PDT)
- Re: [AMBER] Error in MM PBSA Ray Luo (Thu Jun 04 2009 - 14:00:51 PDT)
- Re: [AMBER] Error in MM PBSA Vikas Sharma (Sat Jun 06 2009 - 02:03:22 PDT)
  - Re: [AMBER] Error in MM PBSA Ray Luo (Sat Jun 06 2009 - 07:37:43 PDT)
    - Re: [AMBER] Error in MM PBSA Vikas Sharma (Sun Jun 07 2009 - 10:02:03 PDT)
    - Re: [AMBER] Error in MM PBSA Ray Luo (Sun Jun 07 2009 - 12:17:30 PDT)
    - Re: [AMBER] Error in MM PBSA Vikas Sharma (Mon Jun 08 2009 - 10:44:06 PDT)
    - Re: [AMBER] Error in MM PBSA Ray Luo (Mon Jun 08 2009 - 11:12:22 PDT)
[AMBER] mol2 file to amber pdb file format balaji nagarajan (Thu Jun 04 2009 - 09:32:06 PDT)
- Re: [AMBER] mol2 file to amber pdb file format David A. Case (Thu Jun 04 2009 - 09:55:39 PDT)
[AMBER] rescaling velocities abi ghanem (Thu Jun 04 2009 - 09:39:02 PDT)
- Re: [AMBER] rescaling velocities Carlos Simmerling (Thu Jun 04 2009 - 09:43:20 PDT)
[AMBER] ptraj_hbond_problem balaji nagarajan (Thu Jun 04 2009 - 15:08:24 PDT)
- Re: [AMBER] ptraj_hbond_problem Thomas Cheatham (Thu Jun 04 2009 - 22:28:11 PDT)
[AMBER] Warning: No sp2 improper torsion term for Alan (Fri Jun 05 2009 - 05:26:55 PDT)
- RE: [AMBER] Warning: No sp2 improper torsion term for Ross Walker (Fri Jun 05 2009 - 07:13:53 PDT)
  - Re: [AMBER] Warning: No sp2 improper torsion term for Alan (Mon Jun 08 2009 - 07:54:50 PDT)
[AMBER] parameter for dihedral angle Jorgen Simonsen (Fri Jun 05 2009 - 08:16:56 PDT)
- Re: [AMBER] parameter for dihedral angle David A. Case (Fri Jun 05 2009 - 12:50:03 PDT)
- Re: [AMBER] parameter for dihedral angle raja pandian (Fri Jun 05 2009 - 22:13:52 PDT)
  - Re: [AMBER] parameter for dihedral angle David A. Case (Sat Jun 06 2009 - 05:47:35 PDT)
    - RE: [AMBER] parameter for dihedral angle Catein Catherine (Sun Jun 07 2009 - 20:08:17 PDT)
    - [AMBER] Error message? INFO: Old style inpcrd file read Catein Catherine (Sun Jun 07 2009 - 20:11:27 PDT)
    - Re: [AMBER] Error message? INFO: Old style inpcrd file read Robert Duke (Sun Jun 07 2009 - 20:19:38 PDT)
    - RE: [AMBER] Error message? INFO: Old style inpcrd file read Catein Catherine (Sun Jun 07 2009 - 20:55:28 PDT)
    - [AMBER] What is the parallel efficiency of amber10 Catein Catherine (Sun Jun 07 2009 - 20:19:37 PDT)
    - Re: [AMBER] What is the parallel efficiency of amber10 Tom Joseph (Sun Jun 07 2009 - 23:07:29 PDT)
    - Re: [AMBER] What is the parallel efficiency of amber10 David A. Case (Mon Jun 08 2009 - 05:23:11 PDT)
    - [AMBER] Can we define +1 or -1 charge for an organic drug using GAFF? Catein Catherine (Mon Jun 08 2009 - 08:16:23 PDT)
    - Re: [AMBER] Can we define +1 or -1 charge for an organic drug using GAFF? David A. Case (Mon Jun 08 2009 - 09:47:54 PDT)
    - [AMBER] PDMED Catein Catherine (Mon Jun 08 2009 - 21:28:58 PDT)
    - RE: [AMBER] PDMED Ross Walker (Mon Jun 08 2009 - 22:19:36 PDT)
    - RE: [AMBER] PDMED Catein Catherine (Mon Jun 08 2009 - 23:18:59 PDT)
    - RE: [AMBER] PDMED Ross Walker (Mon Jun 08 2009 - 23:35:25 PDT)
    - Re: [AMBER] What is the parallel efficiency of amber10 Gustavo Seabra (Mon Jun 08 2009 - 06:44:26 PDT)
[AMBER] Proper ISTRNG value ? Marek Maly (Fri Jun 05 2009 - 09:24:58 PDT)
[AMBER] Computational Alanine Scanning using mm_pbsa, any tutorial for amber9 or amber 10 version? Haizhen Zhong (Fri Jun 05 2009 - 16:17:01 PDT)
[AMBER] average torsional energy Francesco Pietra (Sat Jun 06 2009 - 09:57:49 PDT)
- Re: [AMBER] average torsional energy Adrian Roitberg (Sun Jun 07 2009 - 09:09:14 PDT)
  - Re: [AMBER] average torsional energy Carlos Simmerling (Sun Jun 07 2009 - 09:14:17 PDT)
    - Re: [AMBER] average torsional energy Karl Kirschner (Mon Jun 08 2009 - 01:29:05 PDT)
    - Re: [AMBER] average torsional energy Francesco Pietra (Mon Jun 08 2009 - 02:11:52 PDT)
- [AMBER] Fwd: average torsional energy Francesco Pietra (Sun Jun 07 2009 - 09:09:37 PDT)
- [AMBER] How to calculate the distance of CA of all residues in the trajectory Thomas Leonard (Sun Jun 07 2009 - 18:45:54 PDT)
[AMBER] MaxRad ? Marek Maly (Sat Jun 06 2009 - 13:56:44 PDT)
[AMBER] POL3 Hemant Kumar (Sun Jun 07 2009 - 11:27:29 PDT)
[AMBER] vs_vikassharma.yahoo.co.in has sent you a private message Vikas S (Sun Jun 07 2009 - 12:28:03 PDT)
[AMBER] Max filename length in Sander? Paul Mortenson (Mon Jun 08 2009 - 03:59:52 PDT)
- Re: [AMBER] Max filename length in Sander? David A. Case (Mon Jun 08 2009 - 05:28:41 PDT)
- Re: [AMBER] Max filename length in Sander? David A. Case (Mon Jun 08 2009 - 05:36:32 PDT)
- Re: [AMBER] Max filename length in Sander? Robert Duke (Mon Jun 08 2009 - 10:30:47 PDT)
  - RE: [AMBER] Max filename length in Sander? Paul Mortenson (Tue Jun 09 2009 - 07:47:57 PDT)
    - Re: [AMBER] Max filename length in Sander? Robert Duke (Tue Jun 09 2009 - 08:01:39 PDT)
[AMBER] (no subject) Vishal Maingi (Mon Jun 08 2009 - 04:14:22 PDT)
- Re: [AMBER] (no subject) Karl Kirschner (Mon Jun 08 2009 - 04:38:42 PDT)
- Re: [AMBER] (no subject) FyD (Mon Jun 08 2009 - 10:14:05 PDT)
- RE: [AMBER] (no subject) david.lisgarten.canterbury.ac.uk (Tue Jun 09 2009 - 06:56:32 PDT)
- RE: [AMBER] (no subject) david.lisgarten.canterbury.ac.uk (Thu Jun 11 2009 - 01:28:56 PDT)
  - Re: [AMBER] (no subject) David A. Case (Thu Jun 11 2009 - 04:54:38 PDT)
[AMBER] Lost mail Robert Duke (Mon Jun 08 2009 - 04:58:02 PDT)
[AMBER] problem with creation of prmtop and prmcrd files moitrayee.mbu.iisc.ernet.in (Mon Jun 08 2009 - 06:00:18 PDT)
- Re: [AMBER] problem with creation of prmtop and prmcrd files Tom Joseph (Wed Jun 10 2009 - 18:30:19 PDT)
[AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files] moitrayee.mbu.iisc.ernet.in (Mon Jun 08 2009 - 07:28:14 PDT)
[AMBER] sander error Beale, John (Mon Jun 08 2009 - 07:43:24 PDT)
- RE: [AMBER] sander error Ross Walker (Mon Jun 08 2009 - 18:41:06 PDT)
- Re: [AMBER] sander error Robert Duke (Mon Jun 08 2009 - 20:27:52 PDT)
[AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files]] moitrayee.mbu.iisc.ernet.in (Mon Jun 08 2009 - 07:30:21 PDT)
[AMBER] Unknown residue: MOL number: 30 type: Terminal/last Workalemhu Berhanu (Mon Jun 08 2009 - 11:30:43 PDT)
- Re: [AMBER] Unknown residue: MOL number: 30 type: Terminal/last David A. Case (Tue Jun 09 2009 - 04:51:42 PDT)
[AMBER] mm_pbsa_statistics-CALC DELTA parameter ? Marek Maly (Mon Jun 08 2009 - 12:16:19 PDT)
[AMBER] Strange contacts with water molecules Jordan MONNET (Mon Jun 08 2009 - 14:39:26 PDT)
- RE: [AMBER] Strange contacts with water molecules Ross Walker (Mon Jun 08 2009 - 20:16:41 PDT)
  - Re: [AMBER] Strange contacts with water molecules Jordan MONNET (Tue Jun 09 2009 - 09:01:53 PDT)
    - Re: [AMBER] Strange contacts with water molecules Jordan MONNET (Wed Jun 17 2009 - 10:00:46 PDT)
[AMBER] Error in MM PBSA (vertex atom mismatch) Vikas Sharma (Mon Jun 08 2009 - 23:33:38 PDT)
[AMBER] ptraj quasiharmonic analysis Neha Gandhi (Mon Jun 08 2009 - 23:38:01 PDT)
- Re: [AMBER] ptraj quasiharmonic analysis Hannes Loeffler (Tue Jun 09 2009 - 00:19:23 PDT)
[AMBER] (no subject) david.lisgarten.canterbury.ac.uk (Tue Jun 09 2009 - 03:23:57 PDT)
- Re: [AMBER] (no subject) David A. Case (Tue Jun 09 2009 - 04:47:59 PDT)
[AMBER] SOS - too high binding energy Marek Maly (Tue Jun 09 2009 - 03:49:43 PDT)
- Re: [AMBER] SOS - too high binding energy Marek Maly (Wed Jun 10 2009 - 12:47:58 PDT)
[AMBER] unit of charge in prep files moitrayee.mbu.iisc.ernet.in (Tue Jun 09 2009 - 04:35:51 PDT)
- Re: [AMBER] unit of charge in prep files David A. Case (Tue Jun 09 2009 - 06:07:08 PDT)
  - Re: [AMBER] unit of charge in prep files moitrayee.mbu.iisc.ernet.in (Tue Jun 09 2009 - 18:18:58 PDT)
[AMBER] Question of about MM-PBSA and mm_pbsa_createinput.pm script Samuel Genheden (Tue Jun 09 2009 - 05:43:19 PDT)
- Re: [AMBER] Question of about MM-PBSA and mm_pbsa_createinput.pm script David A. Case (Tue Jun 09 2009 - 06:20:22 PDT)
[AMBER] Vertex atom mismatch in Amber Vikas Sharma (Tue Jun 09 2009 - 06:41:33 PDT)
[AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 07:30:39 PDT)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Carlos Simmerling (Tue Jun 09 2009 - 07:38:14 PDT)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 08:33:51 PDT)
  - Re: [AMBER] DNA as well as protein distorted during MD run in sander Carlos Simmerling (Tue Jun 09 2009 - 08:36:50 PDT)
- RE: [AMBER] DNA as well as protein distorted during MD run in sander Jesse Dylan Ziebarth (jziebrth) (Tue Jun 09 2009 - 08:47:34 PDT)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Carlos Simmerling (Tue Jun 09 2009 - 08:48:30 PDT)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 09:02:56 PDT)
[AMBER] Improper dihedrals between residues? Ben Roberts (Tue Jun 09 2009 - 09:11:15 PDT)
- Re: [AMBER] Improper dihedrals between residues? Carlos Simmerling (Tue Jun 09 2009 - 09:28:04 PDT)
  - Re: [AMBER] Improper dihedrals between residues? David A. Case (Tue Jun 09 2009 - 10:14:57 PDT)
    - Re: [AMBER] Improper dihedrals between residues? Carlos Simmerling (Tue Jun 09 2009 - 10:51:40 PDT)
- Re: [AMBER] Improper dihedrals between residues? Bill Ross (Tue Jun 09 2009 - 14:17:03 PDT)
  - [AMBER] radial distribution without normalization CHAMI F. (Wed Jun 10 2009 - 08:48:12 PDT)
    - Re: [AMBER] radial distribution without normalization Thomas Cheatham (Wed Jun 10 2009 - 15:11:40 PDT)
Re: [AMBER] Improper dihedrals between residues? Bill Ross (Tue Jun 09 2009 - 12:04:02 PDT)
- Re: [AMBER] Improper dihedrals between residues? Ben Roberts (Tue Jun 09 2009 - 12:12:07 PDT)
[AMBER] POL3 & SHAKE Hemant Gangwar (Tue Jun 09 2009 - 13:53:27 PDT)
- Re: [AMBER] POL3 & SHAKE David A. Case (Wed Jun 10 2009 - 12:11:40 PDT)
[AMBER] MM PBSA ( Vertex atom mismatch in Amber) Vikas Sharma (Tue Jun 09 2009 - 20:28:22 PDT)
[AMBER] unit of force constant aneesh cna (Tue Jun 09 2009 - 22:06:50 PDT)
[AMBER] GAFF and solvents.lib error Vishal Maingi (Wed Jun 10 2009 - 03:25:38 PDT)
- Re: [AMBER] GAFF and solvents.lib error David A. Case (Wed Jun 10 2009 - 08:54:05 PDT)
[AMBER] Thermodynamic parameters in mm_PBSA - NAB ? Marek Maly (Wed Jun 10 2009 - 03:33:59 PDT)
- Re: [AMBER] Thermodynamic parameters in mm_PBSA - NAB ? David A. Case (Wed Jun 10 2009 - 09:01:26 PDT)
  - Re: [AMBER] Thermodynamic parameters in mm_PBSA - NAB ? Marek Maly (Wed Jun 10 2009 - 12:47:41 PDT)
[AMBER] partial charges from AM1-BCC and RESP differ a lot xueqin pang (Wed Jun 10 2009 - 05:39:31 PDT)
- Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot FyD (Thu Jun 11 2009 - 11:59:27 PDT)
  - RE:Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot xueqin pang (Tue Jun 16 2009 - 00:57:25 PDT)
    - RE:Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot FyD (Tue Jun 16 2009 - 23:32:11 PDT)
[AMBER] force.f routine Brad Dickson (Wed Jun 10 2009 - 05:56:39 PDT)
- Re: [AMBER] force.f routine David A. Case (Wed Jun 10 2009 - 07:09:47 PDT)
[AMBER] Completed installation of AmberTools, version 1.1 Alan (Wed Jun 10 2009 - 06:13:37 PDT)
- Re: [AMBER] Completed installation of AmberTools, version 1.1 David A. Case (Wed Jun 10 2009 - 07:10:22 PDT)
  - [AMBER] ptraj amber 10 file. Catein Catherine (Wed Jun 10 2009 - 09:02:32 PDT)
[AMBER] Error in AMBER ( Vertex atom mismatch in Amber) Vikas Sharma (Wed Jun 10 2009 - 06:14:28 PDT)
[AMBER] question lev kantorovich (Wed Jun 10 2009 - 07:20:08 PDT)
- RE: [AMBER] question Ross Walker (Wed Jun 10 2009 - 20:19:01 PDT)
[AMBER] compiling amber10 with mac intel, ifort/icc and mpi Alan (Wed Jun 10 2009 - 07:47:00 PDT)
- Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi David A. Case (Wed Jun 10 2009 - 08:34:59 PDT)
  - Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi Alan (Wed Jun 10 2009 - 09:26:13 PDT)
    - Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi David A. Case (Wed Jun 10 2009 - 09:54:38 PDT)
    - Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi Alan (Thu Jun 11 2009 - 04:14:42 PDT)
    - Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi David Watson (Thu Jun 11 2009 - 05:43:28 PDT)
    - Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi Alan (Sat Jun 13 2009 - 11:37:54 PDT)
[AMBER] RNA and polarizable force field Abhishek Singh (Wed Jun 10 2009 - 08:30:29 PDT)
[AMBER] glycopeptide Parametrization guardiani.fi.infn.it (Wed Jun 10 2009 - 08:41:14 PDT)
- Re: [AMBER] glycopeptide Parametrization Ahammadunny Pathiaseril (Wed Jun 10 2009 - 13:25:21 PDT)
- Re: [AMBER] glycopeptide Parametrization FyD (Fri Jun 12 2009 - 00:05:51 PDT)
  - Re: [AMBER] glycopeptide Parametrization guardiani.fi.infn.it (Fri Jun 12 2009 - 07:06:24 PDT)
    - Re: [AMBER] glycopeptide Parametrization Karl Kirschner (Fri Jun 12 2009 - 08:06:17 PDT)
    - RE: [AMBER] glycopeptide Parametrization Ross Walker (Fri Jun 12 2009 - 09:09:37 PDT)
    - RE: [AMBER] glycopeptide Parametrization FyD (Sat Jun 13 2009 - 00:40:00 PDT)
    - [AMBER] IGB=7 vs IGB=5 guardiani.fi.infn.it (Thu Jun 25 2009 - 04:20:15 PDT)
[AMBER] GAFF atom type question Cen Gao (Wed Jun 10 2009 - 08:49:00 PDT)
[AMBER] entangle-less building Vishal Maingi (Wed Jun 10 2009 - 10:52:51 PDT)
[AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles (Wed Jun 10 2009 - 11:26:32 PDT)
- Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid David A. Case (Wed Jun 10 2009 - 12:14:49 PDT)
  - Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid David A. Case (Wed Jun 10 2009 - 12:23:36 PDT)
    - RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles (Wed Jun 10 2009 - 12:40:21 PDT)
- Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid FyD (Wed Jun 10 2009 - 23:48:27 PDT)
  - RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles (Thu Jun 18 2009 - 10:38:53 PDT)
    - RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid FyD (Thu Jun 18 2009 - 12:55:34 PDT)
    - RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles (Thu Jun 18 2009 - 14:01:52 PDT)
    - RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid FyD (Thu Jun 18 2009 - 22:41:54 PDT)
    - RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles (Fri Jun 19 2009 - 10:46:25 PDT)
[AMBER] input coordinates for vdW transition step in Amber 10 TI Jodi Hadden (Wed Jun 10 2009 - 13:27:16 PDT)
- Re: [AMBER] input coordinates for vdW transition step in Amber 10 TI Tom Joseph (Wed Jun 10 2009 - 18:02:51 PDT)
- Re: [AMBER] input coordinates for vdW transition step in Amber 10 TI Ye MEI (Thu Jun 11 2009 - 01:22:34 PDT)
- Re: [AMBER] input coordinates for vdW transition step in Amber 10 TI steinbrt.rci.rutgers.edu (Thu Jun 11 2009 - 03:42:51 PDT)
Re: [AMBER] entangle-less building Bill Ross (Wed Jun 10 2009 - 15:38:31 PDT)
- [AMBER] Constant pH simulation Rukman Hertadi (Wed Jun 10 2009 - 17:56:59 PDT)
  - Re: [AMBER] Constant pH simulation Tom Joseph (Wed Jun 10 2009 - 18:08:36 PDT)
[AMBER] Vertex atom mismatch in Amber Vikas Sharma (Wed Jun 10 2009 - 20:29:57 PDT)
[AMBER] zinc coordination of benzimidazole Aust, Susanne (Thu Jun 11 2009 - 00:09:59 PDT)
- Re: [AMBER] zinc coordination of benzimidazole Urszula Uciechowska (Thu Jun 11 2009 - 01:49:45 PDT)
  - [AMBER] ptraj "image" "center" commands Catein Catherine (Thu Jun 11 2009 - 02:13:38 PDT)
    - RE: [AMBER] ptraj "image" "center" commands Ross Walker (Thu Jun 11 2009 - 08:30:08 PDT)
[AMBER] NOE Beale, John (Thu Jun 11 2009 - 05:30:36 PDT)
- Re: [AMBER] NOE David A. Case (Thu Jun 11 2009 - 10:29:06 PDT)
[AMBER] GAFF atom type question Cen Gao (Thu Jun 11 2009 - 06:36:52 PDT)
- RE: [AMBER] GAFF atom type question Ross Walker (Thu Jun 11 2009 - 08:43:50 PDT)
  - Re: [AMBER] GAFF atom type question Cen Gao (Thu Jun 11 2009 - 17:31:25 PDT)
    - [AMBER] Is the result of sander same as that of pmemd? Catein Catherine (Fri Jun 12 2009 - 07:04:38 PDT)
    - Re: [AMBER] Is the result of sander same as that of pmemd? Robert Duke (Fri Jun 12 2009 - 07:09:45 PDT)
    - RE: [AMBER] Is the result of sander same as that of pmemd? Catein Catherine (Fri Jun 12 2009 - 19:55:10 PDT)
    - RE: [AMBER] Is the result of sander same as that of pmemd? Ross Walker (Sat Jun 13 2009 - 09:12:51 PDT)
    - [AMBER] Are ntrp=1000, ntwx=1000, ntwr=500 reasonable for long MD simulations? Catein Catherine (Mon Jun 15 2009 - 03:04:53 PDT)
    - RE: [AMBER] Are ntrp=1000, ntwx=1000, ntwr=500 reasonable for long MD simulations? Ross Walker (Mon Jun 15 2009 - 07:49:43 PDT)
  - Re: [AMBER] GAFF atom type question Cen Gao (Sun Jun 14 2009 - 21:12:19 PDT)
[AMBER] Copper semiempirical parameters Jacopo Sgrignani (Thu Jun 11 2009 - 06:49:50 PDT)
- RE: [AMBER] Copper semiempirical parameters Ross Walker (Thu Jun 11 2009 - 09:09:14 PDT)
[AMBER] PRINCIPAL QUESTION Marek Maly (Thu Jun 11 2009 - 08:41:42 PDT)
[AMBER] setBox truncated octahedron Myunggi Yi (Thu Jun 11 2009 - 10:27:26 PDT)
AW: [AMBER] zinc coordination of benzimidazole Aust, Susanne (Thu Jun 11 2009 - 23:13:19 PDT)
[AMBER] MM PBSA ERROR Vikas Sharma (Fri Jun 12 2009 - 07:04:25 PDT)
[AMBER] Residues KIRTANA S (Fri Jun 12 2009 - 07:10:39 PDT)
- Re: [AMBER] Residues FyD (Fri Jun 12 2009 - 07:24:35 PDT)
  - Re: [AMBER] Residues KIRTANA S (Fri Jun 12 2009 - 08:07:50 PDT)
    - Re: [AMBER] Residues FyD (Fri Jun 12 2009 - 08:36:10 PDT)
    - Re: [AMBER] Residues KIRTANA S (Fri Jun 12 2009 - 12:41:02 PDT)
    - Re: [AMBER] Residues KIRTANA S (Sat Jun 13 2009 - 17:14:31 PDT)
    - Re: [AMBER] Residues FyD (Sun Jun 14 2009 - 00:02:02 PDT)
- Re: [AMBER] Residues Bill Ross (Fri Jun 12 2009 - 12:49:09 PDT)
- [AMBER] Re: Residues KIRTANA S (Fri Jun 12 2009 - 18:15:20 PDT)
- Re: [AMBER] Residues FyD (Sun Jun 14 2009 - 23:51:56 PDT)
- Re: [AMBER] Residues KIRTANA S (Thu Jun 18 2009 - 12:57:11 PDT)
  - Re: [AMBER] Residues FyD (Thu Jun 18 2009 - 13:24:16 PDT)
- Re: [AMBER] Residues Bill Ross (Thu Jun 18 2009 - 14:13:53 PDT)
  - Re: [AMBER] Residues Roman Osman (Thu Jun 18 2009 - 14:58:53 PDT)
[AMBER] help KIRTANA S (Fri Jun 12 2009 - 06:42:04 PDT)
- RE: [AMBER] help Ross Walker (Fri Jun 12 2009 - 09:02:06 PDT)
[AMBER] dipole printing Hemant Kumar (Fri Jun 12 2009 - 08:58:29 PDT)
- RE: [AMBER] dipole printing Ross Walker (Fri Jun 12 2009 - 09:13:30 PDT)
  - RE: [AMBER] dipole printing Hemant Kumar (Fri Jun 12 2009 - 12:03:17 PDT)
[AMBER] AMBER ERROR Vikas Sharma (Sat Jun 13 2009 - 00:16:52 PDT)
[AMBER] Re: [Contact q4md] qurey reagarding RED Server FyD (Sat Jun 13 2009 - 01:08:26 PDT)
[AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee (Sat Jun 13 2009 - 02:53:43 PDT)
- 回复： [AMBER] too high in binding energy (MM-PBSA) 廖青华 (Sat Jun 13 2009 - 05:44:31 PDT)
  - Re: 回复： [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee (Sat Jun 13 2009 - 06:56:16 PDT)
    - 回复：回复： [AMBER] too high in binding energy (MM-PBSA) 廖青华 (Sat Jun 13 2009 - 08:23:38 PDT)
    - Re: 回复：回复： [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee (Sat Jun 13 2009 - 11:02:16 PDT)
    - Re: 回复：回复： [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee (Sat Jun 13 2009 - 11:02:06 PDT)
    - Re: 回复：回复： [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee (Sat Jun 13 2009 - 11:02:57 PDT)
    - Re: 回复：回复： [AMBER] too high in binding energy (MM-PBSA) Ilyas Yildirim (Sat Jun 13 2009 - 11:19:09 PDT)
    - 回复：回复：回复： [AMBER] too high in binding energy (MM-PBSA) 廖青华 (Sat Jun 13 2009 - 17:48:59 PDT)
    - Re: 回复：回复：回复： [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee (Mon Jun 15 2009 - 03:00:50 PDT)
    - 回复：回复：回复：回复： [AMBER] too high in binding energy (MM-PBSA) 廖青华 (Mon Jun 15 2009 - 03:45:09 PDT)
[AMBER] PLEASE HELP - PDB Modification s_bill36.yahoo.co.uk (Sun Jun 14 2009 - 10:29:31 PDT)
- Re: [AMBER] PLEASE HELP - PDB Modification Tom Joseph (Sun Jun 14 2009 - 16:36:16 PDT)
[AMBER] parallel error 廖青华 (Mon Jun 15 2009 - 00:31:27 PDT)
- Re: [AMBER] parallel error Tom Joseph (Mon Jun 15 2009 - 04:54:19 PDT)
  - 回复： [AMBER] parallel error 廖青华 (Mon Jun 15 2009 - 05:08:27 PDT)
    - Re: 回复： [AMBER] parallel error Tom Joseph (Mon Jun 15 2009 - 05:51:49 PDT)
    - 回复：回复： [AMBER] parallel error 廖青华 (Mon Jun 15 2009 - 06:13:56 PDT)
    - Re: 回复：回复： [AMBER] parallel error Tom Joseph (Mon Jun 15 2009 - 06:25:30 PDT)
    - 回复：回复：回复： [AMBER] parallel error 廖青华 (Mon Jun 15 2009 - 06:35:58 PDT)
    - Re: 回复：回复：回复： [AMBER] parallel error Tom Joseph (Mon Jun 15 2009 - 07:06:05 PDT)
    - 回复：回复：回复：回复： [AMBER] parallel error 廖青华 (Mon Jun 15 2009 - 07:20:59 PDT)
[AMBER] covalent interaction 廖青华 (Mon Jun 15 2009 - 01:06:52 PDT)
[AMBER] total charge for NPRO in ff03ua Edyta Malolepsza (Mon Jun 15 2009 - 03:09:35 PDT)
- RE: [AMBER] total charge for NPRO in ff03ua Jun Wang (Mon Jun 15 2009 - 16:35:39 PDT)
  - Re: [AMBER] total charge for NPRO in ff03ua Edyta Malolepsza (Tue Jun 16 2009 - 02:42:55 PDT)
[AMBER] to unsubscribe email Urszula Uciechowska (Mon Jun 15 2009 - 05:59:46 PDT)
- RE: [AMBER] to unsubscribe email Ross Walker (Mon Jun 15 2009 - 09:59:06 PDT)
- [AMBER] to unsubscribe email backy (Wed Jun 17 2009 - 00:13:02 PDT)
  - RE: [AMBER] to unsubscribe email Ross Walker (Wed Jun 17 2009 - 01:09:39 PDT)
- Re: [AMBER] to unsubscribe email backy (Wed Jun 17 2009 - 01:22:19 PDT)
[AMBER] Antechamber am1bcc questions gilbert.bluemarble.net (Mon Jun 15 2009 - 06:04:19 PDT)
[AMBER] to check basepair in ptraj balaji nagarajan (Mon Jun 15 2009 - 07:23:28 PDT)
[AMBER] Histidine, which form? s_bill36.yahoo.co.uk (Mon Jun 15 2009 - 07:54:05 PDT)
- Re: [AMBER] Histidine, which form? Carlos Simmerling (Mon Jun 15 2009 - 07:57:40 PDT)
- RE: [AMBER] Histidine, which form? Ross Walker (Mon Jun 15 2009 - 08:06:49 PDT)
- Re: [AMBER] Histidine, which form? s. Bill (Mon Jun 15 2009 - 09:28:27 PDT)
  - RE: [AMBER] Histidine, which form? Ross Walker (Mon Jun 15 2009 - 09:39:04 PDT)
    - Re: [AMBER] Histidine, which form? M. L. Dodson (Mon Jun 15 2009 - 09:45:25 PDT)
[AMBER] pKa data base.... s. Bill (Mon Jun 15 2009 - 09:01:14 PDT)
[AMBER] Need help with nab code to access the m_prm struct in a molecule M. L. Dodson (Mon Jun 15 2009 - 12:49:02 PDT)
[AMBER] Re: connect KIRTANA S (Mon Jun 15 2009 - 13:18:54 PDT)
- RE: [AMBER] Re: connect Ross Walker (Mon Jun 15 2009 - 18:43:46 PDT)
- [AMBER] Distance-covariance and PCA questions... Cihan Aydin (Mon Jun 15 2009 - 21:18:58 PDT)
  - Re: [AMBER] Distance-covariance and PCA questions... Hannes Loeffler (Wed Jun 17 2009 - 00:41:42 PDT)
Re: [AMBER] Re: connect Bill Ross (Mon Jun 15 2009 - 13:39:32 PDT)
[AMBER] problem in pressure equillibration wong105.llnl.gov (Mon Jun 15 2009 - 23:18:22 PDT)
- Re: [AMBER] problem in pressure equillibration David A. Case (Tue Jun 16 2009 - 04:56:34 PDT)
[AMBER] Fix the local structure as a rigid body Yunjie Zhao (Tue Jun 16 2009 - 06:11:43 PDT)
- Re: [AMBER] Fix the local structure as a rigid body Carlos Simmerling (Tue Jun 16 2009 - 06:15:12 PDT)
  - Re: [AMBER] Fix the local structure as a rigid body Yunjie Zhao (Tue Jun 16 2009 - 06:57:10 PDT)
    - Re: [AMBER] Fix the local structure as a rigid body Carlos Simmerling (Tue Jun 16 2009 - 07:13:45 PDT)
    - Re: [AMBER] Fix the local structure as a rigid body David A. Case (Tue Jun 16 2009 - 08:41:04 PDT)
[AMBER] Sander imin=5 option Paul Mortenson (Tue Jun 16 2009 - 07:46:37 PDT)
- Re: [AMBER] Sander imin=5 option Carlos Simmerling (Tue Jun 16 2009 - 07:50:43 PDT)
  - RE: [AMBER] Sander imin=5 option Paul Mortenson (Tue Jun 16 2009 - 08:09:54 PDT)
[AMBER] MM decomp energy - zero values for Eele, Evdw Thomas Lake (Tue Jun 16 2009 - 08:36:50 PDT)
[AMBER] connecting residues KIRTANA S (Tue Jun 16 2009 - 08:59:37 PDT)
Re: [AMBER] Distance-covariance and PCA questions... Bill Ross (Tue Jun 16 2009 - 09:18:40 PDT)
Re: [AMBER] connecting residues Bill Ross (Tue Jun 16 2009 - 09:37:33 PDT)
- Re: [AMBER] connecting residues Bill Ross (Tue Jun 16 2009 - 09:39:02 PDT)
[AMBER] Seg-fault when creating residue Valla Fatemi (Tue Jun 16 2009 - 18:28:43 PDT)
- [AMBER] Re: Seg-fault when creating residue Valla Fatemi (Wed Jun 17 2009 - 10:41:47 PDT)
[AMBER] improper torsion problem Youn Kyeung Lee (Tue Jun 16 2009 - 19:36:14 PDT)
[AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Tue Jun 16 2009 - 23:38:56 PDT)
- Re: [AMBER] GLYCAM: warnings by writing topology FyD (Wed Jun 17 2009 - 00:30:26 PDT)
  - Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Wed Jun 17 2009 - 00:50:46 PDT)
    - Re: [AMBER] GLYCAM: warnings by writing topology Karl Kirschner (Wed Jun 17 2009 - 01:33:55 PDT)
    - Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Wed Jun 17 2009 - 02:09:23 PDT)
    - Re: [AMBER] GLYCAM: warnings by writing topology Shubhra Gupta (Wed Jun 17 2009 - 03:33:50 PDT)
    - Re: [AMBER] GLYCAM: warnings by writing topology FyD (Wed Jun 17 2009 - 08:40:06 PDT)
  - Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Wed Jun 17 2009 - 01:18:33 PDT)
- Re: [AMBER] GLYCAM: warnings by writing topology Bill Ross (Wed Jun 17 2009 - 01:01:28 PDT)
  - Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Wed Jun 17 2009 - 01:10:33 PDT)
- Re: [AMBER] GLYCAM: warnings by writing topology Bill Ross (Wed Jun 17 2009 - 10:32:43 PDT)
  - Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Thu Jun 18 2009 - 05:49:31 PDT)
[AMBER] How to calculate SASA in vmd Mannan (Tue Jun 16 2009 - 23:40:05 PDT)
Re: [AMBER] improper torsion problem Bill Ross (Wed Jun 17 2009 - 00:47:12 PDT)
Re: [AMBER] Seg-fault when creating residue Bill Ross (Wed Jun 17 2009 - 00:51:02 PDT)
[AMBER] vlimit in TI with soft core potential Ye MEI (Wed Jun 17 2009 - 01:20:31 PDT)
- Re: [AMBER] vlimit in TI with soft core potential steinbrt.rci.rutgers.edu (Wed Jun 17 2009 - 01:47:38 PDT)
  - Re: [AMBER] vlimit in TI with soft core potential Ye MEI (Wed Jun 17 2009 - 02:13:40 PDT)
[AMBER] Antechamber: stuck at bondtype Jack Shultz (Wed Jun 17 2009 - 05:50:11 PDT)
- Re: [AMBER] Antechamber: stuck at bondtype David A. Case (Wed Jun 17 2009 - 06:28:15 PDT)
- Re: [AMBER] Antechamber: stuck at bondtype Ye MEI (Wed Jun 17 2009 - 06:48:18 PDT)
[AMBER] bond length energy Thomas Lake (Wed Jun 17 2009 - 07:04:55 PDT)
- Re: [AMBER] bond length energy Mark Williamson (Wed Jun 17 2009 - 10:29:09 PDT)
- Re: [AMBER] bond length energy Karl Kirschner (Fri Jun 19 2009 - 02:57:04 PDT)
[AMBER] Specifying improper dihedrals Ben Roberts (Wed Jun 17 2009 - 08:24:14 PDT)
- Re: [AMBER] Specifying improper dihedrals Mark Williamson (Wed Jun 17 2009 - 10:12:08 PDT)
  - Re: [AMBER] Specifying improper dihedrals David A. Case (Wed Jun 17 2009 - 10:56:20 PDT)
    - Re: [AMBER] Specifying improper dihedrals Ben Roberts (Wed Jun 17 2009 - 12:17:12 PDT)
- Re: [AMBER] Specifying improper dihedrals Bill Ross (Wed Jun 17 2009 - 10:56:26 PDT)
  - Re: [AMBER] Specifying improper dihedrals Ben Roberts (Wed Jun 17 2009 - 12:18:41 PDT)
- Re: [AMBER] Specifying improper dihedrals Bill Ross (Wed Jun 17 2009 - 12:25:55 PDT)
[AMBER] Coarse grained MD in AMBER ? Siddharth Rastogi (Wed Jun 17 2009 - 11:50:13 PDT)
- Re: [AMBER] Coarse grained MD in AMBER ? Lili Peng (Wed Jun 17 2009 - 11:57:58 PDT)
[AMBER] where to I get the parameters for Mg divalent ion Mannan (Wed Jun 17 2009 - 21:11:19 PDT)
- Re: [AMBER] where to I get the parameters for Mg divalent ion Tom Joseph (Thu Jun 18 2009 - 20:53:01 PDT)
[AMBER] force units Brad Dickson (Thu Jun 18 2009 - 00:14:31 PDT)
- [AMBER] Re: force units Brad Dickson (Thu Jun 18 2009 - 02:31:16 PDT)
  - Re: [AMBER] Re: force units David A. Case (Thu Jun 18 2009 - 04:32:18 PDT)
    - [AMBER] ptraj correlation Catein Catherine (Thu Jun 18 2009 - 06:47:01 PDT)
    - RE: [AMBER] Re: force units Catein Catherine (Thu Jun 18 2009 - 07:01:40 PDT)
  - [AMBER] Re: force units Brad Dickson (Fri Jun 19 2009 - 06:22:40 PDT)
[AMBER] Improper dihedrals from .off and .lib files Johan Sund (Thu Jun 18 2009 - 03:15:37 PDT)
- Re: [AMBER] Improper dihedrals from .off and .lib files David A. Case (Thu Jun 18 2009 - 04:28:40 PDT)
[AMBER] guntheyp.aston.ac.uk (Thu Jun 18 2009 - 04:48:21 PDT)
- Re: [AMBER] Raja Pandian (Thu Jun 18 2009 - 05:35:10 PDT)
[AMBER] how to create prmtop and inpcrd files for covalent neutral phenylalanine Madhurima Jana (Thu Jun 18 2009 - 05:39:03 PDT)
[AMBER] Sulfates parameterization for GAGs in GLYCAM_06 Sergey Samsonov (Thu Jun 18 2009 - 06:07:17 PDT)
[AMBER] Dyndom Chunliyan (Thu Jun 18 2009 - 08:12:44 PDT)
[AMBER] Fix Residue continued... Vishal Maingi (Thu Jun 18 2009 - 11:48:03 PDT)
- Re: [AMBER] Fix Residue continued... Carlos Simmerling (Thu Jun 18 2009 - 11:56:54 PDT)
[AMBER] residue KIRTANA S (Thu Jun 18 2009 - 12:59:50 PDT)
[AMBER] Re: R.E.D. error message FyD (Thu Jun 18 2009 - 13:13:41 PDT)
[AMBER] Postdoc position in biomolecular simulation Ivaylo, Ivanov (Thu Jun 18 2009 - 16:26:05 PDT)
[AMBER] From DLG to Antechamber Jack Shultz (Thu Jun 18 2009 - 17:04:15 PDT)
- Re: [AMBER] From DLG to Antechamber FyD (Fri Jun 19 2009 - 02:26:46 PDT)
  - Re: [AMBER] From DLG to Antechamber Jack Shultz (Fri Jun 19 2009 - 05:27:20 PDT)
- Re: [AMBER] From DLG to Antechamber gilbert.bluemarble.net (Fri Jun 19 2009 - 05:57:04 PDT)
  - Re: [AMBER] From DLG to Antechamber Jack Shultz (Fri Jun 19 2009 - 06:09:06 PDT)
    - Re: [AMBER] From DLG to Antechamber gilbert.bluemarble.net (Fri Jun 19 2009 - 07:17:09 PDT)
    - Re: [AMBER] From DLG to Antechamber Jack Shultz (Fri Jun 19 2009 - 07:21:37 PDT)
    - Re: [AMBER] From DLG to Antechamber Jack Shultz (Fri Jun 19 2009 - 07:34:33 PDT)
- Re: [AMBER] From DLG to Antechamber FyD (Fri Jun 19 2009 - 08:54:05 PDT)
[AMBER] Force field parameter for Unionized Phenylalanine HOOC-CH(NH2)-CH2-C6H5 Madhurima Jana (Thu Jun 18 2009 - 23:40:43 PDT)
- Re: [AMBER] Force field parameter for Unionized Phenylalanine HOOC-CH(NH2)-CH2-C6H5 FyD (Fri Jun 19 2009 - 01:47:39 PDT)
[AMBER] 2 restraints with different force constants Aust, Susanne (Fri Jun 19 2009 - 00:14:50 PDT)
- Re: [AMBER] 2 restraints with different force constants David A. Case (Fri Jun 19 2009 - 04:41:01 PDT)
AW: [AMBER] 2 restraints with different force constants Aust, Susanne (Fri Jun 19 2009 - 04:51:21 PDT)
- Re: [AMBER] 2 restraints with different force constants David A. Case (Fri Jun 19 2009 - 05:06:18 PDT)
[AMBER] methyl group at the N-terminal Francesca Poletti (Fri Jun 19 2009 - 05:03:56 PDT)
- Re: [AMBER] methyl group at the N-terminal FyD (Fri Jun 19 2009 - 05:12:36 PDT)
AW: [AMBER] 2 restraints with different force constants Aust, Susanne (Fri Jun 19 2009 - 05:39:34 PDT)
[AMBER] Re: residue KIRTANA S (Fri Jun 19 2009 - 08:03:31 PDT)
[AMBER] RED Geometry Calculation Error Brothers, Michael Charles (Fri Jun 19 2009 - 11:52:37 PDT)
- Re: [AMBER] RED Geometry Calculation Error FyD (Fri Jun 19 2009 - 12:19:00 PDT)
  - RE: [AMBER] RED Geometry Calculation Error Brothers, Michael Charles (Fri Jun 19 2009 - 14:10:12 PDT)
    - RE: [AMBER] RED Geometry Calculation Error FyD (Fri Jun 19 2009 - 23:41:46 PDT)
    - [AMBER] PTRAJ, rms for separated residues. Catein Catherine (Mon Jun 22 2009 - 02:20:36 PDT)
    - Re: [AMBER] PTRAJ, rms for separated residues. Germain Vallverdu (Mon Jun 22 2009 - 02:27:43 PDT)
[AMBER] atom type no recognize - xleap version 10 but fine in v 9 Peter Gannett (Fri Jun 19 2009 - 12:40:47 PDT)
- Re: [AMBER] atom type no recognize - xleap version 10 but fine in v 9 case (Sat Jun 20 2009 - 11:31:40 PDT)
[AMBER] PMEMD compilation manoj singh (Fri Jun 19 2009 - 15:49:31 PDT)
- RE: [AMBER] PMEMD compilation Ross Walker (Sat Jun 20 2009 - 10:36:14 PDT)
  - Re: [AMBER] PMEMD compilation manoj singh (Sat Jun 20 2009 - 21:05:44 PDT)
    - RE: [AMBER] PMEMD compilation Ross Walker (Sat Jun 20 2009 - 21:15:23 PDT)
    - Re: [AMBER] PMEMD compilation manoj singh (Sat Jun 20 2009 - 21:22:01 PDT)
    - RE: [AMBER] PMEMD compilation Ross Walker (Sat Jun 20 2009 - 21:32:18 PDT)
    - Re: [AMBER] PMEMD compilation manoj singh (Sat Jun 20 2009 - 21:30:17 PDT)
[AMBER] Hard limit in Amber10? Yang, Ping (Fri Jun 19 2009 - 17:21:14 PDT)
- RE: [AMBER] Hard limit in Amber10? Ross Walker (Sat Jun 20 2009 - 10:40:46 PDT)
- RE: [AMBER] Hard limit in Amber10? Yang, Ping (Sat Jun 20 2009 - 16:44:11 PDT)
  - RE: [AMBER] Hard limit in Amber10? Yang, Ping (Mon Jun 22 2009 - 18:52:39 PDT)
    - RE: [AMBER] Hard limit in Amber10? Ross Walker (Wed Jun 24 2009 - 09:02:17 PDT)
R: [AMBER] Amber10 Parallel Installation sgrignani.cerm.unifi.it (Sat Jun 20 2009 - 13:14:38 PDT)
Re: [AMBER] Amber10 Parallel Installation case (Sat Jun 20 2009 - 15:04:14 PDT)
[AMBER] Your private message from Vikas is about to expire Vikas S (Sat Jun 20 2009 - 23:41:57 PDT)
[AMBER] Reference Correction Mahmoud A. A. Ibrahim (Sun Jun 21 2009 - 13:11:34 PDT)
[AMBER] reclaiming space from amber10 installation Alan (Sun Jun 21 2009 - 15:04:53 PDT)
- [AMBER] correlation motion at production simulation period still changing. Is it normal? Catein Catherine (Mon Jun 22 2009 - 02:26:40 PDT)
- RE: [AMBER] reclaiming space from amber10 installation Ross Walker (Mon Jun 22 2009 - 18:26:36 PDT)
[AMBER] parameters Fe4S4 cluster KIRTANA S (Sun Jun 21 2009 - 19:30:08 PDT)
[AMBER] Atom Type List Javier Klett (Mon Jun 22 2009 - 02:54:43 PDT)
- Re: [AMBER] Atom Type List case (Mon Jun 22 2009 - 04:38:24 PDT)
  - Re: [Barracuda SPAM] Re: [AMBER] Atom Type List Javier Klett (Mon Jun 22 2009 - 09:34:43 PDT)
    - Re: [Barracuda SPAM] Re: [AMBER] Atom Type List Bill Ross (Mon Jun 22 2009 - 09:43:39 PDT)
[AMBER] About the Amber tutorial Aurum Bai (Mon Jun 22 2009 - 03:03:49 PDT)
[AMBER] About the "FATAL: Atom err!" Aurum Bai (Mon Jun 22 2009 - 03:12:23 PDT)
[AMBER] About the "FATAL: Atom err"! Aurum Bai (Mon Jun 22 2009 - 03:14:20 PDT)
- Re: [AMBER] About the "FATAL: Atom err"! case (Mon Jun 22 2009 - 04:47:59 PDT)
[AMBER] Error on equilibriation of Amber10 Masakazu SEKIJIMA (Mon Jun 22 2009 - 03:59:55 PDT)
- Re: [AMBER] Problems using nmode in NAB Andreas Svrcek-Seiler (Wed Jun 24 2009 - 01:52:30 PDT)
  - Re: [AMBER] Problems using nmode in NAB E.M. (Wed Jun 24 2009 - 02:09:44 PDT)
  - Re: [AMBER] Problems using nmode in NAB E.M. (Wed Jun 24 2009 - 21:15:38 PDT)
    - Re: [AMBER] Problems using nmode in NAB Andreas Svrcek-Seiler (Thu Jun 25 2009 - 06:03:15 PDT)
- [AMBER] Re: Error on equilibriation of Amber10 Masakazu SEKIJIMA (Thu Jun 25 2009 - 03:45:31 PDT)
  - Re: [AMBER] Re: Error on equilibriation of Amber10 case (Thu Jun 25 2009 - 05:07:20 PDT)
    - Re: [AMBER] Re: Error on equilibriation of Amber10 Masakazu SEKIJIMA (Thu Jun 25 2009 - 10:41:39 PDT)
    - Re: [AMBER] Re: Error on equilibriation of Amber10 case (Fri Jun 26 2009 - 05:17:42 PDT)
[AMBER] max atoms for antechamber Alan (Mon Jun 22 2009 - 05:37:39 PDT)
- Re: [AMBER] max atoms for antechamber case (Mon Jun 22 2009 - 05:48:43 PDT)
  - Re: [AMBER] max atoms for antechamber Alan (Mon Jun 22 2009 - 06:00:48 PDT)
[AMBER] making leap to recognize 5' phosphate Bala subramanian (Mon Jun 22 2009 - 06:45:43 PDT)
- Re: [AMBER] making leap to recognize 5' phosphate FyD (Tue Jun 23 2009 - 00:45:31 PDT)
  - Re: [AMBER] making leap to recognize 5' phosphate Bala subramanian (Tue Jun 23 2009 - 01:49:05 PDT)
    - Re: [AMBER] making leap to recognize 5' phosphate FyD (Tue Jun 23 2009 - 02:48:34 PDT)
- Re: [AMBER] making leap to recognize 5' phosphate FyD (Tue Jun 23 2009 - 23:02:42 PDT)
[AMBER] Re: Regd: Fe4S4 case (Mon Jun 22 2009 - 11:39:57 PDT)
RE: [Subject Filtered] Re: [AMBER] Amber10 Parallel Installation 8% Hopkins, Robert (Mon Jun 22 2009 - 12:54:17 PDT)
[AMBER] bad atom type: MN Edward M (Mon Jun 22 2009 - 16:10:54 PDT)
[AMBER] bad atom type: MN Edward M (Mon Jun 22 2009 - 16:12:09 PDT)
[AMBER] AMBER question: bad atom type: MN Edward M (Mon Jun 22 2009 - 20:05:51 PDT)
[AMBER] REMD Shaikh Abdul R S Ramaju (Mon Jun 22 2009 - 22:32:34 PDT)
- Re: [AMBER] REMD Carlos Simmerling (Tue Jun 23 2009 - 03:07:39 PDT)
[AMBER] guessing the charge of a small molecule Alan (Tue Jun 23 2009 - 01:06:51 PDT)
[AMBER] Compiling amber 9 with openMPI Myunggi Yi (Tue Jun 23 2009 - 06:31:58 PDT)
- Re: [AMBER] Compiling amber 9 with openMPI case (Tue Jun 23 2009 - 07:13:18 PDT)
  - Re: [AMBER] Compiling amber 9 with openMPI Myunggi Yi (Tue Jun 23 2009 - 11:11:46 PDT)
[AMBER] net charge Vishal Maingi (Tue Jun 23 2009 - 07:19:51 PDT)
- Re: [AMBER] net charge case (Tue Jun 23 2009 - 07:34:07 PDT)
[AMBER] SANDER BOMB in subroutine nonbond_list Siddharth Rastogi (Tue Jun 23 2009 - 09:39:58 PDT)
Re: [AMBER] SANDER BOMB in subroutine nonbond_list Bill Ross (Tue Jun 23 2009 - 09:54:30 PDT)
[AMBER] re: net charge Vishal Maingi (Tue Jun 23 2009 - 11:56:52 PDT)
- Re: [AMBER] re: net charge case (Tue Jun 23 2009 - 12:22:28 PDT)
  - Re: [AMBER] re: net charge Junmei Wang (Tue Jun 23 2009 - 13:41:24 PDT)
[AMBER] "loadoff tRNA.lib" in Leap Ju Zhang (Tue Jun 23 2009 - 13:55:25 PDT)
[AMBER] 2-step vs 3-step TI, and softcores question Jodi Hadden (Tue Jun 23 2009 - 15:00:02 PDT)
- Re: [AMBER] 2-step vs 3-step TI, and softcores question steinbrt.rci.rutgers.edu (Tue Jun 23 2009 - 15:27:46 PDT)
[AMBER] How to build amide bond etween two protein chains journal.update (Tue Jun 23 2009 - 21:36:07 PDT)
- Re: [AMBER] How to build amide bond etween two protein chains FyD (Tue Jun 23 2009 - 23:18:25 PDT)
[AMBER] error in tleap of AMBER 10 kureeckal ramesh (Tue Jun 23 2009 - 22:03:55 PDT)
- Re: [AMBER] error in tleap of AMBER 10 case (Thu Jun 25 2009 - 04:54:47 PDT)
[AMBER] Problems using nmode in NAB E.M. (Tue Jun 23 2009 - 23:05:50 PDT)
[AMBER] calculating the hydrogen bonding energy between the two molecule bharat lakhani (Wed Jun 24 2009 - 02:19:01 PDT)
[AMBER] Trying to patch amber 9 Jack Shultz (Wed Jun 24 2009 - 06:24:40 PDT)
- Re: [AMBER] Trying to patch amber 9 case (Wed Jun 24 2009 - 07:58:48 PDT)
  - Re: [AMBER] Trying to patch amber 9 Jack Shultz (Wed Jun 24 2009 - 08:18:23 PDT)
    - Re: [AMBER] Trying to patch amber 9 Jack Shultz (Wed Jun 24 2009 - 08:25:41 PDT)
[AMBER] Half charge reported during NN ? Marek Maly (Wed Jun 24 2009 - 09:33:54 PDT)
- Re: [AMBER] Half charge reported during NN ? case (Wed Jun 24 2009 - 10:31:45 PDT)
  - Re: [AMBER] Half charge reported during NN ? Marek Maly (Wed Jun 24 2009 - 10:43:26 PDT)
[AMBER] problem with parametrization janzso.brc.hu (Wed Jun 24 2009 - 11:24:45 PDT)
- RE: [AMBER] problem with parametrization Brothers, Michael Charles (Wed Jun 24 2009 - 11:34:16 PDT)
- Re: [AMBER] problem with parametrization FyD (Wed Jun 24 2009 - 22:15:23 PDT)
  - Re: [AMBER] problem with parametrization janzso.brc.hu (Thu Jun 25 2009 - 02:49:50 PDT)
- Re: [AMBER] problem with parametrization FyD (Thu Jun 25 2009 - 03:04:27 PDT)
  - Re: [AMBER] problem with parametrization janzso.brc.hu (Thu Jun 25 2009 - 04:40:35 PDT)
    - Re: [AMBER] problem with parametrization FyD (Thu Jun 25 2009 - 04:52:45 PDT)
    - Re: [AMBER] problem with parametrization janzso.brc.hu (Thu Jun 25 2009 - 05:04:27 PDT)
    - Re: [AMBER] problem with parametrization FyD (Thu Jun 25 2009 - 06:47:31 PDT)
    - Re: [AMBER] problem with parametrization janzso.brc.hu (Mon Jun 29 2009 - 02:30:50 PDT)
[AMBER] Amber tools 1.2 , Bug report (PTRAJ: dumpq with strip) Myunggi Yi (Wed Jun 24 2009 - 11:57:25 PDT)
[AMBER] NAB memory increase E.M. (Wed Jun 24 2009 - 13:12:09 PDT)
- Re: [AMBER] NAB memory increase case (Thu Jun 25 2009 - 04:33:03 PDT)
- Re: [AMBER] NAB memory increase Bill Ross (Thu Jun 25 2009 - 09:34:58 PDT)
[AMBER] setting atomic radii for GB version 7 Workalemhu Berhanu (Wed Jun 24 2009 - 20:12:55 PDT)
- Re: [AMBER] setting atomic radii for GB version 7 case (Thu Jun 25 2009 - 05:20:36 PDT)
Re: [AMBER] atomtypes in gaff FyD (Thu Jun 25 2009 - 01:55:03 PDT)
[AMBER] Re: question about ff FyD (Thu Jun 25 2009 - 02:12:40 PDT)
[AMBER] ADD SALT Rilei Yu (Thu Jun 25 2009 - 02:22:20 PDT)
- Re: [AMBER] ADD SALT Simon Becker (Thu Jun 25 2009 - 02:57:37 PDT)
AW: [AMBER] atomtypes in gaff Aust, Susanne (Thu Jun 25 2009 - 02:24:07 PDT)
- Re: AW: [AMBER] atomtypes in gaff FyD (Thu Jun 25 2009 - 03:32:33 PDT)
AW: AW: [AMBER] atomtypes in gaff Aust, Susanne (Thu Jun 25 2009 - 04:27:19 PDT)
- Re: AW: AW: [AMBER] atomtypes in gaff FyD (Thu Jun 25 2009 - 04:36:20 PDT)
- Re: [AMBER] atomtypes in gaff FyD (Thu Jun 25 2009 - 04:45:16 PDT)
[AMBER] PCA for CA of specific resiudes Patrick Gedeon (Thu Jun 25 2009 - 04:43:20 PDT)
- Re: [AMBER] PCA for CA of specific resiudes case (Thu Jun 25 2009 - 05:27:01 PDT)
AW: AW: AW: [AMBER] atomtypes in gaff Aust, Susanne (Thu Jun 25 2009 - 04:44:58 PDT)
AW: [AMBER] atomtypes in gaff Aust, Susanne (Thu Jun 25 2009 - 05:05:10 PDT)
- Re: AW: [AMBER] atomtypes in gaff FyD (Thu Jun 25 2009 - 23:56:35 PDT)
[AMBER] Error when installing amber11 on OpenSuse steinbrt.rci.rutgers.edu (Thu Jun 25 2009 - 05:19:59 PDT)
[AMBER] ADD SALT additional question Simon Becker (Thu Jun 25 2009 - 05:34:36 PDT)
- Re: [AMBER] ADD SALT additional question Vlad Cojocaru (Thu Jun 25 2009 - 07:51:54 PDT)
- Re: [AMBER] ADD SALT additional question Vlad Cojocaru (Thu Jun 25 2009 - 07:55:15 PDT)
[AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice (Thu Jun 25 2009 - 08:24:25 PDT)
- Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error David Watson (Thu Jun 25 2009 - 11:53:16 PDT)
  - Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice (Thu Jun 25 2009 - 17:54:31 PDT)
    - Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error David Watson (Thu Jun 25 2009 - 19:28:22 PDT)
    - Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice (Thu Jun 25 2009 - 19:36:06 PDT)
    - Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error David Watson (Thu Jun 25 2009 - 19:51:11 PDT)
    - Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice (Thu Jun 25 2009 - 20:24:18 PDT)
    - Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error David Watson (Fri Jun 26 2009 - 04:31:26 PDT)
    - Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice (Tue Jun 30 2009 - 08:06:03 PDT)
Re: AW: [AMBER] atomtypes in gaff Bill Ross (Thu Jun 25 2009 - 09:42:01 PDT)
[AMBER] Compiling and running NAB programs in parallel using MPI Kaushik Raha (Thu Jun 25 2009 - 14:36:35 PDT)
- Re: [AMBER] Compiling and running NAB programs in parallel using MPI case (Fri Jun 26 2009 - 06:19:04 PDT)
  - Re: [AMBER] Compiling and running NAB programs in parallel using MPI Kaushik Raha (Fri Jun 26 2009 - 08:12:11 PDT)
    - Re: [AMBER] Compiling and running NAB programs in parallel using MPI case (Mon Jun 29 2009 - 05:19:10 PDT)
    - Re: [AMBER] Compiling and running NAB programs in parallel using MPI Kaushik Raha (Tue Jun 30 2009 - 07:48:11 PDT)
    - Re: [AMBER] Compiling and running NAB programs in parallel using MPI case (Tue Jun 30 2009 - 09:02:57 PDT)
[AMBER] Thanks Simon and Vlad! Rilei Yu (Thu Jun 25 2009 - 16:32:35 PDT)
[AMBER] error in tleap of AMBER 10 kureeckal ramesh (Fri Jun 26 2009 - 00:10:56 PDT)
- Re: [AMBER] error in tleap of AMBER 10 case (Fri Jun 26 2009 - 05:09:58 PDT)
[AMBER] Box Center Jagan Mohan (Fri Jun 26 2009 - 01:02:05 PDT)
[AMBER] installation of RESP programm subarna thakur (Fri Jun 26 2009 - 01:52:57 PDT)
- Re: [AMBER] installation of RESP programm FyD (Fri Jun 26 2009 - 02:15:39 PDT)
[AMBER] Problem with radial distribution function aneesh cna (Fri Jun 26 2009 - 01:56:09 PDT)
[AMBER] query about the charge fitting procedure about C- and N-terminal residues Ye MEI (Fri Jun 26 2009 - 02:19:47 PDT)
- Re: [AMBER] query about the charge fitting procedure about C- and N-terminal residues FyD (Fri Jun 26 2009 - 02:41:52 PDT)
[AMBER] a method or program to try to guess the net charge of a small molecule Alan (Fri Jun 26 2009 - 03:00:48 PDT)
[AMBER] force field choice ahmed said (Fri Jun 26 2009 - 01:21:16 PDT)
[AMBER] NAB memory E.M. (Fri Jun 26 2009 - 11:06:41 PDT)
- Re: [AMBER] NAB memory case (Fri Jun 26 2009 - 11:42:03 PDT)
Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration Cihan Aydin (Sat Jun 27 2009 - 07:29:21 PDT)
- Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration Naser Alijabbari (Sat Jun 27 2009 - 11:19:23 PDT)
  - Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration Cihan Aydin (Sun Jun 28 2009 - 09:19:07 PDT)
[AMBER] explicit solvent NMR refinement Sally Pias (Sun Jun 28 2009 - 01:46:56 PDT)
- Re: [AMBER] explicit solvent NMR refinement Carlos Simmerling (Sun Jun 28 2009 - 05:36:42 PDT)
- Re: [AMBER] explicit solvent NMR refinement case (Sun Jun 28 2009 - 06:19:11 PDT)
[AMBER] Velocity rescaling and ig... Cihan Aydin (Sun Jun 28 2009 - 07:52:30 PDT)
- Re: [AMBER] Velocity rescaling and ig... Carlos Simmerling (Sun Jun 28 2009 - 08:35:37 PDT)
  - Re: [AMBER] Velocity rescaling and ig... Cihan Aydin (Sun Jun 28 2009 - 09:08:32 PDT)
    - RE: [AMBER] Velocity rescaling and ig... Ross Walker (Sun Jun 28 2009 - 09:18:08 PDT)
    - RE: [AMBER] Velocity rescaling and ig... Cihan Aydin (Sun Jun 28 2009 - 09:22:29 PDT)
[AMBER] how to creat an mixture sovlent of hexane and water TaoPaul (Sun Jun 28 2009 - 08:58:19 PDT)
[AMBER] Analysis of the solt-bridge Rilei Yu (Sun Jun 28 2009 - 15:24:28 PDT)
- Re: [AMBER] Analysis of the solt-bridge Alessandro Nascimento (Mon Jun 29 2009 - 05:58:49 PDT)
  - Re: [AMBER] Analysis of the solt-bridge Rilei Yu (Mon Jun 29 2009 - 15:42:23 PDT)
[AMBER] Simulations including RNA-protein complexes... Cihan Aydin (Sun Jun 28 2009 - 15:29:10 PDT)
[AMBER] RESP Syed Tarique Moin (Mon Jun 29 2009 - 00:42:51 PDT)
- Re: [AMBER] RESP case (Mon Jun 29 2009 - 04:52:19 PDT)
[AMBER] Steps for NMR structure minimization Prem Prakash Pathak (Mon Jun 29 2009 - 07:09:34 PDT)
[AMBER] steps for NMR structure minimization of protein Prem Prakash Pathak (Mon Jun 29 2009 - 07:12:40 PDT)
[AMBER] steps for NMR structure minimization of protein Prem Prakash Pathak (Mon Jun 29 2009 - 07:13:33 PDT)
[AMBER] problems with ptraj option IMAGE Antonija Tomić (Mon Jun 29 2009 - 07:48:54 PDT)
- Re: [AMBER] problems with ptraj option IMAGE Carlos Simmerling (Mon Jun 29 2009 - 08:00:59 PDT)
  - Re: [AMBER] problems with ptraj option IMAGE Antonija Tomić (Mon Jun 29 2009 - 08:27:54 PDT)
[AMBER] Regd: parameter Fe4S4 KIRTANA S (Mon Jun 29 2009 - 09:11:49 PDT)
- Re: [AMBER] Regd: parameter Fe4S4 FyD (Mon Jun 29 2009 - 12:03:22 PDT)
[AMBER] Nonstandard molecules simulated with parm99EP ? Marek Maly (Mon Jun 29 2009 - 10:06:27 PDT)
- Re: [AMBER] Nonstandard molecules simulated with parm99EP ? FyD (Mon Jun 29 2009 - 11:28:19 PDT)
  - Re: [AMBER] Nonstandard molecules simulated with parm99EP ? Marek Maly (Mon Jun 29 2009 - 13:48:52 PDT)
    - Re: [AMBER] Nonstandard molecules simulated with parm99EP ? FyD (Tue Jun 30 2009 - 00:31:53 PDT)
    - Re: [AMBER] Nonstandard molecules simulated with parm99EP ? case (Tue Jun 30 2009 - 09:19:00 PDT)
[AMBER] Fe-S topology subarna thakur (Mon Jun 29 2009 - 23:29:16 PDT)
- Re: [AMBER] Fe-S topology Markus Kaukonen (Tue Jun 30 2009 - 00:28:51 PDT)
  - Re: [AMBER] Fe-S topology case (Tue Jun 30 2009 - 10:45:27 PDT)
[AMBER] Saccharides chains termini Sergey Samsonov (Tue Jun 30 2009 - 07:32:53 PDT)
- Re: [AMBER] Saccharides chains termini Lachele Foley (Lists) (Tue Jun 30 2009 - 07:46:09 PDT)
- Re: [AMBER] Saccharides chains termini Karl Kirschner (Tue Jun 30 2009 - 07:57:46 PDT)
- Re: [AMBER] Saccharides chains termini FyD (Tue Jun 30 2009 - 08:47:04 PDT)
[AMBER] Partial charges of heme Justine Shaw Condo (Tue Jun 30 2009 - 11:28:11 PDT)
[AMBER] Fe and Mn simulations Alessandro Nascimento (Tue Jun 30 2009 - 13:22:14 PDT)

Amber Archive Jun 2009 by thread