Amber Archive Jul 2010: by thread

[AMBER] maintaining temperature scheme missing_grace.sina.com (Wed Jun 30 2010 - 21:05:21 PDT)
- Re: [AMBER] maintaining temperature scheme Jason Swails (Wed Jun 30 2010 - 23:11:16 PDT)
Re: [AMBER] regarding mmpbsa Asfa Ali (Wed Jun 30 2010 - 22:01:45 PDT)
- Re: [AMBER] regarding mmpbsa Dwight McGee (Thu Jul 01 2010 - 07:09:20 PDT)
Re: [AMBER] vlimit exceeded for step Homa Azizian (Wed Jun 30 2010 - 22:22:04 PDT)
- Re: [AMBER] vlimit exceeded for step case (Thu Jul 01 2010 - 05:03:09 PDT)
Re: [AMBER] adding counterions Jason Swails (Wed Jun 30 2010 - 22:49:33 PDT)
- Re: [AMBER] adding counterions Bill Ross (Thu Jul 01 2010 - 10:40:27 PDT)
- Re: [AMBER] adding counterions Ping (Thu Jul 01 2010 - 11:12:24 PDT)
- Re: [AMBER] adding counterions Bill Ross (Thu Jul 01 2010 - 11:19:58 PDT)
  - Re: [AMBER] adding counterions Ping (Thu Jul 01 2010 - 11:37:47 PDT)
    - Re: [AMBER] adding counterions Paul S. Nerenberg (Thu Jul 01 2010 - 11:39:44 PDT)
- Re: [AMBER] adding counterions Bill Ross (Thu Jul 01 2010 - 11:41:40 PDT)
Re: [AMBER] AmberTools installation in Cygwin Jason Swails (Wed Jun 30 2010 - 22:59:45 PDT)
- Re: [AMBER] AmberTools installation in Cygwin Yan Gao (Thu Jul 01 2010 - 10:22:02 PDT)
- Re: [AMBER] AmberTools installation in Cygwin Yan Gao (Thu Jul 01 2010 - 11:52:51 PDT)
  - Re: [AMBER] AmberTools installation in Cygwin case (Thu Jul 01 2010 - 13:21:21 PDT)
    - Re: [AMBER] AmberTools installation in Cygwin Yan Gao (Thu Jul 01 2010 - 14:11:33 PDT)
Re: [AMBER] Questions with input file in constant pH MD nicholus bhattacharjee (Wed Jun 30 2010 - 23:53:26 PDT)
- Re: [AMBER] Questions with input file in constant pH MD Bill Miller III (Thu Jul 01 2010 - 06:28:50 PDT)
[AMBER] File MAKE_CRD is not found fancy2012 (Wed Jun 30 2010 - 23:59:21 PDT)
- Re: [AMBER] File MAKE_CRD is not found Jason Swails (Thu Jul 01 2010 - 06:41:31 PDT)
[AMBER] Regarding Antechamber Tutorial sonali dhindwal (Thu Jul 01 2010 - 00:23:09 PDT)
- Re: [AMBER] Regarding Antechamber Tutorial vaibhav dixit (Thu Jul 01 2010 - 00:49:30 PDT)
  - Re: [AMBER] Regarding Antechamber Tutorial sonali dhindwal (Thu Jul 01 2010 - 01:43:05 PDT)
- Re: [AMBER] Regarding Antechamber Tutorial case (Thu Jul 01 2010 - 05:17:09 PDT)
Re: [AMBER] mmgbsa tricky output Amor San Juan (Thu Jul 01 2010 - 00:39:51 PDT)
- Re: [AMBER] mmgbsa tricky output Bill Ross (Thu Jul 01 2010 - 10:09:39 PDT)
- Re: [AMBER] mmgbsa tricky output Ray Luo (Thu Jul 01 2010 - 15:46:37 PDT)
  - Re: [AMBER] mmgbsa tricky output Amor San Juan (Sun Jul 04 2010 - 20:49:01 PDT)
    - Re: [AMBER] mmgbsa tricky output Amor San Juan (Sun Jul 04 2010 - 23:22:13 PDT)
    - Re: [AMBER] mmgbsa tricky output: PART 2 Amor San Juan (Mon Jul 05 2010 - 23:48:35 PDT)
    - Re: [AMBER] mmgbsa tricky output: PART 2 Jason Swails (Tue Jul 06 2010 - 06:00:59 PDT)
    - Re: [AMBER] mmgbsa tricky output: PART 2 Amor San Juan (Wed Jul 07 2010 - 03:03:10 PDT)
    - [AMBER] mmgbsa for ternary system Amor San Juan (Wed Jul 07 2010 - 03:42:50 PDT)
    - Re: [AMBER] mmgbsa for ternary system Jason Swails (Wed Jul 07 2010 - 07:15:08 PDT)
    - Re: [AMBER] mmgbsa for ternary system Amor San Juan (Thu Jul 08 2010 - 03:23:16 PDT)
    - [AMBER] MMPBSA.PY with two parts receptor Amor San Juan (Tue Jul 13 2010 - 22:48:57 PDT)
    - Re: [AMBER] MMPBSA.PY with two parts receptor Bill Miller III (Wed Jul 14 2010 - 03:21:48 PDT)
    - Re: [AMBER] MMPBSA.PY with two parts receptor Amor San Juan (Mon Jul 19 2010 - 01:05:43 PDT)
    - Re: [AMBER] MMPBSA.PY with two parts receptor Jason Swails (Mon Jul 19 2010 - 07:57:29 PDT)
    - [AMBER] Segmentation fault in MMPBSA.PY with two parts receptor Amor San Juan (Tue Jul 20 2010 - 03:16:57 PDT)
    - Re: [AMBER] Segmentation fault in MMPBSA.PY with two parts receptor Oliver Grant (Tue Jul 20 2010 - 03:30:45 PDT)
    - [AMBER] Thank you Jason, Bill and Oliver Amor San Juan (Wed Jul 21 2010 - 00:12:51 PDT)
    - Re: [AMBER] mmgbsa tricky output: PART 2 Jason Swails (Wed Jul 07 2010 - 07:04:56 PDT)
    - [AMBER] MMPBSA.py source files Amor San Juan (Fri Jul 09 2010 - 01:36:35 PDT)
    - [AMBER] What is the way to change from MMPBSA+GBSA to MMGBSA only input file. Catein Catherine (Fri Jul 09 2010 - 03:50:40 PDT)
    - Re: [AMBER] What is the way to change from MMPBSA+GBSA to MMGBSA only input file. Oliver Grant (Fri Jul 09 2010 - 03:57:02 PDT)
    - [AMBER] How to find the angle bond etc parameters used for practicular atom type used in AMBER? Catein Catherine (Fri Jul 09 2010 - 04:23:22 PDT)
    - Re: [AMBER] How to find the angle bond etc parameters used for practicular atom type used in AMBER? James Maier (Fri Jul 09 2010 - 07:21:55 PDT)
    - Re: [AMBER] How to find the angle bond etc parameters used for practicular atom type used in AMBER? Catein Catherine (Fri Jul 09 2010 - 08:11:58 PDT)
    - [AMBER] Do I have to keep the Na+ counterions in prmtop and snapshot generation when I do mmGBSA/PBSA calculation? Catein Catherine (Fri Jul 09 2010 - 04:14:24 PDT)
    - Re: [AMBER] Do I have to keep the Na+ counterions in prmtop and snapshot generation when I do mmGBSA/PBSA calculation? Oliver Grant (Fri Jul 09 2010 - 04:24:38 PDT)
    - Re: [AMBER] Do I have to keep the Na+ counterions in prmtop and snapshot generation when I do mmGBSA/PBSA calculation? Mahmoud A. A. Ibrahim (Fri Jul 09 2010 - 04:29:37 PDT)
    - Re: [AMBER] Do I have to keep the Na+ counterions in prmtop and snapshot generation when I do mmGBSA/PBSA calculation? Oliver Grant (Fri Jul 09 2010 - 04:42:32 PDT)
    - Re: [AMBER] MMPBSA.py source files case (Fri Jul 09 2010 - 05:26:43 PDT)
    - Re: [AMBER] mmgbsa tricky output Mannan (Wed Jul 07 2010 - 20:08:01 PDT)
Re: [AMBER] installing AmberTools 1.4 on AIX Mirko Cestari (Thu Jul 01 2010 - 00:44:23 PDT)
- Re: [AMBER] installing AmberTools 1.4 on AIX case (Thu Jul 01 2010 - 05:26:01 PDT)
  - Re: [AMBER] installing AmberTools 1.4 on AIX Mirko Cestari (Wed Jul 07 2010 - 05:52:27 PDT)
Re: [AMBER] force field parameter and resp charge calculation colvin (Thu Jul 01 2010 - 04:00:34 PDT)
[AMBER] hydrogen bond printout Beale, John (Thu Jul 01 2010 - 04:29:14 PDT)
Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o case (Thu Jul 01 2010 - 05:58:33 PDT)
- Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Yu Chen (Thu Jul 01 2010 - 06:58:33 PDT)
  - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o case (Thu Jul 01 2010 - 07:52:30 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Jason Swails (Thu Jul 01 2010 - 08:00:16 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Yu Chen (Thu Jul 01 2010 - 08:24:09 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Yu Chen (Thu Jul 01 2010 - 08:37:46 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o case (Thu Jul 01 2010 - 09:52:11 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Yu Chen (Thu Jul 01 2010 - 14:16:04 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o case (Thu Jul 01 2010 - 14:58:56 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Jason Swails (Thu Jul 01 2010 - 20:55:20 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Yu Chen (Fri Jul 02 2010 - 06:50:24 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Jason Swails (Fri Jul 02 2010 - 07:19:51 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Yu Chen (Fri Jul 02 2010 - 06:31:44 PDT)
[AMBER] results calculated by mmpbsa.pl and mmpbsa.py lidansa.mail.ustc.edu.cn (Thu Jul 01 2010 - 07:18:09 PDT)
- Re: [AMBER] results calculated by mmpbsa.pl and mmpbsa.py Jason Swails (Thu Jul 01 2010 - 07:55:50 PDT)
Re: [AMBER] make test.parallel case (Thu Jul 01 2010 - 07:39:15 PDT)
[AMBER] 3D-RISM in NAB AmberTools: what is tolerance and initial guess Andrey Frolov (Thu Jul 01 2010 - 09:09:51 PDT)
- Re: [AMBER] 3D-RISM in NAB AmberTools: what is tolerance and initial guess Tyler Luchko (Fri Jul 02 2010 - 06:39:18 PDT)
[AMBER] 3D-RISM in NAB AmberTools: 2) what is tolerance Andrey Frolov (Thu Jul 01 2010 - 09:16:38 PDT)
- Re: [AMBER] 3D-RISM in NAB AmberTools: 2) what is tolerance Tyler Luchko (Fri Jul 02 2010 - 07:08:41 PDT)
Re: [AMBER] AmberTools installation in Cygwin --- thanks and new errors Yan Gao (Thu Jul 01 2010 - 11:53:34 PDT)
[AMBER] Conformation capture in molecular dynamics Yuqin Cai (Thu Jul 01 2010 - 18:46:01 PDT)
- [AMBER] create a prmtop file without water & ions, Homa Azizian (Thu Jul 01 2010 - 20:13:52 PDT)
  - Re: [AMBER] create a prmtop file without water & ions, Jason Swails (Thu Jul 01 2010 - 22:46:17 PDT)
[AMBER] About the ptraj problem c00jsw00 (Thu Jul 01 2010 - 22:12:40 PDT)
- Re: [AMBER] About the ptraj problem Jason Swails (Thu Jul 01 2010 - 22:48:06 PDT)
  - Re: [AMBER] About the ptraj problem c00jsw00 (Fri Jul 02 2010 - 00:13:34 PDT)
    - Re: [AMBER] About the ptraj problem Jason Swails (Fri Jul 02 2010 - 07:24:59 PDT)
- Re: [AMBER] About the ptraj problem Bill Ross (Fri Jul 02 2010 - 10:18:41 PDT)
[AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! sunita gupta (Fri Jul 02 2010 - 00:43:25 PDT)
- Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! steinbrt.rci.rutgers.edu (Fri Jul 02 2010 - 01:33:19 PDT)
  - Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! sunita gupta (Fri Jul 02 2010 - 02:01:51 PDT)
    - [AMBER] Any parameters for Mg2+? Catein Catherine (Fri Jul 02 2010 - 02:30:24 PDT)
    - [AMBER] What ab initio methods can be choose for QM/MM package in AMBER10? Catein Catherine (Fri Jul 02 2010 - 02:34:31 PDT)
    - Re: [AMBER] What ab initio methods can be choose for QM/MM package in AMBER10? Gustavo Seabra (Fri Jul 02 2010 - 03:40:03 PDT)
    - Re: [AMBER] Any parameters for Mg2+? Jason Swails (Fri Jul 02 2010 - 07:28:41 PDT)
    - Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! steinbrt.rci.rutgers.edu (Fri Jul 02 2010 - 03:43:09 PDT)
    - Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! sunita gupta (Thu Jul 08 2010 - 01:10:27 PDT)
    - Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! steinbrt.rci.rutgers.edu (Thu Jul 08 2010 - 01:49:49 PDT)
    - Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! sunita gupta (Fri Jul 09 2010 - 05:11:40 PDT)
    - Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! case (Fri Jul 09 2010 - 05:36:01 PDT)
    - Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! steinbrt.rci.rutgers.edu (Fri Jul 09 2010 - 05:43:47 PDT)
Re: [AMBER] Adding Ions. Ajay Ummat (Fri Jul 02 2010 - 07:45:03 PDT)
- Re: [AMBER] Adding Ions. Jason Swails (Fri Jul 02 2010 - 09:00:47 PDT)
  - [AMBER] MMPBSA.py install error Catein Catherine (Sat Jul 03 2010 - 04:38:33 PDT)
    - Re: [AMBER] MMPBSA.py install error Jason Swails (Sat Jul 03 2010 - 07:44:41 PDT)
    - [AMBER] How do define phospho-tyrosine-DA linkage? Catein Catherine (Sat Jul 03 2010 - 10:38:41 PDT)
    - [AMBER] Amber web page is slow David A. Case (Sat Jul 03 2010 - 11:00:13 PDT)
    - [AMBER] Question about xleap: How to define a linkage between DNA and phosphotyrosine. Catein Catherine (Sun Jul 04 2010 - 01:06:27 PDT)
    - Re: [AMBER] Question about xleap: How to define a linkage between DNA and phosphotyrosine. FyD (Sun Jul 04 2010 - 23:44:44 PDT)
    - Re: [AMBER] Question about xleap: How to define a linkage between DNA and phosphotyrosine. Catein Catherine (Mon Jul 05 2010 - 02:39:58 PDT)
    - [AMBER] Should I define drug intercalation site of a DNA as internal (DT/DA) or terminal (DT3/DA5) unit ? Catein Catherine (Mon Jul 05 2010 - 02:59:23 PDT)
    - Re: [AMBER] Should I define drug intercalation site of a DNA as internal (DT/DA) or terminal (DT3/DA5) unit ? ros (Mon Jul 05 2010 - 06:27:01 PDT)
    - Re: [AMBER] Should I define drug intercalation site of a DNA as internal (DT/DA) or terminal (DT3/DA5) unit ? Jason Swails (Mon Jul 05 2010 - 07:15:51 PDT)
    - Re: [AMBER] Question about xleap: How to define a linkage between DNA and phosphotyrosine. FyD (Mon Jul 05 2010 - 23:32:17 PDT)
    - [AMBER] What is the command to add two tails for a new residue in xleap? Catein Catherine (Mon Jul 05 2010 - 02:42:36 PDT)
    - Re: [AMBER] What is the command to add two tails for a new residue in xleap? Bill Ross (Mon Jul 05 2010 - 13:38:53 PDT)
    - Re: [AMBER] How do define phospho-tyrosine-DA linkage? Bill Ross (Sat Jul 03 2010 - 11:02:46 PDT)
[AMBER] Solvation in water Hoshin Kim (Thu Jul 01 2010 - 19:39:42 PDT)
- Re: [AMBER] Solvation in water Jason Swails (Fri Jul 02 2010 - 08:57:37 PDT)
[AMBER] nmode problem with mm_pbsa.pl RANAJIT SHINDE (Fri Jul 02 2010 - 11:51:12 PDT)
[AMBER] Checking multiple production run nicholus bhattacharjee (Sat Jul 03 2010 - 01:41:11 PDT)
- Re: [AMBER] Checking multiple production run Jason Swails (Sat Jul 03 2010 - 04:22:04 PDT)
- Re: [AMBER] Checking multiple production run Gustavo Seabra (Sat Jul 03 2010 - 06:18:11 PDT)
[AMBER] PMEMD installation error M. Reza Ganjalikhany (Sat Jul 03 2010 - 01:51:14 PDT)
- Re: [AMBER] PMEMD installation error M. Reza Ganjalikhany (Sun Jul 04 2010 - 01:26:14 PDT)
[AMBER] simulations in urea monica.imtech.res.in (Sat Jul 03 2010 - 05:14:38 PDT)
- Re: [AMBER] simulations in urea Bill Ross (Sat Jul 03 2010 - 10:58:38 PDT)
[AMBER] h bond analysis REENU KHATTRI (Sat Jul 03 2010 - 20:45:25 PDT)
[AMBER] WARNING: Local coordinate 382 differs from partner coordinate 382 ! kirsten (Sun Jul 04 2010 - 05:07:08 PDT)
- Re: [AMBER] WARNING: Local coordinate 382 differs from partner coordinate 382 ! steinbrt.rci.rutgers.edu (Sun Jul 04 2010 - 07:53:00 PDT)
[AMBER] RESP charges outside Gaussian Francesco Pietra (Sun Jul 04 2010 - 08:13:20 PDT)
- Re: [AMBER] RESP charges outside Gaussian Jason Swails (Sun Jul 04 2010 - 09:01:22 PDT)
  - Re: [AMBER] RESP charges outside Gaussian FyD (Sun Jul 04 2010 - 09:11:41 PDT)
[AMBER] Steered MD calc eduardo.troche.uvigo.es (Sun Jul 04 2010 - 09:24:55 PDT)
- Re: [AMBER] Steered MD calc Jason Swails (Sun Jul 04 2010 - 16:16:27 PDT)
- Re: [AMBER] Steered MD calc Adrian Roitberg (Sun Jul 04 2010 - 20:12:49 PDT)
[AMBER] No potential terms in sander output! Check out put files - MMPBSA.py.MPI kamlesh sahu (Sun Jul 04 2010 - 18:56:21 PDT)
- Re: [AMBER] No potential terms in sander output! Check out put files - MMPBSA.py.MPI Jason Swails (Sun Jul 04 2010 - 20:04:45 PDT)
  - Re: [AMBER] No potential terms in sander output! Check out put files - MMPBSA.py.MPI kamlesh sahu (Sun Jul 04 2010 - 23:08:08 PDT)
[AMBER] Problems using library file containing multiple residues to make a complex Chris Whittleston (Mon Jul 05 2010 - 08:57:13 PDT)
- Re: [AMBER] Problems using library file containing multiple residues to make a complex Daniel Roe (Mon Jul 05 2010 - 10:53:57 PDT)
  - Re: [AMBER] Problems using library file containing multiple residues to make a complex Chris Whittleston (Tue Jul 06 2010 - 02:05:30 PDT)
    - Re: [AMBER] Problems using library file containing multiple residues to make a complex Daniel Roe (Tue Jul 06 2010 - 05:54:28 PDT)
Re: [AMBER] Davies Bouldin Index with DME in ptraj Geoffrey Wood (Mon Jul 05 2010 - 10:15:26 PDT)
[AMBER] AMBER purchase ros (Mon Jul 05 2010 - 10:40:07 PDT)
[AMBER] step 0 of minimization ? balaji nagarajan (Mon Jul 05 2010 - 12:28:06 PDT)
- Re: [AMBER] step 0 of minimization ? James Maier (Mon Jul 05 2010 - 17:55:37 PDT)
[AMBER] H3O+ force field file 강지영 (Mon Jul 05 2010 - 17:52:17 PDT)
Re: [AMBER] Segmentation fault Jagdeesh C (Mon Jul 05 2010 - 20:10:11 PDT)
[AMBER] error massage in constant pH simulation nicholus bhattacharjee (Tue Jul 06 2010 - 02:16:35 PDT)
- Re: [AMBER] error massage in constant pH simulation Jason Swails (Tue Jul 06 2010 - 05:53:07 PDT)
[AMBER] License sonali dhindwal (Tue Jul 06 2010 - 07:01:38 PDT)
- Re: [AMBER] License Ross Walker (Tue Jul 06 2010 - 08:06:26 PDT)
  - Re: [AMBER] License sonali dhindwal (Tue Jul 06 2010 - 09:37:24 PDT)
[AMBER] Restrain with PMEMD Giovanni Doni (Tue Jul 06 2010 - 09:08:18 PDT)
- Re: [AMBER] Restrain with PMEMD Ross Walker (Tue Jul 06 2010 - 09:19:30 PDT)
[AMBER] segmentation fault David A. Case (Tue Jul 06 2010 - 10:37:32 PDT)
- Re: [AMBER] segmentation fault Jagdeesh C (Thu Jul 22 2010 - 02:51:15 PDT)
  - Re: [AMBER] segmentation fault case (Thu Jul 22 2010 - 06:53:22 PDT)
[AMBER] dyld: lazy symbol binding failed: Symbol not found: _iconv_open Yu Chen (Tue Jul 06 2010 - 11:17:51 PDT)
- Re: [AMBER] dyld: lazy symbol binding failed: Symbol not found: _iconv_open Yu Chen (Tue Jul 06 2010 - 13:26:42 PDT)
[AMBER] Release of the R.E.D.-III.4 tools FyD (Wed Jul 07 2010 - 00:04:36 PDT)
[AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration g t (Wed Jul 07 2010 - 11:07:33 PDT)
- Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration steinbrt.rci.rutgers.edu (Thu Jul 08 2010 - 01:53:53 PDT)
  - Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration g t (Thu Jul 08 2010 - 03:07:58 PDT)
- Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration 冉挺 (Fri Jul 09 2010 - 19:52:33 PDT)
- Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration Bill Ross (Fri Jul 09 2010 - 22:22:01 PDT)
- Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration Bill Ross (Fri Jul 09 2010 - 22:58:16 PDT)
[AMBER] rfree: Error decoding variable 2 2 Vaibhav Jain (Wed Jul 07 2010 - 11:43:28 PDT)
- Re: [AMBER] rfree: Error decoding variable 2 2 David A. Case (Wed Jul 07 2010 - 14:06:13 PDT)
  - [AMBER] rms command Homa Azizian (Wed Jul 07 2010 - 21:57:40 PDT)
    - Re: [AMBER] rms command Jason Swails (Thu Jul 08 2010 - 04:18:46 PDT)
    - Re: [AMBER] rms command Daniel Roe (Thu Jul 08 2010 - 04:48:03 PDT)
[AMBER] problem with 2d-rmsd based clustering moitrayee.mbu.iisc.ernet.in (Wed Jul 07 2010 - 12:37:06 PDT)
[AMBER] compile ambertools on mac Jorgen Simonsen (Wed Jul 07 2010 - 16:21:28 PDT)
- Re: [AMBER] compile ambertools on mac Jason Swails (Wed Jul 07 2010 - 17:58:22 PDT)
  - [AMBER] analysising trajectory Homa Azizian (Wed Jul 07 2010 - 19:05:30 PDT)
  - Re: [AMBER] compile ambertools on mac Jorgen Simonsen (Thu Jul 08 2010 - 03:42:16 PDT)
    - Re: [AMBER] compile ambertools on mac Jason Swails (Thu Jul 08 2010 - 04:14:26 PDT)
    - Re: [AMBER] compile ambertools on mac Jorgen Simonsen (Thu Jul 08 2010 - 05:41:04 PDT)
    - Re: [AMBER] compile ambertools on mac Jason Swails (Thu Jul 08 2010 - 05:52:07 PDT)
    - Re: [AMBER] compile ambertools on mac Jorgen Simonsen (Sun Jul 11 2010 - 13:56:46 PDT)
    - Re: [AMBER] compile ambertools on mac case (Mon Jul 12 2010 - 05:31:18 PDT)
    - Re: [AMBER] compile ambertools on mac Jorgen Simonsen (Mon Jul 12 2010 - 05:57:58 PDT)
    - Re: [AMBER] compile ambertools on mac case (Mon Jul 12 2010 - 06:08:02 PDT)
    - Re: [AMBER] compile ambertools on mac Jorgen Simonsen (Mon Jul 12 2010 - 13:50:13 PDT)
    - Re: [AMBER] compile ambertools on mac Jason Swails (Mon Jul 12 2010 - 14:03:17 PDT)
    - Re: [AMBER] compile ambertools on mac Jorgen Simonsen (Mon Jul 12 2010 - 14:34:39 PDT)
    - Re: [AMBER] compile ambertools on mac case (Tue Jul 13 2010 - 05:05:04 PDT)
    - Re: [AMBER] compile ambertools on mac Jorgen Simonsen (Tue Jul 13 2010 - 05:22:49 PDT)
    - Re: [AMBER] compile ambertools on mac case (Tue Jul 13 2010 - 05:47:51 PDT)
    - Re: [AMBER] compile ambertools on mac Mengjuei Hsieh (Tue Jul 13 2010 - 11:55:05 PDT)
    - Re: [AMBER] compile ambertools on mac Mengjuei Hsieh (Thu Jul 15 2010 - 11:22:33 PDT)
    - Re: [AMBER] compile ambertools on mac Mengjuei Hsieh (Thu Jul 15 2010 - 16:11:19 PDT)
    - Re: [AMBER] compile ambertools on mac Mengjuei Hsieh (Sun Jul 25 2010 - 04:54:38 PDT)
    - Re: [AMBER] compile ambertools on mac case (Mon Jul 26 2010 - 07:06:27 PDT)
    - Re: [AMBER] compile ambertools on mac Adelene Sim (Mon Jul 26 2010 - 09:37:11 PDT)
    - Re: [AMBER] compile ambertools on mac Paul S. Nerenberg (Mon Jul 26 2010 - 09:57:57 PDT)
    - Re: [AMBER] compile ambertools on mac Mengjuei Hsieh (Mon Jul 26 2010 - 14:32:53 PDT)
    - Re: [AMBER] compile ambertools on mac Mengjuei Hsieh (Mon Jul 26 2010 - 14:17:09 PDT)
[AMBER] Is It Possible to Prevent Center-of-Mass Rotation During MD? Logan Ahlstrom (Wed Jul 07 2010 - 19:41:47 PDT)
- Re: [AMBER] Is It Possible to Prevent Center-of-Mass Rotation During MD? Jason Swails (Wed Jul 07 2010 - 21:15:03 PDT)
  - Re: [AMBER] Is It Possible to Prevent Center-of-Mass Rotation During MD? Gustavo Seabra (Thu Jul 08 2010 - 05:30:31 PDT)
Re: [AMBER] atom-type cz ??? M. Shahid (Thu Jul 08 2010 - 06:43:39 PDT)
- Re: [AMBER] atom-type cz ??? David A. Case (Thu Jul 08 2010 - 13:06:23 PDT)
  - Re: [AMBER] atom-type cz ??? Jason Swails (Thu Jul 08 2010 - 13:13:32 PDT)
    - Re: [AMBER] atom-type cz ??? M. Shahid (Thu Jul 08 2010 - 15:02:31 PDT)
    - Re: [AMBER] atom-type cz ??? Jason Swails (Thu Jul 08 2010 - 15:25:56 PDT)
    - Re: [AMBER] atom-type cz ??? case (Fri Jul 09 2010 - 05:20:46 PDT)
Re: [AMBER] Combine trajectory files error Daniel Roe (Thu Jul 08 2010 - 07:35:09 PDT)
- Re: [AMBER] Combine trajectory files error Steve Seibold (Fri Jul 09 2010 - 05:32:45 PDT)
[AMBER] 1D-RISM in AmberTools: atom order in output, a bug? Andrey Frolov (Thu Jul 08 2010 - 08:04:06 PDT)
- Re: [AMBER] 1D-RISM in AmberTools: atom order in output, a bug? Tyler Luchko (Fri Jul 09 2010 - 08:06:30 PDT)
[AMBER] 1D-RISM in AmberTools: the reference for ion parameters and LJ parameters Andrey Frolov (Thu Jul 08 2010 - 08:23:55 PDT)
- Re: [AMBER] 1D-RISM in AmberTools: the reference for ion parameters and LJ parameters Tyler Luchko (Fri Jul 09 2010 - 08:21:27 PDT)
  - [AMBER] Missing BELE for MM in 1 ( residue 1) Catein Catherine (Fri Jul 09 2010 - 08:48:47 PDT)
[AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes Yan Gao (Thu Jul 08 2010 - 10:20:35 PDT)
- [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes Yan Gao (Thu Jul 08 2010 - 10:21:21 PDT)
- [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes Yan Gao (Thu Jul 08 2010 - 13:57:34 PDT)
  - Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes Bill Ross (Thu Jul 08 2010 - 14:28:25 PDT)
[AMBER] OpenMP programs Marc Moreau (Thu Jul 08 2010 - 10:46:21 PDT)
- Re: [AMBER] OpenMP programs Ross Walker (Thu Jul 08 2010 - 12:23:04 PDT)
- Re: [AMBER] OpenMP programs David A. Case (Thu Jul 08 2010 - 13:14:21 PDT)
  - Re: [AMBER] OpenMP programs Marc Moreau (Thu Jul 08 2010 - 14:10:49 PDT)
Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files Daniel Roe (Thu Jul 08 2010 - 12:42:13 PDT)
- Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files Daniel Roe (Sun Jul 18 2010 - 06:37:47 PDT)
Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Yan Gao (Thu Jul 08 2010 - 16:26:55 PDT)
- Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Bill Ross (Thu Jul 08 2010 - 16:46:29 PDT)
  - Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Yan Gao (Thu Jul 08 2010 - 21:41:23 PDT)
- Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Jason Swails (Thu Jul 08 2010 - 20:26:08 PDT)
  - Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Yan Gao (Thu Jul 08 2010 - 21:51:24 PDT)
    - Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Gustavo Seabra (Fri Jul 09 2010 - 03:50:06 PDT)
    - Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Yan Gao (Fri Jul 09 2010 - 06:45:41 PDT)
    - Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Jason Swails (Fri Jul 09 2010 - 08:09:00 PDT)
    - Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Yan Gao (Fri Jul 09 2010 - 08:57:00 PDT)
[AMBER] counterions placings Jio M (Thu Jul 08 2010 - 23:46:48 PDT)
- [AMBER] MMPBSA using counterions Giorgos Lamprinidis (Fri Jul 09 2010 - 00:08:33 PDT)
  - Re: [AMBER] MMPBSA using counterions Jason Swails (Fri Jul 09 2010 - 07:44:04 PDT)
    - [AMBER] Are there any GPU clusters that offer compute time? Sasha Buzko (Fri Jul 09 2010 - 17:09:52 PDT)
    - Re: [AMBER] Are there any GPU clusters that offer compute time? Carlos Simmerling (Fri Jul 09 2010 - 17:30:41 PDT)
    - Re: [AMBER] Are there any GPU clusters that offer compute time? Sasha Buzko (Fri Jul 09 2010 - 17:33:49 PDT)
    - Re: [AMBER] Are there any GPU clusters that offer compute time? Ross Walker (Fri Jul 09 2010 - 19:08:40 PDT)
    - [AMBER] The system size limitations for Tesla C2050 ? Marek Maly (Mon Jul 12 2010 - 01:37:43 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Dairsie Latimer (Mon Jul 12 2010 - 02:04:12 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Marek Maly (Mon Jul 12 2010 - 06:59:10 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Scott Le Grand (Mon Jul 12 2010 - 09:13:05 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Marek Maly (Mon Jul 12 2010 - 09:49:55 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Scott Le Grand (Mon Jul 12 2010 - 10:23:53 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Ross Walker (Mon Jul 12 2010 - 11:02:19 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Scott Le Grand (Mon Jul 12 2010 - 11:27:35 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Marek Maly (Tue Jul 13 2010 - 09:45:37 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Scott Le Grand (Tue Jul 13 2010 - 14:37:19 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Marek Maly (Tue Jul 13 2010 - 14:47:17 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Scott Le Grand (Tue Jul 13 2010 - 15:13:14 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Marek Maly (Tue Jul 13 2010 - 16:04:01 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Scott Le Grand (Mon Jul 12 2010 - 09:11:27 PDT)
- Re: [AMBER] counterions placings Jason Swails (Fri Jul 09 2010 - 07:48:22 PDT)
- Re: [AMBER] counterions placings Bill Ross (Fri Jul 09 2010 - 10:11:02 PDT)
  - Re: [AMBER] counterions placings Jio M (Fri Jul 09 2010 - 21:45:52 PDT)
- Re: [AMBER] counterions placings Bill Ross (Fri Jul 09 2010 - 22:45:52 PDT)
  - Re: [AMBER] counterions placings Jio M (Sat Jul 10 2010 - 03:23:00 PDT)
- Re: [AMBER] counterions placings Bill Ross (Sat Jul 10 2010 - 10:32:06 PDT)
[AMBER] distance between two residues from their center of mass Siddharth Rastogi (Fri Jul 09 2010 - 02:28:10 PDT)
- Re: [AMBER] distance between two residues from their center of mass v.satish.iitg.ernet.in (Fri Jul 09 2010 - 05:13:19 PDT)
- Re: [AMBER] distance between two residues from their center of mass Bill Ross (Fri Jul 09 2010 - 09:39:36 PDT)
[AMBER] ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption moitrayee.mbu.iisc.ernet.in (Fri Jul 09 2010 - 05:12:18 PDT)
- Re: [AMBER] ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption Daniel Roe (Fri Jul 09 2010 - 05:41:00 PDT)
- Re: [AMBER] ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption Daniel Roe (Fri Jul 09 2010 - 09:07:01 PDT)
  - Re: [AMBER] ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption moitrayee.mbu.iisc.ernet.in (Fri Jul 09 2010 - 11:14:31 PDT)
[AMBER] No solvent overlap Thomas Exner (Fri Jul 09 2010 - 07:13:31 PDT)
- Re: [AMBER] No solvent overlap Jason Swails (Fri Jul 09 2010 - 07:58:36 PDT)
- Re: [AMBER] No solvent overlap Bill Ross (Fri Jul 09 2010 - 09:56:12 PDT)
  - Re: [AMBER] No solvent overlap Thomas Exner (Sat Jul 10 2010 - 00:23:01 PDT)
- Re: [AMBER] No solvent overlap case (Sat Jul 10 2010 - 07:37:51 PDT)
- Re: [AMBER] No solvent overlap Bill Ross (Sat Jul 10 2010 - 10:29:24 PDT)
[AMBER] xleap error Steve Seibold (Fri Jul 09 2010 - 08:38:31 PDT)
- Re: [AMBER] xleap error Daniel Roe (Fri Jul 09 2010 - 08:48:15 PDT)
  - Re: [AMBER] xleap error Steve Seibold (Fri Jul 09 2010 - 09:21:33 PDT)
  - Re: [AMBER] xleap error Steve Seibold (Fri Jul 09 2010 - 10:05:23 PDT)
    - Re: [AMBER] xleap error case (Fri Jul 09 2010 - 11:28:21 PDT)
- Re: [AMBER] xleap error Bill Ross (Fri Jul 09 2010 - 10:16:28 PDT)
  - Re: [AMBER] xleap error Steve Seibold (Fri Jul 09 2010 - 10:26:13 PDT)
- Re: [AMBER] xleap error Bill Ross (Fri Jul 09 2010 - 10:41:29 PDT)
[AMBER] compiling amber 10 with mpi Jorgen Simonsen (Fri Jul 09 2010 - 10:13:37 PDT)
- Re: [AMBER] compiling amber 10 with mpi ros (Fri Jul 09 2010 - 11:54:33 PDT)
  - Re: [AMBER] compiling amber 10 with mpi Jorgen Simonsen (Fri Jul 09 2010 - 12:53:57 PDT)
    - Re: [AMBER] compiling amber 10 with mpi Jason Swails (Fri Jul 09 2010 - 13:13:12 PDT)
[AMBER] Align two ligands Yubo Fan (Fri Jul 09 2010 - 10:43:10 PDT)
[AMBER] Question about increasing the max number of atoms in mopac in antechamber Guoxiong Su (Fri Jul 09 2010 - 12:47:16 PDT)
- Re: [AMBER] Question about increasing the max number of atoms in mopac in antechamber case (Fri Jul 09 2010 - 13:39:13 PDT)
[AMBER] (no subject) llduan.itcs.ecnu.edu.cn (Sat Jul 10 2010 - 00:04:33 PDT)
- Re: [AMBER] (no subject) case (Sat Jul 10 2010 - 05:55:54 PDT)
- [AMBER] amber02pol: sequence: Illegal UNIT named: NHE llduan.itcs.ecnu.edu.cn (Tue Jul 13 2010 - 07:49:05 PDT)
  - Re: [AMBER] amber02pol: sequence: Illegal UNIT named: NHE Paul S. Nerenberg (Tue Jul 13 2010 - 07:52:40 PDT)
    - Re: [AMBER] amber02pol: sequence: Illegal UNIT named: NHE llduan.itcs.ecnu.edu.cn (Wed Jul 14 2010 - 00:19:09 PDT)
    - Re: [AMBER] amber02pol: sequence: Illegal UNIT named: NHE Paul S. Nerenberg (Wed Jul 14 2010 - 07:53:54 PDT)
    - Re: [AMBER] amber02pol: sequence: Illegal UNIT named: NHE cieplak.cgl.ucsf.edu (Thu Jul 15 2010 - 14:39:24 PDT)
[AMBER] same dihedral with different parameter in FRCMOD file Xioling Chuang (Sat Jul 10 2010 - 05:39:14 PDT)
- Re: [AMBER] same dihedral with different parameter in FRCMOD file case (Sat Jul 10 2010 - 06:52:48 PDT)
  - Re: [AMBER] same dihedral with different parameter in FRCMOD file Xioling Chuang (Sun Jul 11 2010 - 06:57:59 PDT)
- Re: [AMBER] same dihedral with different parameter in FRCMOD file Dmitry Mukha (Sat Jul 10 2010 - 07:21:22 PDT)
  - Re: [AMBER] same dihedral with different parameter in FRCMOD file case (Sat Jul 10 2010 - 07:43:22 PDT)
[AMBER] [Fwd: Re: ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption] moitrayee.mbu.iisc.ernet.in (Sat Jul 10 2010 - 05:45:54 PDT)
[AMBER] problem in converting cprestrt to cpin2 file in constant pH md nicholus bhattacharjee (Sun Jul 11 2010 - 21:23:25 PDT)
- Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md Jason Swails (Mon Jul 12 2010 - 07:04:30 PDT)
  - Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md nicholus bhattacharjee (Wed Jul 21 2010 - 06:37:26 PDT)
    - Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md Jason Swails (Wed Jul 21 2010 - 09:33:03 PDT)
    - Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md nicholus bhattacharjee (Thu Jul 22 2010 - 02:37:35 PDT)
    - Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md nicholus bhattacharjee (Thu Jul 22 2010 - 04:41:31 PDT)
    - Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md Jason Swails (Thu Jul 22 2010 - 05:06:00 PDT)
    - Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md nicholus bhattacharjee (Thu Jul 22 2010 - 06:42:39 PDT)
    - Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md Jason Swails (Thu Jul 22 2010 - 07:26:56 PDT)
[AMBER] residue wise rmsd, not getting expected results vaibhav dixit (Mon Jul 12 2010 - 01:30:55 PDT)
- Re: [AMBER] residue wise rmsd, not getting expected results Daniel Roe (Mon Jul 12 2010 - 06:47:14 PDT)
  - Re: [AMBER] residue wise rmsd, not getting expected results Daniel Roe (Mon Jul 12 2010 - 06:48:01 PDT)
    - Re: [AMBER] residue wise rmsd, not getting expected results vaibhav dixit (Mon Jul 12 2010 - 06:57:16 PDT)
    - Re: [AMBER] residue wise rmsd, not getting expected results Jason Swails (Mon Jul 12 2010 - 06:59:39 PDT)
    - Re: [AMBER] residue wise rmsd, not getting expected results vaibhav dixit (Mon Jul 12 2010 - 09:19:45 PDT)
    - [AMBER] mm_pbsa.pl in PARALLEL does not finish Anselm Horn (Mon Jul 12 2010 - 09:55:32 PDT)
    - Re: [AMBER] mm_pbsa.pl in PARALLEL does not finish Jason Swails (Mon Jul 12 2010 - 10:32:57 PDT)
    - Re: [AMBER] mm_pbsa.pl in PARALLEL does not finish Anselm Horn (Mon Jul 12 2010 - 12:23:37 PDT)
    - Re: [AMBER] mm_pbsa.pl in PARALLEL does not finish Thomas Zeiser (Thu Jul 22 2010 - 07:22:38 PDT)
- Re: [AMBER] residue wise rmsd, not getting expected results Bill Ross (Mon Jul 12 2010 - 09:41:29 PDT)
[AMBER] simulation runs very slow.. Vijay Manickam Achari (Mon Jul 12 2010 - 01:54:24 PDT)
- Re: [AMBER] simulation runs very slow.. James Maier (Mon Jul 12 2010 - 08:11:47 PDT)
  - Re: [AMBER] simulation runs very slow.. Catein Catherine (Mon Jul 12 2010 - 08:18:02 PDT)
    - Re: [AMBER] simulation runs very slow.. Jason Swails (Mon Jul 12 2010 - 08:22:09 PDT)
- Re: [AMBER] simulation runs very slow.. Bill Ross (Mon Jul 12 2010 - 08:16:28 PDT)
- Re: [AMBER] simulation runs very slow.. Bill Ross (Mon Jul 12 2010 - 08:41:43 PDT)
[AMBER] ptraj Steve Seibold (Mon Jul 12 2010 - 09:52:07 PDT)
[AMBER] AmberTools citation Jason Swails (Mon Jul 12 2010 - 13:00:05 PDT)
[AMBER] source code to calculate electrostatic interaction in amber6 Qian Wang (Mon Jul 12 2010 - 13:37:51 PDT)
- Re: [AMBER] source code to calculate electrostatic interaction in amber6 Bill Ross (Mon Jul 12 2010 - 13:41:58 PDT)
  - Re: [AMBER] source code to calculate electrostatic interaction in amber6 Qian Wang (Mon Jul 12 2010 - 13:48:32 PDT)
[AMBER] Units for mass weighted covariance matrix in ptraj Lekpa Duukori (Mon Jul 12 2010 - 18:34:38 PDT)
- Re: [AMBER] Units for mass weighted covariance matrix in ptraj Jason Swails (Mon Jul 12 2010 - 19:56:23 PDT)
  - Re: [AMBER] Units for mass weighted covariance matrix in ptraj Lekpa Duukori (Tue Jul 13 2010 - 08:27:36 PDT)
    - Re: [AMBER] Units for mass weighted covariance matrix in ptraj Lekpa Duukori (Tue Jul 13 2010 - 11:16:54 PDT)
[AMBER] error 126 when install AmberTool1.4 Yan Gao (Mon Jul 12 2010 - 22:42:31 PDT)
- [AMBER] reference structure Homa Azizian (Mon Jul 12 2010 - 23:42:15 PDT)
  - Re: [AMBER] reference structure Ross Walker (Mon Jul 12 2010 - 23:54:39 PDT)
    - Re: [AMBER] reference structure Homa Azizian (Tue Jul 13 2010 - 00:09:47 PDT)
- Re: [AMBER] error 126 when install AmberTool1.4 case (Tue Jul 13 2010 - 05:18:34 PDT)
  - Re: [AMBER] error 126 when install AmberTool1.4 Yan Gao (Tue Jul 13 2010 - 09:07:01 PDT)
    - Re: [AMBER] error 126 when install AmberTool1.4 case (Tue Jul 13 2010 - 09:34:09 PDT)
- Re: [AMBER] error 126 when install AmberTool1.4 Daniel Roe (Tue Jul 13 2010 - 05:44:37 PDT)
  - Re: [AMBER] error 126 when install AmberTool1.4 Yan Gao (Tue Jul 13 2010 - 09:09:23 PDT)
[AMBER] 3D-RISM disabled? Daniel Sindhikara (Tue Jul 13 2010 - 01:26:29 PDT)
- Re: [AMBER] 3D-RISM disabled? case (Tue Jul 13 2010 - 05:24:20 PDT)
  - Re: [AMBER] 3D-RISM disabled? Daniel Sindhikara (Tue Jul 13 2010 - 19:05:52 PDT)
[AMBER] Periodic Neighbor Distance Logan Ahlstrom (Tue Jul 13 2010 - 16:23:58 PDT)
- Re: [AMBER] Periodic Neighbor Distance Paul S. Nerenberg (Tue Jul 13 2010 - 16:49:00 PDT)
[AMBER] please, units of LENNARD_JONES_ACOEF in prmptop? Jose Borreguero (Tue Jul 13 2010 - 16:45:07 PDT)
- Re: [AMBER] please, units of LENNARD_JONES_ACOEF in prmptop? Paul S. Nerenberg (Tue Jul 13 2010 - 17:31:13 PDT)
  - Re: [AMBER] please, units of LENNARD_JONES_ACOEF in prmptop? Jose Borreguero (Wed Jul 14 2010 - 07:56:08 PDT)
[AMBER] general enquiry monica.imtech.res.in (Wed Jul 14 2010 - 00:40:40 PDT)
- Re: [AMBER] general enquiry Jason Swails (Wed Jul 14 2010 - 03:56:34 PDT)
[AMBER] Error Compiling NAB o AMBER Tools 1.2 Giorgos Lamprinidis (Wed Jul 14 2010 - 03:02:16 PDT)
- Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 Jason Swails (Wed Jul 14 2010 - 03:47:36 PDT)
  - Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 Giorgos Lamprinidis (Wed Jul 14 2010 - 07:30:25 PDT)
    - Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 Jason Swails (Wed Jul 14 2010 - 08:24:27 PDT)
    - Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 Giorgos Lamprinidis (Wed Jul 14 2010 - 08:44:59 PDT)
    - Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 Jason Swails (Wed Jul 14 2010 - 12:18:53 PDT)
- Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 case (Wed Jul 14 2010 - 13:26:49 PDT)
  - Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 Giorgos Lamprinidis (Thu Jul 15 2010 - 07:34:59 PDT)
    - Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 Jason Swails (Thu Jul 15 2010 - 08:56:31 PDT)
[AMBER] NAB rdparm seg fault Josh Berryman (Wed Jul 14 2010 - 05:03:41 PDT)
- Re: [AMBER] NAB rdparm seg fault case (Wed Jul 14 2010 - 09:36:36 PDT)
  - Re: [AMBER] NAB rdparm seg fault Josh Berryman (Thu Jul 15 2010 - 04:49:13 PDT)
    - Re: [AMBER] NAB rdparm seg fault case (Thu Jul 15 2010 - 05:37:20 PDT)
    - Re: [AMBER] NAB rdparm seg fault case (Thu Jul 15 2010 - 06:02:31 PDT)
    - Re: [AMBER] NAB rdparm seg fault Josh Berryman (Mon Jul 26 2010 - 04:54:47 PDT)
[AMBER] Query regarding Abscissa and their corresponding weights in Thermodynamic Integration sunita gupta (Wed Jul 14 2010 - 05:16:05 PDT)
- Re: [AMBER] Query regarding Abscissa and their corresponding weights in Thermodynamic Integration Jason Swails (Wed Jul 14 2010 - 08:18:23 PDT)
[AMBER] mm_pbsa.pl in PARALLEL - part 2 Anselm Horn (Wed Jul 14 2010 - 05:26:53 PDT)
[AMBER] problem with tleap and xleap moacyr comar (Wed Jul 14 2010 - 07:05:38 PDT)
- Re: [AMBER] problem with tleap and xleap Jason Swails (Wed Jul 14 2010 - 08:22:32 PDT)
[AMBER] RDF analysis of glucose made by GLYCAM problem Hoshin Kim (Tue Jul 13 2010 - 18:10:30 PDT)
- Re: [AMBER] RDF analysis of glucose made by GLYCAM problem Lachele Foley (Lists) (Wed Jul 14 2010 - 07:53:54 PDT)
[AMBER] sign me off please~ Qiuting Hong (Wed Jul 14 2010 - 09:35:00 PDT)
- Re: [AMBER] sign me off please~ Paul S. Nerenberg (Wed Jul 14 2010 - 09:47:48 PDT)
[AMBER] entropy from mass weighted covariance matrix Lekpa Duukori (Wed Jul 14 2010 - 09:50:41 PDT)
- Re: [AMBER] entropy from mass weighted covariance matrix Jason Swails (Wed Jul 14 2010 - 12:30:32 PDT)
  - Re: [AMBER] entropy from mass weighted covariance matrix Lekpa Duukori (Wed Jul 14 2010 - 14:29:18 PDT)
[AMBER] TIP4P question hong-bin Xie (Wed Jul 14 2010 - 10:16:33 PDT)
- Re: [AMBER] TIP4P question case (Wed Jul 14 2010 - 10:46:24 PDT)
  - Re: [AMBER] TIP4P question hong-bin Xie (Wed Jul 14 2010 - 10:53:17 PDT)
[AMBER] The atom number exceeds the MAXATOM, reallocate memory Segmentation fault (core dumped) Yan Gao (Wed Jul 14 2010 - 11:02:12 PDT)
- Re: [AMBER] The atom number exceeds the MAXATOM, reallocate memory Segmentation fault (core dumped) Bill Ross (Wed Jul 14 2010 - 11:27:04 PDT)
Re: [AMBER] The atom number exceeds the MAXATOM, reallocate memory Segmentation fault (core dumped) --- thank you and more questions! Yan Gao (Wed Jul 14 2010 - 12:12:42 PDT)
- Re: [AMBER] The atom number exceeds the MAXATOM, reallocate memory Segmentation fault (core dumped) --- thank you and more questions! Bill Ross (Wed Jul 14 2010 - 13:12:53 PDT)
[AMBER] how to create a mixture solvent of hexane and water setyanto tri wahyudi (Wed Jul 14 2010 - 20:43:24 PDT)
- [AMBER] amber tool installing problem Homa Azizian (Wed Jul 14 2010 - 22:11:39 PDT)
  - [AMBER] About RAMD gokul algates (Wed Jul 14 2010 - 23:03:15 PDT)
    - Re: [AMBER] About RAMD Jason Swails (Thu Jul 15 2010 - 04:41:12 PDT)
    - Re: [AMBER] About RAMD gokul algates (Thu Jul 15 2010 - 07:34:44 PDT)
  - Re: [AMBER] amber tool installing problem Jason Swails (Thu Jul 15 2010 - 04:37:35 PDT)
  - Re: [AMBER] amber tool installing problem case (Thu Jul 15 2010 - 04:54:14 PDT)
- Re: [AMBER] how to create a mixture solvent of hexane and water case (Thu Jul 15 2010 - 05:16:10 PDT)
  - Re: [AMBER] how to create a mixture solvent of hexane and water setyanto tri wahyudi (Fri Jul 23 2010 - 03:21:41 PDT)
[AMBER] vlimit exceeding situtaion with ntt option Vijay Manickam Achari (Thu Jul 15 2010 - 01:30:20 PDT)
[AMBER] Simulation cell reduction Lorenzo Gontrani (Thu Jul 15 2010 - 03:15:47 PDT)
[AMBER] About RAMD gokul algates (Thu Jul 15 2010 - 07:46:06 PDT)
Re: [AMBER] problems with NAB and SHIFTS Xinfu Xia (Thu Jul 15 2010 - 08:30:41 PDT)
- Re: [AMBER] problems with NAB and SHIFTS Jason Swails (Thu Jul 15 2010 - 08:54:49 PDT)
- Re: [AMBER] problems with NAB and SHIFTS Xinfu Xia (Thu Jul 15 2010 - 10:31:08 PDT)
  - Re: [AMBER] problems with NAB and SHIFTS case (Thu Jul 15 2010 - 11:28:47 PDT)
- Re: [AMBER] problems with NAB and SHIFTS case (Thu Jul 15 2010 - 10:32:06 PDT)
[AMBER] website down Sidney Elmer (Thu Jul 15 2010 - 18:17:57 PDT)
- Re: [AMBER] website down Yan Gao (Thu Jul 15 2010 - 19:17:11 PDT)
- [AMBER] Can I calculate the interaction energy between two connected domains of a protein? Catein Catherine (Mon Jul 19 2010 - 00:40:54 PDT)
  - Re: [AMBER] Can I calculate the interaction energy between two connected domains of a protein? Rubben Torella (Mon Jul 19 2010 - 00:45:08 PDT)
    - Re: [AMBER] Can I calculate the interaction energy between two connected domains of a protein? Catein Catherine (Mon Jul 19 2010 - 01:04:23 PDT)
    - Re: [AMBER] Can I calculate the interaction energy between two connected domains of a protein? Jason Swails (Mon Jul 19 2010 - 08:12:43 PDT)
    - [AMBER] Can I calculate the interaction energy between two connected domains of a protein using mmpbsa.py? Catein Catherine (Mon Jul 19 2010 - 08:12:55 PDT)
    - Re: [AMBER] Can I calculate the interaction energy between two connected domains of a protein using mmpbsa.py? Jason Swails (Mon Jul 19 2010 - 10:54:32 PDT)
    - Re: [AMBER] Can I calculate the interaction energy between two connected domains of a protein? Purisima, Enrico (Mon Jul 19 2010 - 08:56:39 PDT)
[AMBER] residues lacking connect Jorgen Simonsen (Sat Jul 17 2010 - 11:54:06 PDT)
- Re: [AMBER] residues lacking connect case (Sun Jul 18 2010 - 15:24:28 PDT)
- Re: [AMBER] residues lacking connect Bill Ross (Sun Jul 18 2010 - 20:26:20 PDT)
[AMBER] Problem with sander.MPI moacyr comar (Sat Jul 17 2010 - 12:15:42 PDT)
- Re: [AMBER] Problem with sander.MPI Ross Walker (Sun Jul 18 2010 - 02:21:16 PDT)
[AMBER] questions of decomposition using mm/gbsa fancy2012 (Sun Jul 18 2010 - 00:01:45 PDT)
- Re: [AMBER] questions of decomposition using mm/gbsa fancy2012 (Sun Jul 18 2010 - 00:11:39 PDT)
[AMBER] How to remove PBC effects? Oliver Kuhn (Mon Jul 19 2010 - 05:04:23 PDT)
- Re: [AMBER] How to remove PBC effects? Daniel Sindhikara (Mon Jul 19 2010 - 06:06:11 PDT)
  - Re: [AMBER] How to remove PBC effects? Oliver Kuhn (Mon Jul 19 2010 - 06:55:31 PDT)
    - Re: [AMBER] How to remove PBC effects? Jason Swails (Mon Jul 19 2010 - 08:08:07 PDT)
    - Re: [AMBER] How to remove PBC effects? Oliver Kuhn (Tue Jul 20 2010 - 01:36:10 PDT)
[AMBER] protein distance constraints Beale, John (Mon Jul 19 2010 - 08:18:11 PDT)
- Re: [AMBER] protein distance constraints case (Mon Jul 19 2010 - 10:40:50 PDT)
[AMBER] Problem with pmemd.cuda ros (Mon Jul 19 2010 - 09:11:12 PDT)
- Re: [AMBER] Problem with pmemd.cuda case (Mon Jul 19 2010 - 10:34:57 PDT)
  - Re: [AMBER] Problem with pmemd.cuda ros (Mon Jul 19 2010 - 11:34:02 PDT)
    - Re: [AMBER] Problem with pmemd.cuda case (Mon Jul 19 2010 - 12:30:54 PDT)
    - Re: [AMBER] Problem with pmemd.cuda Levi Pierce (Mon Jul 19 2010 - 12:49:19 PDT)
    - Re: [AMBER] Problem with pmemd.cuda ros (Mon Jul 19 2010 - 13:14:18 PDT)
- Re: [AMBER] Problem with pmemd.cuda Bill Ross (Mon Jul 19 2010 - 13:18:32 PDT)
  - Re: [AMBER] Problem with pmemd.cuda ros (Mon Jul 19 2010 - 13:55:26 PDT)
- Re: [AMBER] Problem with pmemd.cuda Bill Ross (Mon Jul 19 2010 - 14:15:52 PDT)
  - Re: [AMBER] Problem with pmemd.cuda ros (Mon Jul 19 2010 - 14:42:58 PDT)
    - Re: [AMBER] Problem with pmemd.cuda case (Mon Jul 19 2010 - 17:41:37 PDT)
    - Re: [AMBER] Problem with pmemd.cuda ros (Mon Jul 19 2010 - 22:16:45 PDT)
    - Re: [AMBER] Problem with pmemd.cuda ros (Mon Jul 19 2010 - 22:53:36 PDT)
    - Re: [AMBER] Problem with pmemd.cuda ros (Mon Jul 19 2010 - 23:30:02 PDT)
[AMBER] Head-Tail covalently bound substrate and arikcohen (Mon Jul 19 2010 - 11:04:24 PDT)
- Re: [AMBER] Head-Tail covalently bound substrate and Jason Swails (Mon Jul 19 2010 - 11:20:34 PDT)
  - Re: [AMBER] Head-Tail covalently bound substrate and arikcohen (Mon Jul 19 2010 - 11:47:29 PDT)
    - [AMBER] Parameters missing after changing topology arikcohen (Mon Jul 19 2010 - 14:45:36 PDT)
    - Re: [AMBER] Parameters missing after changing topology Jason Swails (Mon Jul 19 2010 - 18:36:05 PDT)
[AMBER] problem with the total charge Yan Gao (Mon Jul 19 2010 - 20:25:37 PDT)
- Re: [AMBER] problem with the total charge Jason Swails (Mon Jul 19 2010 - 21:27:08 PDT)
- Re: [AMBER] problem with the total charge case (Tue Jul 20 2010 - 04:44:48 PDT)
  - Re: [AMBER] problem with the total charge Yan Gao (Tue Jul 20 2010 - 09:48:44 PDT)
[AMBER] adding ion concentration Neha Gandhi (Tue Jul 20 2010 - 02:08:05 PDT)
- Re: [AMBER] adding ion concentration Jason Swails (Tue Jul 20 2010 - 05:36:04 PDT)
[AMBER] Performance from pmemd.cuda Gould, Ian R (Tue Jul 20 2010 - 02:36:46 PDT)
- Re: [AMBER] Performance from pmemd.cuda Ross Walker (Tue Jul 20 2010 - 11:01:33 PDT)
[AMBER] How to calculate the radial distribution function of one of the atom(say P) of one residue ( say R1) to the center of the another residue (R2) Siddharth Rastogi (Tue Jul 20 2010 - 04:48:14 PDT)
[AMBER] ANALYSES LIGAND EXIT TRAJECTORIES sophie fourtanier (Tue Jul 20 2010 - 05:49:16 PDT)
[AMBER] radial distribution function Siddharth Rastogi (Tue Jul 20 2010 - 06:06:20 PDT)
[AMBER] Warning: Input error! "nmode_igb=1" is an invalid option. Sushil Mishra (Tue Jul 20 2010 - 08:24:08 PDT)
- Re: [AMBER] Warning: Input error! "nmode_igb=1" is an invalid option. Bill Miller III (Tue Jul 20 2010 - 08:32:19 PDT)
[AMBER] problem about cyclic peptide Rebeca García Fandiño (Tue Jul 20 2010 - 08:33:15 PDT)
- Re: [AMBER] problem about cyclic peptide Levi Pierce (Tue Jul 20 2010 - 09:37:32 PDT)
  - Re: [AMBER] problem about cyclic peptide Rebeca García Fandiño (Tue Jul 20 2010 - 09:43:59 PDT)
[AMBER] L and D peptides Jorgen Simonsen (Tue Jul 20 2010 - 09:52:30 PDT)
- Re: [AMBER] L and D peptides Jason Swails (Tue Jul 20 2010 - 12:51:41 PDT)
- Re: [AMBER] L and D peptides Bill Ross (Tue Jul 20 2010 - 13:12:08 PDT)
  - Re: [AMBER] L and D peptides Jorgen Simonsen (Tue Jul 20 2010 - 14:20:05 PDT)
- Re: [AMBER] L and D peptides Bill Ross (Tue Jul 20 2010 - 14:34:16 PDT)
- Re: [AMBER] L and D peptides case (Tue Jul 20 2010 - 18:18:32 PDT)
  - Re: [AMBER] L and D peptides FyD (Wed Jul 21 2010 - 00:39:32 PDT)
    - Re: [AMBER] L and D peptides Jason Swails (Wed Jul 21 2010 - 07:51:15 PDT)
    - Re: [AMBER] L and D peptides Roman Osman (Wed Jul 21 2010 - 08:13:00 PDT)
- Re: [AMBER] L and D peptides Karl N. Kirschner (Wed Jul 21 2010 - 03:26:21 PDT)
[AMBER] Workaround for gfortran-4.1.2? Marc Moreau (Tue Jul 20 2010 - 16:19:53 PDT)
- Re: [AMBER] Workaround for gfortran-4.1.2? Mark Williamson (Tue Jul 20 2010 - 16:51:43 PDT)
- Re: [AMBER] Workaround for gfortran-4.1.2? case (Tue Jul 20 2010 - 18:31:06 PDT)
  - Re: [AMBER] Workaround for gfortran-4.1.2? Marc Moreau (Tue Jul 20 2010 - 18:39:11 PDT)
    - Re: [AMBER] Workaround for gfortran-4.1.2? Marc Moreau (Wed Jul 21 2010 - 18:38:38 PDT)
  - [AMBER] Enquiry about NED calculation in AMBER10 Catein Catherine (Tue Jul 20 2010 - 19:53:08 PDT)
    - Re: [AMBER] Enquiry about NED calculation in AMBER10 case (Wed Jul 21 2010 - 05:04:31 PDT)
[AMBER] errors of energy decomposition fancy2012 (Tue Jul 20 2010 - 23:20:30 PDT)
- Re: [AMBER] errors of energy decomposition Amor San Juan (Tue Jul 20 2010 - 23:58:36 PDT)
  - Re: [AMBER] errors of energy decomposition fancy2012 (Wed Jul 21 2010 - 00:23:38 PDT)
[AMBER] Getting missing force constants for Amber from Gaussian? Markus Knauth (Wed Jul 21 2010 - 01:00:02 PDT)
[AMBER] mm_pbsa.pl in PARALLEL - part 3 Anselm Horn (Wed Jul 21 2010 - 03:33:00 PDT)
- Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3 Asfa Ali (Wed Jul 21 2010 - 04:05:57 PDT)
- Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3 Anselm Horn (Wed Jul 21 2010 - 04:21:20 PDT)
  - Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3 Asfa Ali (Wed Jul 21 2010 - 04:32:05 PDT)
    - Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3 Bill Miller III (Wed Jul 21 2010 - 04:48:18 PDT)
    - Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3 Jason Swails (Wed Jul 21 2010 - 07:59:52 PDT)
- Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3 Thomas Zeiser (Thu Jul 22 2010 - 05:13:08 PDT)
[AMBER] FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type. kamlesh sahu (Wed Jul 21 2010 - 05:11:34 PDT)
- Re: [AMBER] FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type. case (Wed Jul 21 2010 - 06:09:11 PDT)
  - Re: [AMBER] FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type. Jason Swails (Wed Jul 21 2010 - 08:10:56 PDT)
    - Re: [AMBER] FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type. kamlesh sahu (Wed Jul 21 2010 - 20:06:36 PDT)
[AMBER] external electric field? Wong, Sergio E. (Wed Jul 21 2010 - 11:42:08 PDT)
[AMBER] Issue with preparing pdb, top and crd files via leap for a non-standard residue Valerie Fako (Wed Jul 21 2010 - 14:29:54 PDT)
- Re: [AMBER] Issue with preparing pdb, top and crd files via leap for a non-standard residue Levi Pierce (Wed Jul 21 2010 - 14:40:11 PDT)
[AMBER] How to make oligo-peptides using AMBER ? Siddharth Rastogi (Wed Jul 21 2010 - 15:51:02 PDT)
- Re: [AMBER] How to make oligo-peptides using AMBER ? Gustavo Seabra (Wed Jul 21 2010 - 16:07:09 PDT)
[AMBER] POPC parameters Vasillis Myrianthopoulos (Thu Jul 22 2010 - 04:57:27 PDT)
- Re: [AMBER] POPC parameters Hannes Loeffler (Thu Jul 22 2010 - 05:33:40 PDT)
[AMBER] scee EEL and scnb VDW 1-4 CHAMI F. (Thu Jul 22 2010 - 05:34:36 PDT)
[AMBER] minimization segmentation fault Jorgen Simonsen (Thu Jul 22 2010 - 06:16:02 PDT)
- Re: [AMBER] minimization segmentation fault Daniel Roe (Thu Jul 22 2010 - 06:33:30 PDT)
- Re: [AMBER] minimization segmentation fault Jason Swails (Thu Jul 22 2010 - 07:42:00 PDT)
- Re: [AMBER] minimization segmentation fault Bill Ross (Thu Jul 22 2010 - 10:03:27 PDT)
  - Re: [AMBER] minimization segmentation fault Jorgen Simonsen (Tue Jul 27 2010 - 11:37:24 PDT)
- Re: [AMBER] minimization segmentation fault Bill Ross (Tue Jul 27 2010 - 11:53:25 PDT)
  - Re: [AMBER] minimization segmentation fault Jorgen Simonsen (Fri Jul 30 2010 - 04:11:31 PDT)
- Re: [AMBER] minimization segmentation fault Bill Ross (Fri Jul 30 2010 - 09:52:50 PDT)
[AMBER] pmemd amber10 compilation error Marcela Madrid (Thu Jul 22 2010 - 07:49:00 PDT)
- Re: [AMBER] pmemd amber10 compilation error Jason Swails (Thu Jul 22 2010 - 07:54:21 PDT)
  - Re: [AMBER] pmemd amber10 compilation error Jason Swails (Thu Jul 22 2010 - 07:55:40 PDT)
- Re: [AMBER] pmemd amber10 compilation error Ross Walker (Thu Jul 22 2010 - 07:57:51 PDT)
[AMBER] file format monica.imtech.res.in (Thu Jul 22 2010 - 08:12:37 PDT)
- Re: [AMBER] file format James Maier (Thu Jul 22 2010 - 12:31:06 PDT)
- Re: [AMBER] file format Jason Swails (Thu Jul 22 2010 - 16:00:46 PDT)
Re: [AMBER] Compiling failure of Amber 9 Yubo Fan (Thu Jul 22 2010 - 08:43:18 PDT)
- Re: [AMBER] Compiling failure of Amber 9 David Watson (Thu Jul 22 2010 - 09:22:56 PDT)
  - Re: [AMBER] Compiling failure of Amber 9 Yubo Fan (Fri Jul 23 2010 - 07:17:08 PDT)
    - Re: [AMBER] Compiling failure of Amber 9 case (Fri Jul 23 2010 - 11:52:16 PDT)
[AMBER] question about bond command Philippe Pinard (Thu Jul 22 2010 - 10:36:38 PDT)
- Re: [AMBER] question about bond command Bill Ross (Thu Jul 22 2010 - 10:43:58 PDT)
- Re: [AMBER] question about bond command ros (Thu Jul 22 2010 - 11:06:19 PDT)
  - Re: [AMBER] question about bond command Philippe Pinard (Thu Jul 22 2010 - 11:34:11 PDT)
- Re: [AMBER] question about bond command Bill Ross (Thu Jul 22 2010 - 11:50:28 PDT)
  - Re: [AMBER] question about bond command Philippe Pinard (Thu Jul 22 2010 - 12:16:38 PDT)
- Re: [AMBER] question about bond command Bill Ross (Thu Jul 22 2010 - 11:54:31 PDT)
- Re: [AMBER] question about bond command Bill Ross (Thu Jul 22 2010 - 12:38:28 PDT)
  - Re: [AMBER] question about bond command Philippe Pinard (Thu Jul 22 2010 - 14:41:26 PDT)
    - Re: [AMBER] question about bond command case (Thu Jul 22 2010 - 18:58:12 PDT)
    - Re: [AMBER] question about bond command Philippe Pinard (Thu Jul 22 2010 - 19:38:33 PDT)
    - [AMBER] mandatory command lines in MMPBSA.PY Amor San Juan (Thu Jul 22 2010 - 21:16:25 PDT)
    - Re: [AMBER] mandatory command lines in MMPBSA.PY Oliver Grant (Fri Jul 23 2010 - 03:55:56 PDT)
    - Re: [AMBER] mandatory command lines in MMPBSA.PY Jason Swails (Fri Jul 23 2010 - 05:06:24 PDT)
    - Re: [AMBER] question about bond command case (Fri Jul 23 2010 - 04:36:00 PDT)
- Re: [AMBER] question about bond command Bill Ross (Thu Jul 22 2010 - 14:55:48 PDT)
- Re: [AMBER] question about bond command Bill Ross (Fri Jul 23 2010 - 09:36:47 PDT)
  - Re: [AMBER] question about bond command Philippe Pinard (Sat Jul 24 2010 - 09:34:19 PDT)
    - Re: [AMBER] question about bond command Jason Swails (Sat Jul 24 2010 - 22:04:18 PDT)
    - Re: [AMBER] question about bond command Philippe Pinard (Sun Jul 25 2010 - 20:52:21 PDT)
    - Re: [AMBER] question about bond command Jason Swails (Sat Jul 24 2010 - 22:13:51 PDT)
- Re: [AMBER] question about bond command Bill Ross (Fri Jul 23 2010 - 09:44:08 PDT)
- Re: [AMBER] question about bond command Bill Ross (Fri Jul 23 2010 - 10:00:49 PDT)
- Re: [AMBER] question about bond command Bill Ross (Sat Jul 24 2010 - 13:57:32 PDT)
  - Re: [AMBER] question about bond command Philippe Pinard (Sat Jul 24 2010 - 17:13:45 PDT)
- Re: [AMBER] question about bond command Bill Ross (Sat Jul 24 2010 - 17:22:44 PDT)
  - Re: [AMBER] question about bond command Philippe Pinard (Sat Jul 24 2010 - 19:38:39 PDT)
    - Re: [AMBER] question about bond command case (Sat Jul 24 2010 - 20:44:40 PDT)
- Re: [AMBER] question about bond command Bill Ross (Sat Jul 24 2010 - 20:05:24 PDT)
[AMBER] Coulson vs. Mulliken, CM1, etc. in antechamber + mopac Don.Bashford.stjude.org (Thu Jul 22 2010 - 13:59:42 PDT)
- Re: [AMBER] Coulson vs. Mulliken, CM1, etc. in antechamber + mopac case (Thu Jul 22 2010 - 19:32:55 PDT)
- Re: [AMBER] Coulson vs. Mulliken, CM1, etc. in antechamber + mopac Timothy J Giese (Mon Jul 26 2010 - 08:22:50 PDT)
[AMBER] clustering analysis changes my coordinates Geoffrey Wood (Thu Jul 22 2010 - 18:55:46 PDT)
- Re: [AMBER] clustering analysis changes my coordinates Daniel Roe (Fri Jul 23 2010 - 07:46:04 PDT)
  - Re: [AMBER] clustering analysis changes my coordinates Geoffrey Wood (Fri Jul 23 2010 - 08:14:28 PDT)
    - Re: [AMBER] clustering analysis changes my coordinates Thomas Cheatham III (Fri Jul 23 2010 - 08:51:43 PDT)
    - Re: [AMBER] clustering analysis changes my coordinates Geoffrey Wood (Sat Jul 24 2010 - 18:06:52 PDT)
    - [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER? Catein Catherine (Fri Jul 23 2010 - 08:54:49 PDT)
    - Re: [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER? hannes.loeffler.stfc.ac.uk (Fri Jul 23 2010 - 10:43:57 PDT)
    - Re: [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER? Catein Catherine (Fri Jul 23 2010 - 20:47:43 PDT)
    - Re: [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER? hannes.loeffler.stfc.ac.uk (Sat Jul 24 2010 - 00:26:27 PDT)
    - Re: [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER? Catein Catherine (Sun Jul 25 2010 - 01:09:17 PDT)
    - Re: [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER? hannes.loeffler.stfc.ac.uk (Sun Jul 25 2010 - 03:10:18 PDT)
[AMBER] ptraj-clustering Necmettin Pirinccioglu (Fri Jul 23 2010 - 00:28:30 PDT)
- Re: [AMBER] ptraj-clustering Daniel Roe (Fri Jul 23 2010 - 07:36:22 PDT)
- Re: [AMBER] ptraj-clustering Necmettin Pirinccioglu (Sun Jul 25 2010 - 23:46:12 PDT)
- Re: [AMBER] ptraj-clustering Daniel Roe (Mon Jul 26 2010 - 20:14:20 PDT)
  - Re: [AMBER] ptraj-clustering Jianyin Shao (Tue Jul 27 2010 - 12:37:22 PDT)
[AMBER] atomic radii of ions Xioling Chuang (Fri Jul 23 2010 - 01:04:41 PDT)
- Re: [AMBER] atomic radii of ions case (Fri Jul 23 2010 - 04:44:28 PDT)
  - Re: [AMBER] atomic radii of ions Xioling Chuang (Sun Jul 25 2010 - 08:27:52 PDT)
    - Re: [AMBER] atomic radii of ions Paul S. Nerenberg (Sun Jul 25 2010 - 08:46:30 PDT)
    - Re: [AMBER] atomic radii of ions case (Sun Jul 25 2010 - 13:28:06 PDT)
[AMBER] test of parallel NAB and PTRAJ Vlad Cojocaru (Fri Jul 23 2010 - 02:52:25 PDT)
- Re: [AMBER] test of parallel NAB and PTRAJ Vlad Cojocaru (Fri Jul 23 2010 - 03:09:08 PDT)
[AMBER] How to make hexane parameter using antechamber ? setyanto tri wahyudi (Fri Jul 23 2010 - 03:42:05 PDT)
- Re: [AMBER] How to make hexane parameter using antechamber ? case (Fri Jul 23 2010 - 04:47:15 PDT)
- Re: [AMBER] How to make hexane parameter using antechamber ? FyD (Fri Jul 23 2010 - 05:28:32 PDT)
  - Re: [AMBER] How to make hexane parameter using antechamber ? setyanto tri wahyudi (Sun Jul 25 2010 - 18:21:24 PDT)
[AMBER] PM6 in Amber 11 Zora Strelcova (Fri Jul 23 2010 - 06:13:34 PDT)
- Re: [AMBER] PM6 in Amber 11 Jason Swails (Fri Jul 23 2010 - 06:39:45 PDT)
  - Re: [AMBER] PM6 in Amber 11 Zora Strelcova (Fri Jul 23 2010 - 06:54:58 PDT)
    - Re: [AMBER] PM6 in Amber 11 Jason Swails (Fri Jul 23 2010 - 07:05:54 PDT)
- Re: [AMBER] PM6 in Amber 11 case (Fri Jul 23 2010 - 12:25:46 PDT)
  - Re: [AMBER] PM6 in Amber 11 Zora Strelcova (Mon Jul 26 2010 - 00:32:27 PDT)
[AMBER] b-factor Syed Tarique Moin (Fri Jul 23 2010 - 06:42:41 PDT)
[AMBER] Relax command for tleap Valerie Fako (Fri Jul 23 2010 - 09:11:43 PDT)
- Re: [AMBER] Relax command for tleap Paul S. Nerenberg (Fri Jul 23 2010 - 09:33:04 PDT)
- Re: [AMBER] Relax command for tleap Bill Ross (Fri Jul 23 2010 - 09:56:27 PDT)
  - Re: [AMBER] Relax command for tleap Paul S. Nerenberg (Fri Jul 23 2010 - 10:32:42 PDT)
[AMBER] antechamber vs. REDDB ros (Fri Jul 23 2010 - 11:19:16 PDT)
- Re: [AMBER] antechamber vs. RED FyD (Sun Jul 25 2010 - 01:46:42 PDT)
[AMBER] random number seed - range g t (Sat Jul 24 2010 - 05:21:51 PDT)
- Re: [AMBER] random number seed - range case (Sat Jul 24 2010 - 06:22:14 PDT)
  - Re: [AMBER] random number seed - range g t (Sat Jul 24 2010 - 12:45:57 PDT)
    - Re: [AMBER] random number seed - range Tom Joseph (Sat Jul 24 2010 - 15:27:14 PDT)
    - Re: [AMBER] random number seed - range Ross Walker (Sat Jul 24 2010 - 16:12:15 PDT)
    - Re: [AMBER] random number seed - range Paul S. Nerenberg (Sat Jul 24 2010 - 18:11:00 PDT)
    - Re: [AMBER] random number seed - range g t (Sun Jul 25 2010 - 06:30:30 PDT)
    - Re: [AMBER] random number seed - range Keith Van Nostrand (Tue Jul 27 2010 - 07:25:19 PDT)
    - Re: [AMBER] random number seed - range Paul S. Nerenberg (Tue Jul 27 2010 - 07:44:38 PDT)
    - Re: [AMBER] random number seed - range case (Tue Jul 27 2010 - 12:02:54 PDT)
- Re: [AMBER] random number seed - range Bill Ross (Sat Jul 24 2010 - 13:54:59 PDT)
- Re: [AMBER] random number seed - range Robert Duke (Tue Jul 27 2010 - 12:13:00 PDT)
[AMBER] about grid & radial distribution function M. Reza Ganjalikhany (Sun Jul 25 2010 - 03:59:36 PDT)
- Re: [AMBER] about grid & radial distribution function Thomas Cheatham (Thu Jul 29 2010 - 19:03:07 PDT)
[AMBER] Mutation of DNA sudipta (Sun Jul 25 2010 - 05:15:03 PDT)
- Re: [AMBER] Mutation of DNA kurisaki ikuo (Sun Jul 25 2010 - 17:57:42 PDT)
[AMBER] Check out my photos on Facebook Ashish Pandey (Sun Jul 25 2010 - 06:43:22 PDT)
[AMBER] Check out my photos on Facebook Ashish Pandey (Sun Jul 25 2010 - 06:50:09 PDT)
[AMBER] MM-PBSA/MM-GBSA: mono valent salt Xioling Chuang (Sun Jul 25 2010 - 08:45:38 PDT)
- Re: [AMBER] MM-PBSA/MM-GBSA: mono valent salt case (Sun Jul 25 2010 - 13:32:21 PDT)
[AMBER] gbsa for 1 or 2 fancy2012 (Sun Jul 25 2010 - 09:19:41 PDT)
[AMBER] For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+ Jorgen Simonsen (Sun Jul 25 2010 - 10:45:27 PDT)
- Re: [AMBER] For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+ Bill Ross (Sun Jul 25 2010 - 11:01:10 PDT)
  - Re: [AMBER] For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+ Jorgen Simonsen (Sun Jul 25 2010 - 11:27:38 PDT)
- Re: [AMBER] For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+ Bill Ross (Sun Jul 25 2010 - 11:34:38 PDT)
  - Re: [AMBER] For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+ case (Sun Jul 25 2010 - 13:52:30 PDT)
[AMBER] AmberTools1.3 with amber9 Xioling Chuang (Sun Jul 25 2010 - 20:47:31 PDT)
- Re: [AMBER] AmberTools1.3 with amber9 case (Mon Jul 26 2010 - 04:44:32 PDT)
[AMBER] Error report please fix it Shubhra Gupta (Mon Jul 26 2010 - 00:25:42 PDT)
- Re: [AMBER] Error report please fix it case (Mon Jul 26 2010 - 04:47:51 PDT)
  - Re: [AMBER] Error report please fix it Shubhra Gupta (Mon Jul 26 2010 - 22:42:13 PDT)
    - Re: [AMBER] Error report please fix it Shubhra Gupta (Mon Jul 26 2010 - 22:45:54 PDT)
    - [AMBER] Fwd: Error report please fix it Shubhra Gupta (Tue Jul 27 2010 - 21:25:24 PDT)
    - Re: [AMBER] Fwd: Error report please fix it Daniel Roe (Tue Jul 27 2010 - 22:22:51 PDT)
    - Re: [AMBER] Fwd: Error report please fix it Shubhra Gupta (Wed Jul 28 2010 - 00:28:34 PDT)
[AMBER] radius of K+ ions Asfa Ali (Mon Jul 26 2010 - 03:06:16 PDT)
- Re: [AMBER] radius of K+ ions Jorgen Simonsen (Mon Jul 26 2010 - 03:19:36 PDT)
  - Re: [AMBER] radius of K+ ions Asfa Ali (Mon Jul 26 2010 - 03:42:36 PDT)
- Re: [AMBER] radius of K+ ions case (Mon Jul 26 2010 - 04:54:23 PDT)
[AMBER] NAB: pbc calculations available after all? Josh Berryman (Mon Jul 26 2010 - 05:06:20 PDT)
- Re: [AMBER] NAB: pbc calculations available after all? case (Mon Jul 26 2010 - 07:03:46 PDT)
  - Re: [AMBER] NAB: pbc calculations available after all? Josh Berryman (Mon Jul 26 2010 - 07:24:57 PDT)
[AMBER] regarding remd Jorgen Simonsen (Mon Jul 26 2010 - 06:29:31 PDT)
- Re: [AMBER] regarding remd Daniel Sindhikara (Mon Jul 26 2010 - 07:24:14 PDT)
- Re: [AMBER] regarding remd Carlos Simmerling (Mon Jul 26 2010 - 07:44:47 PDT)
  - Re: [AMBER] regarding remd Jorgen Simonsen (Mon Jul 26 2010 - 12:44:46 PDT)
[AMBER] energies in amber, namd and gromacs Alan (Mon Jul 26 2010 - 07:50:18 PDT)
[AMBER] Question about sqm in antechamber Guoxiong Su (Mon Jul 26 2010 - 09:45:20 PDT)
- Re: [AMBER] Question about sqm in antechamber case (Mon Jul 26 2010 - 11:01:37 PDT)
  - Re: [AMBER] Question about sqm in antechamber Guoxiong Su (Mon Jul 26 2010 - 11:25:49 PDT)
- [AMBER] RDF 3 files and 3 columns Philippe Pinard (Mon Jul 26 2010 - 15:19:33 PDT)
  - Re: [AMBER] RDF 3 files and 3 columns Bill Ross (Tue Jul 27 2010 - 10:48:59 PDT)
  - Re: [AMBER] RDF 3 files and 3 columns Bill Ross (Thu Jul 29 2010 - 13:28:42 PDT)
[AMBER] simulate large molecules with implicit water model (GB) Yan Gao (Mon Jul 26 2010 - 10:42:59 PDT)
- Re: [AMBER] simulate large molecules with implicit water model (GB) Carlos Simmerling (Mon Jul 26 2010 - 10:46:50 PDT)
  - Re: [AMBER] simulate large molecules with implicit water model (GB) Yan Gao (Mon Jul 26 2010 - 11:28:23 PDT)
[AMBER] Segmentation fault with translate command Yan Gao (Mon Jul 26 2010 - 11:28:30 PDT)
- Re: [AMBER] Segmentation fault with translate command case (Tue Jul 27 2010 - 04:53:44 PDT)
  - Re: [AMBER] Segmentation fault with translate command Yan Gao (Tue Jul 27 2010 - 08:43:05 PDT)
[AMBER] Permission to post Admin processes? Marc Moreau (Mon Jul 26 2010 - 12:31:05 PDT)
- Re: [AMBER] Permission to post Admin processes? case (Mon Jul 26 2010 - 13:19:32 PDT)
  - Re: [AMBER] Permission to post Admin processes? Marc Moreau (Mon Jul 26 2010 - 13:33:32 PDT)
    - Re: [AMBER] Permission to post Admin processes? case (Tue Jul 27 2010 - 04:55:20 PDT)
[AMBER] vlimit exceeded after 10ns MD Siddharth Rastogi (Mon Jul 26 2010 - 14:37:36 PDT)
- Re: [AMBER] vlimit exceeded after 10ns MD Bill Ross (Mon Jul 26 2010 - 17:21:02 PDT)
- Re: [AMBER] vlimit exceeded after 10ns MD case (Mon Jul 26 2010 - 18:05:33 PDT)
- Re: [AMBER] vlimit exceeded after 10ns MD Bill Ross (Mon Jul 26 2010 - 18:13:30 PDT)
[AMBER] RDF 3 files and 3 columns Philippe Pinard (Mon Jul 26 2010 - 14:43:12 PDT)
- Re: [AMBER] RDF 3 files and 3 columns Thomas Cheatham III (Mon Jul 26 2010 - 15:49:24 PDT)
  - Re: [AMBER] RDF 3 files and 3 columns Philippe Pinard (Tue Jul 27 2010 - 06:37:37 PDT)
    - Re: [AMBER] RDF 3 files and 3 columns Daniel Roe (Tue Jul 27 2010 - 06:47:29 PDT)
    - Re: [AMBER] RDF 3 files and 3 columns Thomas Cheatham III (Tue Jul 27 2010 - 08:39:29 PDT)
    - Re: [AMBER] RDF 3 files and 3 columns Philippe Pinard (Tue Jul 27 2010 - 09:48:19 PDT)
    - Re: [AMBER] RDF 3 files and 3 columns Thomas Cheatham III (Tue Jul 27 2010 - 10:11:15 PDT)
    - Re: [AMBER] RDF 3 files and 3 columns Philippe Pinard (Thu Jul 29 2010 - 12:50:55 PDT)
    - Re: [AMBER] RDF 3 files and 3 columns Thomas Cheatham (Thu Jul 29 2010 - 18:44:56 PDT)
    - Re: [AMBER] RDF 3 files and 3 columns Philippe Pinard (Sat Jul 31 2010 - 17:03:39 PDT)
    - Re: [AMBER] RDF 3 files and 3 columns Thomas Cheatham III (Tue Jul 27 2010 - 08:41:30 PDT)
[AMBER] A clear procedure to do WHAM based on the REMD simulations outputs Dongshan Wei (Mon Jul 26 2010 - 15:43:58 PDT)
- Re: [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs Daniel Sindhikara (Tue Jul 27 2010 - 04:15:10 PDT)
  - Re: [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs Carlos Simmerling (Tue Jul 27 2010 - 04:18:41 PDT)
    - Re: [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs Daniel Sindhikara (Tue Jul 27 2010 - 04:34:29 PDT)
    - Re: [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs Dongshan Wei (Sat Jul 31 2010 - 12:19:00 PDT)
[AMBER] mpi with openmpi Yan Gao (Mon Jul 26 2010 - 18:26:55 PDT)
- Re: [AMBER] mpi with openmpi Bill Ross (Mon Jul 26 2010 - 18:39:11 PDT)
- Re: [AMBER] mpi with openmpi David Watson (Mon Jul 26 2010 - 18:47:59 PDT)
  - Re: [AMBER] mpi with openmpi Yan Gao (Mon Jul 26 2010 - 19:38:35 PDT)
    - Re: [AMBER] mpi with openmpi David Watson (Mon Jul 26 2010 - 20:04:50 PDT)
Re: [AMBER] mpi with openmpi - with input files Yan Gao (Mon Jul 26 2010 - 18:45:25 PDT)
- Re: [AMBER] mpi with openmpi - with input files Jason Swails (Tue Jul 27 2010 - 10:57:32 PDT)
  - Re: [AMBER] mpi with openmpi - with input files Yan Gao (Tue Jul 27 2010 - 12:15:00 PDT)
[AMBER] very high and unstable RMSD Sangita Kachhap (Tue Jul 27 2010 - 03:15:20 PDT)
- Re: [AMBER] very high and unstable RMSD Jason Swails (Tue Jul 27 2010 - 09:07:41 PDT)
  - Re: [AMBER] very high and unstable RMSD Sangita Kachhap (Wed Jul 28 2010 - 12:06:12 PDT)
    - Re: [AMBER] very high and unstable RMSD Jason Swails (Wed Jul 28 2010 - 13:56:51 PDT)
    - Re: [AMBER] very high and unstable RMSD Sangita Kachhap (Wed Jul 28 2010 - 21:17:24 PDT)
    - Re: [AMBER] very high and unstable RMSD Kevin Hauser (Wed Jul 28 2010 - 21:32:21 PDT)
    - Re: [AMBER] very high and unstable RMSD Kevin Hauser (Wed Jul 28 2010 - 21:34:36 PDT)
    - Re: [AMBER] very high and unstable RMSD Sangita Kachhap (Wed Jul 28 2010 - 21:44:49 PDT)
[AMBER] make test trouble with Amber11 池田輝彦 (Tue Jul 27 2010 - 05:46:46 PDT)
- Re: [AMBER] make test trouble with Amber11 case (Tue Jul 27 2010 - 06:16:01 PDT)
[AMBER] Calculation of Intramolecular hydrogen bonding using ptraj Sudha Mani Karra (Tue Jul 27 2010 - 07:20:05 PDT)
- Re: [AMBER] Calculation of Intramolecular hydrogen bonding using ptraj Thomas Cheatham III (Tue Jul 27 2010 - 08:46:12 PDT)
  - Re: [AMBER] Calculation of Intramolecular hydrogen bonding using ptraj Sudha Mani Karra (Tue Jul 27 2010 - 09:51:55 PDT)
    - Re: [AMBER] Calculation of Intramolecular hydrogen bonding using ptraj Thomas Cheatham III (Tue Jul 27 2010 - 10:15:43 PDT)
[AMBER] MM-PBSA per residue decompostion manoj singh (Tue Jul 27 2010 - 08:39:08 PDT)
- Re: [AMBER] MM-PBSA per residue decompostion Catein Catherine (Tue Jul 27 2010 - 21:19:55 PDT)
  - [AMBER] How to prepare the same prmtop from two PDBs for NED analysis? Catein Catherine (Tue Jul 27 2010 - 21:27:55 PDT)
    - Re: [AMBER] How to prepare the same prmtop from two PDBs for NED analysis? case (Wed Jul 28 2010 - 05:08:32 PDT)
[AMBER] cumulative patch with two bugfixes for threaded mm_pbsa.pl Thomas Zeiser (Tue Jul 27 2010 - 09:13:57 PDT)
Re: [AMBER] mpi with openmpi - SGE error Yan Gao (Tue Jul 27 2010 - 19:47:05 PDT)
[AMBER] about dielectric constant.. Wookyung Yu (Tue Jul 27 2010 - 20:18:19 PDT)
- Re: [AMBER] about dielectric constant.. Jason Swails (Wed Jul 28 2010 - 04:59:16 PDT)
- Re: [AMBER] about dielectric constant.. case (Wed Jul 28 2010 - 05:32:24 PDT)
- Re: [AMBER] about dielectric constant.. Robert Duke (Wed Jul 28 2010 - 06:09:59 PDT)
[AMBER] Reference of ion parameters employed in parm99 kurisaki ikuo (Tue Jul 27 2010 - 20:21:09 PDT)
- Re: [AMBER] Reference of ion parameters employed in parm99 Paul S. Nerenberg (Tue Jul 27 2010 - 21:04:12 PDT)
  - Re: [AMBER] Reference of ion parameters employed in parm99 kurisaki ikuo (Tue Jul 27 2010 - 21:33:54 PDT)
    - Re: [AMBER] Reference of ion parameters employed in parm99 Paul S. Nerenberg (Tue Jul 27 2010 - 21:45:38 PDT)
    - Re: [AMBER] Reference of ion parameters employed in parm99 kurisaki ikuo (Tue Jul 27 2010 - 22:13:44 PDT)
- Re: [AMBER] Reference of ion parameters employed in parm99 kurisaki ikuo (Tue Jul 27 2010 - 22:22:00 PDT)
[AMBER] how to develop parameter for organotin Shulin Zhuang (Wed Jul 28 2010 - 00:04:31 PDT)
- Re: [AMBER] how to develop parameter for organotin FyD (Wed Jul 28 2010 - 01:51:35 PDT)
[AMBER] calculation of sasa Asfa Ali (Wed Jul 28 2010 - 07:06:56 PDT)
- Re: [AMBER] calculation of sasa case (Wed Jul 28 2010 - 18:43:31 PDT)
  - [AMBER] What is the max atom can be run by addles in amber10? Catein Catherine (Wed Jul 28 2010 - 20:42:25 PDT)
  - Re: [AMBER] calculation of sasa Asfa Ali (Wed Jul 28 2010 - 23:47:59 PDT)
    - Re: [AMBER] calculation of sasa case (Thu Jul 29 2010 - 04:45:01 PDT)
[AMBER] Invitation to connect on LinkedIn rameshwar prajapati (Wed Jul 28 2010 - 09:39:52 PDT)
[AMBER] Parallel test times Marc Moreau (Wed Jul 28 2010 - 10:03:42 PDT)
- Re: [AMBER] Parallel test times Marc Moreau (Wed Jul 28 2010 - 10:08:17 PDT)
  - Re: [AMBER] Parallel test times Daniel Roe (Wed Jul 28 2010 - 10:14:08 PDT)
[AMBER] RESP "too many charge-group constraints" error Justine Shaw (Wed Jul 28 2010 - 13:24:05 PDT)
- Re: [AMBER] RESP "too many charge-group constraints" error FyD (Wed Jul 28 2010 - 13:32:49 PDT)
  - Re: [AMBER] RESP "too many charge-group constraints" error Justine Shaw (Wed Jul 28 2010 - 13:51:57 PDT)
    - Re: [AMBER] RESP "too many charge-group constraints" error FyD (Wed Jul 28 2010 - 14:04:11 PDT)
    - Re: [AMBER] RESP "too many charge-group constraints" error Justine Shaw (Wed Jul 28 2010 - 14:18:19 PDT)
    - Re: [AMBER] RESP "too many charge-group constraints" error Justine Shaw (Thu Jul 29 2010 - 09:37:38 PDT)
[AMBER] NAB problem with a metallic atom InSuk Joung (Wed Jul 28 2010 - 14:34:19 PDT)
- Re: [AMBER] NAB problem with a metallic atom Bill Ross (Wed Jul 28 2010 - 14:49:13 PDT)
  - Re: [AMBER] NAB problem with a metallic atom InSuk Joung (Wed Jul 28 2010 - 14:59:15 PDT)
- Re: [AMBER] NAB problem with a metallic atom Bill Ross (Wed Jul 28 2010 - 15:19:25 PDT)
  - Re: [AMBER] NAB problem with a metallic atom InSuk Joung (Wed Jul 28 2010 - 16:16:46 PDT)
[AMBER] PMF from EVB calculations Ewa Chudyk (Wed Jul 28 2010 - 15:13:31 PDT)
[AMBER] PMF from EVB calculations Ewa Chudyk (Thu Jul 29 2010 - 04:57:13 PDT)
[AMBER] 1D PMF D.J. Cole (Thu Jul 29 2010 - 07:03:52 PDT)
[AMBER] how to generate porcupine plot Jia Xu (Thu Jul 29 2010 - 09:31:36 PDT)
- Re: [AMBER] how to generate porcupine plot Hector A. Baldoni (Thu Jul 29 2010 - 15:43:24 PDT)
  - [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests? Sasha Buzko (Thu Jul 29 2010 - 16:52:01 PDT)
    - Re: [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests? Ross Walker (Thu Jul 29 2010 - 19:09:20 PDT)
    - Re: [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests? Scott Le Grand (Sat Jul 31 2010 - 10:12:29 PDT)
[AMBER] Minor Typo bug. Marc Moreau (Thu Jul 29 2010 - 10:20:22 PDT)
- Re: [AMBER] Minor Typo bug. Mengjuei Hsieh (Thu Jul 29 2010 - 11:59:04 PDT)
[AMBER] tleap and sander minimization Hegazy,Lamees (Thu Jul 29 2010 - 11:35:45 PDT)
- Re: [AMBER] tleap and sander minimization Ben Roberts (Thu Jul 29 2010 - 11:52:06 PDT)
- Re: [AMBER] tleap and sander minimization Bill Ross (Thu Jul 29 2010 - 11:53:49 PDT)
- Re: [AMBER] tleap and sander minimization Hegazy,Lamees (Thu Jul 29 2010 - 12:02:06 PDT)
[AMBER] Which one, ESP calculation? William Flak (Thu Jul 29 2010 - 20:41:50 PDT)
[AMBER] how to prepare a system with solvent of ethanol + water ? vasu mathi (Fri Jul 30 2010 - 03:06:37 PDT)
- Re: [AMBER] how to prepare a system with solvent of ethanol + water ? setyanto tri wahyudi (Fri Jul 30 2010 - 04:00:30 PDT)
- Re: [AMBER] how to prepare a system with solvent of ethanol + water ? vasu mathi (Sat Jul 31 2010 - 09:57:31 PDT)
[AMBER] dipole moment of binary mixture box Ganesh Kamath (Fri Jul 30 2010 - 05:33:03 PDT)
[AMBER] addles Hegazy,Lamees (Fri Jul 30 2010 - 10:23:42 PDT)
- Re: [AMBER] addles Carlos Simmerling (Fri Jul 30 2010 - 10:28:11 PDT)
[AMBER] fix CM riya david (Fri Jul 30 2010 - 12:43:16 PDT)
- Re: [AMBER] fix CM Jason Swails (Fri Jul 30 2010 - 13:14:28 PDT)
[AMBER] regarding IWRAP in Sander aneesh cna (Fri Jul 30 2010 - 22:50:23 PDT)
- Re: [AMBER] regarding IWRAP in Sander case (Sat Jul 31 2010 - 06:03:17 PDT)
[AMBER] Constant pH simulation at pH 7 nicholus bhattacharjee (Sat Jul 31 2010 - 07:19:00 PDT)
- Re: [AMBER] Constant pH simulation at pH 7 Jason Swails (Sat Jul 31 2010 - 07:39:55 PDT)
Re: [AMBER] obtain a .pdb file from a .prepin/.frcmod file Alessandro Nascimento (Sat Jul 31 2010 - 12:56:27 PDT)
- Re: [AMBER] obtain a .pdb file from a .prepin/.frcmod file Jason Swails (Sat Jul 31 2010 - 13:45:57 PDT)

Amber Archive Jul 2010 by thread