Amber Archive Jul 2010 by author
772 messages
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Starting
Wed Jun 30 2010 - 21:30:03 PDT,
Ending
Sat Jul 31 2010 - 17:30:03 PDT
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Adelene Sim
Re: [AMBER] compile ambertools on mac
(Mon Jul 26 2010 - 09:37:11 PDT)
Adrian Roitberg
Re: [AMBER] Steered MD calc
(Sun Jul 04 2010 - 20:12:49 PDT)
Ajay Ummat
Re: [AMBER] Adding Ions.
(Fri Jul 02 2010 - 07:45:03 PDT)
Alan
[AMBER] energies in amber, namd and gromacs
(Mon Jul 26 2010 - 07:50:18 PDT)
Alessandro Nascimento
Re: [AMBER] obtain a .pdb file from a .prepin/.frcmod file
(Sat Jul 31 2010 - 12:56:27 PDT)
Amor San Juan
[AMBER] mandatory command lines in MMPBSA.PY
(Thu Jul 22 2010 - 21:16:25 PDT)
[AMBER] Thank you Jason, Bill and Oliver
(Wed Jul 21 2010 - 00:12:51 PDT)
Re: [AMBER] errors of energy decomposition
(Tue Jul 20 2010 - 23:58:36 PDT)
[AMBER] Segmentation fault in MMPBSA.PY with two parts receptor
(Tue Jul 20 2010 - 03:16:57 PDT)
Re: [AMBER] MMPBSA.PY with two parts receptor
(Mon Jul 19 2010 - 01:05:43 PDT)
[AMBER] MMPBSA.PY with two parts receptor
(Tue Jul 13 2010 - 22:48:57 PDT)
[AMBER] MMPBSA.py source files
(Fri Jul 09 2010 - 01:36:35 PDT)
Re: [AMBER] mmgbsa for ternary system
(Thu Jul 08 2010 - 03:23:16 PDT)
[AMBER] mmgbsa for ternary system
(Wed Jul 07 2010 - 03:42:50 PDT)
Re: [AMBER] mmgbsa tricky output: PART 2
(Wed Jul 07 2010 - 03:03:10 PDT)
Re: [AMBER] mmgbsa tricky output: PART 2
(Mon Jul 05 2010 - 23:48:35 PDT)
Re: [AMBER] mmgbsa tricky output
(Sun Jul 04 2010 - 23:22:13 PDT)
Re: [AMBER] mmgbsa tricky output
(Sun Jul 04 2010 - 20:49:01 PDT)
Re: [AMBER] mmgbsa tricky output
(Thu Jul 01 2010 - 00:39:51 PDT)
Andrey Frolov
[AMBER] 1D-RISM in AmberTools: the reference for ion parameters and LJ parameters
(Thu Jul 08 2010 - 08:23:55 PDT)
[AMBER] 1D-RISM in AmberTools: atom order in output, a bug?
(Thu Jul 08 2010 - 08:04:06 PDT)
[AMBER] 3D-RISM in NAB AmberTools: 2) what is tolerance
(Thu Jul 01 2010 - 09:16:38 PDT)
[AMBER] 3D-RISM in NAB AmberTools: what is tolerance and initial guess
(Thu Jul 01 2010 - 09:09:51 PDT)
aneesh cna
[AMBER] regarding IWRAP in Sander
(Fri Jul 30 2010 - 22:50:23 PDT)
Anselm Horn
Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3
(Wed Jul 21 2010 - 04:21:20 PDT)
[AMBER] mm_pbsa.pl in PARALLEL - part 3
(Wed Jul 21 2010 - 03:33:00 PDT)
[AMBER] mm_pbsa.pl in PARALLEL - part 2
(Wed Jul 14 2010 - 05:26:53 PDT)
Re: [AMBER] mm_pbsa.pl in PARALLEL does not finish
(Mon Jul 12 2010 - 12:23:37 PDT)
[AMBER] mm_pbsa.pl in PARALLEL does not finish
(Mon Jul 12 2010 - 09:55:32 PDT)
arikcohen
[AMBER] Parameters missing after changing topology
(Mon Jul 19 2010 - 14:45:36 PDT)
Re: [AMBER] Head-Tail covalently bound substrate and
(Mon Jul 19 2010 - 11:47:29 PDT)
[AMBER] Head-Tail covalently bound substrate and
(Mon Jul 19 2010 - 11:04:24 PDT)
Asfa Ali
Re: [AMBER] calculation of sasa
(Wed Jul 28 2010 - 23:47:59 PDT)
[AMBER] calculation of sasa
(Wed Jul 28 2010 - 07:06:56 PDT)
Re: [AMBER] radius of K+ ions
(Mon Jul 26 2010 - 03:42:36 PDT)
[AMBER] radius of K+ ions
(Mon Jul 26 2010 - 03:06:16 PDT)
Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3
(Wed Jul 21 2010 - 04:32:05 PDT)
Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3
(Wed Jul 21 2010 - 04:05:57 PDT)
Re: [AMBER] regarding mmpbsa
(Wed Jun 30 2010 - 22:01:45 PDT)
Ashish Pandey
[AMBER] Check out my photos on Facebook
(Sun Jul 25 2010 - 06:50:09 PDT)
[AMBER] Check out my photos on Facebook
(Sun Jul 25 2010 - 06:43:22 PDT)
balaji nagarajan
[AMBER] step 0 of minimization ?
(Mon Jul 05 2010 - 12:28:06 PDT)
Beale, John
[AMBER] protein distance constraints
(Mon Jul 19 2010 - 08:18:11 PDT)
[AMBER] hydrogen bond printout
(Thu Jul 01 2010 - 04:29:14 PDT)
Ben Roberts
Re: [AMBER] tleap and sander minimization
(Thu Jul 29 2010 - 11:52:06 PDT)
Bill Miller III
Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3
(Wed Jul 21 2010 - 04:48:18 PDT)
Re: [AMBER] Warning: Input error! "nmode_igb=1" is an invalid option.
(Tue Jul 20 2010 - 08:32:19 PDT)
Re: [AMBER] MMPBSA.PY with two parts receptor
(Wed Jul 14 2010 - 03:21:48 PDT)
Re: [AMBER] Questions with input file in constant pH MD
(Thu Jul 01 2010 - 06:28:50 PDT)
Bill Ross
Re: [AMBER] minimization segmentation fault
(Fri Jul 30 2010 - 09:52:50 PDT)
Re: [AMBER] RDF 3 files and 3 columns
(Thu Jul 29 2010 - 13:28:42 PDT)
Re: [AMBER] tleap and sander minimization
(Thu Jul 29 2010 - 11:53:49 PDT)
Re: [AMBER] NAB problem with a metallic atom
(Wed Jul 28 2010 - 15:19:25 PDT)
Re: [AMBER] NAB problem with a metallic atom
(Wed Jul 28 2010 - 14:49:13 PDT)
Re: [AMBER] minimization segmentation fault
(Tue Jul 27 2010 - 11:53:25 PDT)
Re: [AMBER] RDF 3 files and 3 columns
(Tue Jul 27 2010 - 10:48:59 PDT)
Re: [AMBER] mpi with openmpi
(Mon Jul 26 2010 - 18:39:11 PDT)
Re: [AMBER] vlimit exceeded after 10ns MD
(Mon Jul 26 2010 - 18:13:30 PDT)
Re: [AMBER] vlimit exceeded after 10ns MD
(Mon Jul 26 2010 - 17:21:02 PDT)
Re: [AMBER] For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+
(Sun Jul 25 2010 - 11:34:38 PDT)
Re: [AMBER] For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+
(Sun Jul 25 2010 - 11:01:10 PDT)
Re: [AMBER] question about bond command
(Sat Jul 24 2010 - 20:05:24 PDT)
Re: [AMBER] question about bond command
(Sat Jul 24 2010 - 17:22:44 PDT)
Re: [AMBER] question about bond command
(Sat Jul 24 2010 - 13:57:32 PDT)
Re: [AMBER] random number seed - range
(Sat Jul 24 2010 - 13:54:59 PDT)
Re: [AMBER] question about bond command
(Fri Jul 23 2010 - 10:00:49 PDT)
Re: [AMBER] Relax command for tleap
(Fri Jul 23 2010 - 09:56:27 PDT)
Re: [AMBER] question about bond command
(Fri Jul 23 2010 - 09:44:08 PDT)
Re: [AMBER] question about bond command
(Fri Jul 23 2010 - 09:36:47 PDT)
Re: [AMBER] question about bond command
(Thu Jul 22 2010 - 14:55:48 PDT)
Re: [AMBER] question about bond command
(Thu Jul 22 2010 - 12:38:28 PDT)
Re: [AMBER] question about bond command
(Thu Jul 22 2010 - 11:54:31 PDT)
Re: [AMBER] question about bond command
(Thu Jul 22 2010 - 11:50:28 PDT)
Re: [AMBER] question about bond command
(Thu Jul 22 2010 - 10:43:58 PDT)
Re: [AMBER] minimization segmentation fault
(Thu Jul 22 2010 - 10:03:27 PDT)
Re: [AMBER] L and D peptides
(Tue Jul 20 2010 - 14:34:16 PDT)
Re: [AMBER] L and D peptides
(Tue Jul 20 2010 - 13:12:08 PDT)
Re: [AMBER] Problem with pmemd.cuda
(Mon Jul 19 2010 - 14:15:52 PDT)
Re: [AMBER] Problem with pmemd.cuda
(Mon Jul 19 2010 - 13:18:32 PDT)
Re: [AMBER] residues lacking connect
(Sun Jul 18 2010 - 20:26:20 PDT)
Re: [AMBER] The atom number exceeds the MAXATOM, reallocate memory Segmentation fault (core dumped) --- thank you and more questions!
(Wed Jul 14 2010 - 13:12:53 PDT)
Re: [AMBER] The atom number exceeds the MAXATOM, reallocate memory Segmentation fault (core dumped)
(Wed Jul 14 2010 - 11:27:04 PDT)
Re: [AMBER] source code to calculate electrostatic interaction in amber6
(Mon Jul 12 2010 - 13:41:58 PDT)
Re: [AMBER] residue wise rmsd, not getting expected results
(Mon Jul 12 2010 - 09:41:29 PDT)
Re: [AMBER] simulation runs very slow..
(Mon Jul 12 2010 - 08:41:43 PDT)
Re: [AMBER] simulation runs very slow..
(Mon Jul 12 2010 - 08:16:28 PDT)
Re: [AMBER] counterions placings
(Sat Jul 10 2010 - 10:32:06 PDT)
Re: [AMBER] No solvent overlap
(Sat Jul 10 2010 - 10:29:24 PDT)
Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration
(Fri Jul 09 2010 - 22:58:16 PDT)
Re: [AMBER] counterions placings
(Fri Jul 09 2010 - 22:45:52 PDT)
Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration
(Fri Jul 09 2010 - 22:22:01 PDT)
Re: [AMBER] xleap error
(Fri Jul 09 2010 - 10:41:29 PDT)
Re: [AMBER] xleap error
(Fri Jul 09 2010 - 10:16:28 PDT)
Re: [AMBER] counterions placings
(Fri Jul 09 2010 - 10:11:02 PDT)
Re: [AMBER] No solvent overlap
(Fri Jul 09 2010 - 09:56:12 PDT)
Re: [AMBER] distance between two residues from their center of mass
(Fri Jul 09 2010 - 09:39:36 PDT)
Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions
(Thu Jul 08 2010 - 16:46:29 PDT)
Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes
(Thu Jul 08 2010 - 14:28:25 PDT)
Re: [AMBER] What is the command to add two tails for a new residue in xleap?
(Mon Jul 05 2010 - 13:38:53 PDT)
Re: [AMBER] How do define phospho-tyrosine-DA linkage?
(Sat Jul 03 2010 - 11:02:46 PDT)
Re: [AMBER] simulations in urea
(Sat Jul 03 2010 - 10:58:38 PDT)
Re: [AMBER] About the ptraj problem
(Fri Jul 02 2010 - 10:18:41 PDT)
Re: [AMBER] adding counterions
(Thu Jul 01 2010 - 11:41:40 PDT)
Re: [AMBER] adding counterions
(Thu Jul 01 2010 - 11:19:58 PDT)
Re: [AMBER] adding counterions
(Thu Jul 01 2010 - 10:40:27 PDT)
Re: [AMBER] mmgbsa tricky output
(Thu Jul 01 2010 - 10:09:39 PDT)
c00jsw00
Re: [AMBER] About the ptraj problem
(Fri Jul 02 2010 - 00:13:34 PDT)
[AMBER] About the ptraj problem
(Thu Jul 01 2010 - 22:12:40 PDT)
Carlos Simmerling
Re: [AMBER] addles
(Fri Jul 30 2010 - 10:28:11 PDT)
Re: [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs
(Tue Jul 27 2010 - 04:18:41 PDT)
Re: [AMBER] simulate large molecules with implicit water model (GB)
(Mon Jul 26 2010 - 10:46:50 PDT)
Re: [AMBER] regarding remd
(Mon Jul 26 2010 - 07:44:47 PDT)
Re: [AMBER] Are there any GPU clusters that offer compute time?
(Fri Jul 09 2010 - 17:30:41 PDT)
case
Re: [AMBER] regarding IWRAP in Sander
(Sat Jul 31 2010 - 06:03:17 PDT)
Re: [AMBER] calculation of sasa
(Thu Jul 29 2010 - 04:45:01 PDT)
Re: [AMBER] calculation of sasa
(Wed Jul 28 2010 - 18:43:31 PDT)
Re: [AMBER] about dielectric constant..
(Wed Jul 28 2010 - 05:32:24 PDT)
Re: [AMBER] How to prepare the same prmtop from two PDBs for NED analysis?
(Wed Jul 28 2010 - 05:08:32 PDT)
Re: [AMBER] random number seed - range
(Tue Jul 27 2010 - 12:02:54 PDT)
Re: [AMBER] make test trouble with Amber11
(Tue Jul 27 2010 - 06:16:01 PDT)
Re: [AMBER] Permission to post Admin processes?
(Tue Jul 27 2010 - 04:55:20 PDT)
Re: [AMBER] Segmentation fault with translate command
(Tue Jul 27 2010 - 04:53:44 PDT)
Re: [AMBER] vlimit exceeded after 10ns MD
(Mon Jul 26 2010 - 18:05:33 PDT)
Re: [AMBER] Permission to post Admin processes?
(Mon Jul 26 2010 - 13:19:32 PDT)
Re: [AMBER] Question about sqm in antechamber
(Mon Jul 26 2010 - 11:01:37 PDT)
Re: [AMBER] compile ambertools on mac
(Mon Jul 26 2010 - 07:06:27 PDT)
Re: [AMBER] NAB: pbc calculations available after all?
(Mon Jul 26 2010 - 07:03:46 PDT)
Re: [AMBER] radius of K+ ions
(Mon Jul 26 2010 - 04:54:23 PDT)
Re: [AMBER] Error report please fix it
(Mon Jul 26 2010 - 04:47:51 PDT)
Re: [AMBER] AmberTools1.3 with amber9
(Mon Jul 26 2010 - 04:44:32 PDT)
Re: [AMBER] For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+
(Sun Jul 25 2010 - 13:52:30 PDT)
Re: [AMBER] MM-PBSA/MM-GBSA: mono valent salt
(Sun Jul 25 2010 - 13:32:21 PDT)
Re: [AMBER] atomic radii of ions
(Sun Jul 25 2010 - 13:28:06 PDT)
Re: [AMBER] question about bond command
(Sat Jul 24 2010 - 20:44:40 PDT)
Re: [AMBER] random number seed - range
(Sat Jul 24 2010 - 06:22:14 PDT)
Re: [AMBER] PM6 in Amber 11
(Fri Jul 23 2010 - 12:25:46 PDT)
Re: [AMBER] Compiling failure of Amber 9
(Fri Jul 23 2010 - 11:52:16 PDT)
Re: [AMBER] How to make hexane parameter using antechamber ?
(Fri Jul 23 2010 - 04:47:15 PDT)
Re: [AMBER] atomic radii of ions
(Fri Jul 23 2010 - 04:44:28 PDT)
Re: [AMBER] question about bond command
(Fri Jul 23 2010 - 04:36:00 PDT)
Re: [AMBER] Coulson vs. Mulliken, CM1, etc. in antechamber + mopac
(Thu Jul 22 2010 - 19:32:55 PDT)
Re: [AMBER] question about bond command
(Thu Jul 22 2010 - 18:58:12 PDT)
Re: [AMBER] segmentation fault
(Thu Jul 22 2010 - 06:53:22 PDT)
Re: [AMBER] FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type.
(Wed Jul 21 2010 - 06:09:11 PDT)
Re: [AMBER] Enquiry about NED calculation in AMBER10
(Wed Jul 21 2010 - 05:04:31 PDT)
Re: [AMBER] Workaround for gfortran-4.1.2?
(Tue Jul 20 2010 - 18:31:06 PDT)
Re: [AMBER] L and D peptides
(Tue Jul 20 2010 - 18:18:32 PDT)
Re: [AMBER] problem with the total charge
(Tue Jul 20 2010 - 04:44:48 PDT)
Re: [AMBER] Problem with pmemd.cuda
(Mon Jul 19 2010 - 17:41:37 PDT)
Re: [AMBER] Problem with pmemd.cuda
(Mon Jul 19 2010 - 12:30:54 PDT)
Re: [AMBER] protein distance constraints
(Mon Jul 19 2010 - 10:40:50 PDT)
Re: [AMBER] Problem with pmemd.cuda
(Mon Jul 19 2010 - 10:34:57 PDT)
Re: [AMBER] residues lacking connect
(Sun Jul 18 2010 - 15:24:28 PDT)
Re: [AMBER] problems with NAB and SHIFTS
(Thu Jul 15 2010 - 11:28:47 PDT)
Re: [AMBER] problems with NAB and SHIFTS
(Thu Jul 15 2010 - 10:32:06 PDT)
Re: [AMBER] NAB rdparm seg fault
(Thu Jul 15 2010 - 06:02:31 PDT)
Re: [AMBER] NAB rdparm seg fault
(Thu Jul 15 2010 - 05:37:20 PDT)
Re: [AMBER] how to create a mixture solvent of hexane and water
(Thu Jul 15 2010 - 05:16:10 PDT)
Re: [AMBER] amber tool installing problem
(Thu Jul 15 2010 - 04:54:14 PDT)
Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2
(Wed Jul 14 2010 - 13:26:49 PDT)
Re: [AMBER] TIP4P question
(Wed Jul 14 2010 - 10:46:24 PDT)
Re: [AMBER] NAB rdparm seg fault
(Wed Jul 14 2010 - 09:36:36 PDT)
Re: [AMBER] error 126 when install AmberTool1.4
(Tue Jul 13 2010 - 09:34:09 PDT)
Re: [AMBER] compile ambertools on mac
(Tue Jul 13 2010 - 05:47:51 PDT)
Re: [AMBER] 3D-RISM disabled?
(Tue Jul 13 2010 - 05:24:20 PDT)
Re: [AMBER] error 126 when install AmberTool1.4
(Tue Jul 13 2010 - 05:18:34 PDT)
Re: [AMBER] compile ambertools on mac
(Tue Jul 13 2010 - 05:05:04 PDT)
Re: [AMBER] compile ambertools on mac
(Mon Jul 12 2010 - 06:08:02 PDT)
Re: [AMBER] compile ambertools on mac
(Mon Jul 12 2010 - 05:31:18 PDT)
Re: [AMBER] same dihedral with different parameter in FRCMOD file
(Sat Jul 10 2010 - 07:43:22 PDT)
Re: [AMBER] No solvent overlap
(Sat Jul 10 2010 - 07:37:51 PDT)
Re: [AMBER] same dihedral with different parameter in FRCMOD file
(Sat Jul 10 2010 - 06:52:48 PDT)
Re: [AMBER] (no subject)
(Sat Jul 10 2010 - 05:55:54 PDT)
Re: [AMBER] Question about increasing the max number of atoms in mopac in antechamber
(Fri Jul 09 2010 - 13:39:13 PDT)
Re: [AMBER] xleap error
(Fri Jul 09 2010 - 11:28:21 PDT)
Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 !
(Fri Jul 09 2010 - 05:36:01 PDT)
Re: [AMBER] MMPBSA.py source files
(Fri Jul 09 2010 - 05:26:43 PDT)
Re: [AMBER] atom-type cz ???
(Fri Jul 09 2010 - 05:20:46 PDT)
Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o
(Thu Jul 01 2010 - 14:58:56 PDT)
Re: [AMBER] AmberTools installation in Cygwin
(Thu Jul 01 2010 - 13:21:21 PDT)
Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o
(Thu Jul 01 2010 - 09:52:11 PDT)
Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o
(Thu Jul 01 2010 - 07:52:30 PDT)
Re: [AMBER] make test.parallel
(Thu Jul 01 2010 - 07:39:15 PDT)
Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o
(Thu Jul 01 2010 - 05:58:33 PDT)
Re: [AMBER] installing AmberTools 1.4 on AIX
(Thu Jul 01 2010 - 05:26:01 PDT)
Re: [AMBER] Regarding Antechamber Tutorial
(Thu Jul 01 2010 - 05:17:09 PDT)
Re: [AMBER] vlimit exceeded for step
(Thu Jul 01 2010 - 05:03:09 PDT)
Catein Catherine
[AMBER] What is the max atom can be run by addles in amber10?
(Wed Jul 28 2010 - 20:42:25 PDT)
[AMBER] How to prepare the same prmtop from two PDBs for NED analysis?
(Tue Jul 27 2010 - 21:27:55 PDT)
Re: [AMBER] MM-PBSA per residue decompostion
(Tue Jul 27 2010 - 21:19:55 PDT)
Re: [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER?
(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?
(Fri Jul 23 2010 - 20:47:43 PDT)
[AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER?
(Fri Jul 23 2010 - 08:54:49 PDT)
[AMBER] Enquiry about NED calculation in AMBER10
(Tue Jul 20 2010 - 19:53:08 PDT)
[AMBER] Can I calculate the interaction energy between two connected domains of a protein using mmpbsa.py?
(Mon Jul 19 2010 - 08:12:55 PDT)
Re: [AMBER] Can I calculate the interaction energy between two connected domains of a protein?
(Mon Jul 19 2010 - 01:04:23 PDT)
[AMBER] Can I calculate the interaction energy between two connected domains of a protein?
(Mon Jul 19 2010 - 00:40:54 PDT)
Re: [AMBER] simulation runs very slow..
(Mon Jul 12 2010 - 08:18:02 PDT)
[AMBER] Missing BELE for MM in 1 ( residue 1)
(Fri Jul 09 2010 - 08:48:47 PDT)
Re: [AMBER] How to find the angle bond etc parameters used for practicular atom type used in AMBER?
(Fri Jul 09 2010 - 08:11:58 PDT)
[AMBER] How to find the angle bond etc parameters used for practicular atom type used in AMBER?
(Fri Jul 09 2010 - 04:23:22 PDT)
[AMBER] Do I have to keep the Na+ counterions in prmtop and snapshot generation when I do mmGBSA/PBSA calculation?
(Fri Jul 09 2010 - 04:14:24 PDT)
[AMBER] What is the way to change from MMPBSA+GBSA to MMGBSA only input file.
(Fri Jul 09 2010 - 03:50:40 PDT)
[AMBER] Should I define drug intercalation site of a DNA as internal (DT/DA) or terminal (DT3/DA5) unit ?
(Mon Jul 05 2010 - 02:59:23 PDT)
[AMBER] What is the command to add two tails for a new residue in xleap?
(Mon Jul 05 2010 - 02:42:36 PDT)
Re: [AMBER] Question about xleap: How to define a linkage between DNA and phosphotyrosine.
(Mon Jul 05 2010 - 02:39:58 PDT)
[AMBER] Question about xleap: How to define a linkage between DNA and phosphotyrosine.
(Sun Jul 04 2010 - 01:06:27 PDT)
[AMBER] How do define phospho-tyrosine-DA linkage?
(Sat Jul 03 2010 - 10:38:41 PDT)
[AMBER] MMPBSA.py install error
(Sat Jul 03 2010 - 04:38:33 PDT)
[AMBER] What ab initio methods can be choose for QM/MM package in AMBER10?
(Fri Jul 02 2010 - 02:34:31 PDT)
[AMBER] Any parameters for Mg2+?
(Fri Jul 02 2010 - 02:30:24 PDT)
CHAMI F.
[AMBER] scee EEL and scnb VDW 1-4
(Thu Jul 22 2010 - 05:34:36 PDT)
Chris Whittleston
Re: [AMBER] Problems using library file containing multiple residues to make a complex
(Tue Jul 06 2010 - 02:05:30 PDT)
[AMBER] Problems using library file containing multiple residues to make a complex
(Mon Jul 05 2010 - 08:57:13 PDT)
cieplak.cgl.ucsf.edu
Re: [AMBER] amber02pol: sequence: Illegal UNIT named: NHE
(Thu Jul 15 2010 - 14:39:24 PDT)
colvin
Re: [AMBER] force field parameter and resp charge calculation
(Thu Jul 01 2010 - 04:00:34 PDT)
D.J. Cole
[AMBER] 1D PMF
(Thu Jul 29 2010 - 07:03:52 PDT)
Dairsie Latimer
Re: [AMBER] The system size limitations for Tesla C2050 ?
(Mon Jul 12 2010 - 02:04:12 PDT)
Daniel Roe
Re: [AMBER] Parallel test times
(Wed Jul 28 2010 - 10:14:08 PDT)
Re: [AMBER] Fwd: Error report please fix it
(Tue Jul 27 2010 - 22:22:51 PDT)
Re: [AMBER] RDF 3 files and 3 columns
(Tue Jul 27 2010 - 06:47:29 PDT)
Re: [AMBER] ptraj-clustering
(Mon Jul 26 2010 - 20:14:20 PDT)
Re: [AMBER] clustering analysis changes my coordinates
(Fri Jul 23 2010 - 07:46:04 PDT)
Re: [AMBER] ptraj-clustering
(Fri Jul 23 2010 - 07:36:22 PDT)
Re: [AMBER] minimization segmentation fault
(Thu Jul 22 2010 - 06:33:30 PDT)
Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files
(Sun Jul 18 2010 - 06:37:47 PDT)
Re: [AMBER] error 126 when install AmberTool1.4
(Tue Jul 13 2010 - 05:44:37 PDT)
Re: [AMBER] residue wise rmsd, not getting expected results
(Mon Jul 12 2010 - 06:48:01 PDT)
Re: [AMBER] residue wise rmsd, not getting expected results
(Mon Jul 12 2010 - 06:47:14 PDT)
Re: [AMBER] ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption
(Fri Jul 09 2010 - 09:07:01 PDT)
Re: [AMBER] xleap error
(Fri Jul 09 2010 - 08:48:15 PDT)
Re: [AMBER] ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption
(Fri Jul 09 2010 - 05:41:00 PDT)
Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files
(Thu Jul 08 2010 - 12:42:13 PDT)
Re: [AMBER] Combine trajectory files error
(Thu Jul 08 2010 - 07:35:09 PDT)
Re: [AMBER] rms command
(Thu Jul 08 2010 - 04:48:03 PDT)
Re: [AMBER] Problems using library file containing multiple residues to make a complex
(Tue Jul 06 2010 - 05:54:28 PDT)
Re: [AMBER] Problems using library file containing multiple residues to make a complex
(Mon Jul 05 2010 - 10:53:57 PDT)
Daniel Sindhikara
Re: [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs
(Tue Jul 27 2010 - 04:34:29 PDT)
Re: [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs
(Tue Jul 27 2010 - 04:15:10 PDT)
Re: [AMBER] regarding remd
(Mon Jul 26 2010 - 07:24:14 PDT)
Re: [AMBER] How to remove PBC effects?
(Mon Jul 19 2010 - 06:06:11 PDT)
Re: [AMBER] 3D-RISM disabled?
(Tue Jul 13 2010 - 19:05:52 PDT)
[AMBER] 3D-RISM disabled?
(Tue Jul 13 2010 - 01:26:29 PDT)
David A. Case
Re: [AMBER] OpenMP programs
(Thu Jul 08 2010 - 13:14:21 PDT)
Re: [AMBER] atom-type cz ???
(Thu Jul 08 2010 - 13:06:23 PDT)
Re: [AMBER] rfree: Error decoding variable 2 2
(Wed Jul 07 2010 - 14:06:13 PDT)
[AMBER] segmentation fault
(Tue Jul 06 2010 - 10:37:32 PDT)
[AMBER] Amber web page is slow
(Sat Jul 03 2010 - 11:00:13 PDT)
David Watson
Re: [AMBER] mpi with openmpi
(Mon Jul 26 2010 - 20:04:50 PDT)
Re: [AMBER] mpi with openmpi
(Mon Jul 26 2010 - 18:47:59 PDT)
Re: [AMBER] Compiling failure of Amber 9
(Thu Jul 22 2010 - 09:22:56 PDT)
Dmitry Mukha
Re: [AMBER] same dihedral with different parameter in FRCMOD file
(Sat Jul 10 2010 - 07:21:22 PDT)
Don.Bashford.stjude.org
[AMBER] Coulson vs. Mulliken, CM1, etc. in antechamber + mopac
(Thu Jul 22 2010 - 13:59:42 PDT)
Dongshan Wei
Re: [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs
(Sat Jul 31 2010 - 12:19:00 PDT)
[AMBER] A clear procedure to do WHAM based on the REMD simulations outputs
(Mon Jul 26 2010 - 15:43:58 PDT)
Dwight McGee
Re: [AMBER] regarding mmpbsa
(Thu Jul 01 2010 - 07:09:20 PDT)
eduardo.troche.uvigo.es
[AMBER] Steered MD calc
(Sun Jul 04 2010 - 09:24:55 PDT)
Ewa Chudyk
[AMBER] PMF from EVB calculations
(Thu Jul 29 2010 - 04:57:13 PDT)
[AMBER] PMF from EVB calculations
(Wed Jul 28 2010 - 15:13:31 PDT)
fancy2012
[AMBER] gbsa for 1 or 2
(Sun Jul 25 2010 - 09:19:41 PDT)
Re: [AMBER] errors of energy decomposition
(Wed Jul 21 2010 - 00:23:38 PDT)
[AMBER] errors of energy decomposition
(Tue Jul 20 2010 - 23:20:30 PDT)
Re: [AMBER] questions of decomposition using mm/gbsa
(Sun Jul 18 2010 - 00:11:39 PDT)
[AMBER] questions of decomposition using mm/gbsa
(Sun Jul 18 2010 - 00:01:45 PDT)
[AMBER] File MAKE_CRD is not found
(Wed Jun 30 2010 - 23:59:21 PDT)
Francesco Pietra
[AMBER] RESP charges outside Gaussian
(Sun Jul 04 2010 - 08:13:20 PDT)
FyD
Re: [AMBER] RESP "too many charge-group constraints" error
(Wed Jul 28 2010 - 14:04:11 PDT)
Re: [AMBER] RESP "too many charge-group constraints" error
(Wed Jul 28 2010 - 13:32:49 PDT)
Re: [AMBER] how to develop parameter for organotin
(Wed Jul 28 2010 - 01:51:35 PDT)
Re: [AMBER] antechamber vs. RED
(Sun Jul 25 2010 - 01:46:42 PDT)
Re: [AMBER] How to make hexane parameter using antechamber ?
(Fri Jul 23 2010 - 05:28:32 PDT)
Re: [AMBER] L and D peptides
(Wed Jul 21 2010 - 00:39:32 PDT)
[AMBER] Release of the R.E.D.-III.4 tools
(Wed Jul 07 2010 - 00:04:36 PDT)
Re: [AMBER] Question about xleap: How to define a linkage between DNA and phosphotyrosine.
(Mon Jul 05 2010 - 23:32:17 PDT)
Re: [AMBER] Question about xleap: How to define a linkage between DNA and phosphotyrosine.
(Sun Jul 04 2010 - 23:44:44 PDT)
Re: [AMBER] RESP charges outside Gaussian
(Sun Jul 04 2010 - 09:11:41 PDT)
g t
Re: [AMBER] random number seed - range
(Sun Jul 25 2010 - 06:30:30 PDT)
Re: [AMBER] random number seed - range
(Sat Jul 24 2010 - 12:45:57 PDT)
[AMBER] random number seed - range
(Sat Jul 24 2010 - 05:21:51 PDT)
Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration
(Thu Jul 08 2010 - 03:07:58 PDT)
[AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration
(Wed Jul 07 2010 - 11:07:33 PDT)
Ganesh Kamath
[AMBER] dipole moment of binary mixture box
(Fri Jul 30 2010 - 05:33:03 PDT)
Geoffrey Wood
Re: [AMBER] clustering analysis changes my coordinates
(Sat Jul 24 2010 - 18:06:52 PDT)
Re: [AMBER] clustering analysis changes my coordinates
(Fri Jul 23 2010 - 08:14:28 PDT)
[AMBER] clustering analysis changes my coordinates
(Thu Jul 22 2010 - 18:55:46 PDT)
Re: [AMBER] Davies Bouldin Index with DME in ptraj
(Mon Jul 05 2010 - 10:15:26 PDT)
Giorgos Lamprinidis
Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2
(Thu Jul 15 2010 - 07:34:59 PDT)
Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2
(Wed Jul 14 2010 - 08:44:59 PDT)
Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2
(Wed Jul 14 2010 - 07:30:25 PDT)
[AMBER] Error Compiling NAB o AMBER Tools 1.2
(Wed Jul 14 2010 - 03:02:16 PDT)
[AMBER] MMPBSA using counterions
(Fri Jul 09 2010 - 00:08:33 PDT)
Giovanni Doni
[AMBER] Restrain with PMEMD
(Tue Jul 06 2010 - 09:08:18 PDT)
gokul algates
[AMBER] About RAMD
(Thu Jul 15 2010 - 07:46:06 PDT)
Re: [AMBER] About RAMD
(Thu Jul 15 2010 - 07:34:44 PDT)
[AMBER] About RAMD
(Wed Jul 14 2010 - 23:03:15 PDT)
Gould, Ian R
[AMBER] Performance from pmemd.cuda
(Tue Jul 20 2010 - 02:36:46 PDT)
Guoxiong Su
Re: [AMBER] Question about sqm in antechamber
(Mon Jul 26 2010 - 11:25:49 PDT)
[AMBER] Question about sqm in antechamber
(Mon Jul 26 2010 - 09:45:20 PDT)
[AMBER] Question about increasing the max number of atoms in mopac in antechamber
(Fri Jul 09 2010 - 12:47:16 PDT)
Gustavo Seabra
Re: [AMBER] How to make oligo-peptides using AMBER ?
(Wed Jul 21 2010 - 16:07:09 PDT)
Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions
(Fri Jul 09 2010 - 03:50:06 PDT)
Re: [AMBER] Is It Possible to Prevent Center-of-Mass Rotation During MD?
(Thu Jul 08 2010 - 05:30:31 PDT)
Re: [AMBER] Checking multiple production run
(Sat Jul 03 2010 - 06:18:11 PDT)
Re: [AMBER] What ab initio methods can be choose for QM/MM package in AMBER10?
(Fri Jul 02 2010 - 03:40:03 PDT)
Hannes Loeffler
Re: [AMBER] POPC parameters
(Thu Jul 22 2010 - 05:33:40 PDT)
hannes.loeffler.stfc.ac.uk
Re: [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER?
(Sun Jul 25 2010 - 03:10:18 PDT)
Re: [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER?
(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?
(Fri Jul 23 2010 - 10:43:57 PDT)
Hector A. Baldoni
Re: [AMBER] how to generate porcupine plot
(Thu Jul 29 2010 - 15:43:24 PDT)
Hegazy,Lamees
[AMBER] addles
(Fri Jul 30 2010 - 10:23:42 PDT)
Re: [AMBER] tleap and sander minimization
(Thu Jul 29 2010 - 12:02:06 PDT)
[AMBER] tleap and sander minimization
(Thu Jul 29 2010 - 11:35:45 PDT)
Homa Azizian
[AMBER] amber tool installing problem
(Wed Jul 14 2010 - 22:11:39 PDT)
Re: [AMBER] reference structure
(Tue Jul 13 2010 - 00:09:47 PDT)
[AMBER] reference structure
(Mon Jul 12 2010 - 23:42:15 PDT)
[AMBER] rms command
(Wed Jul 07 2010 - 21:57:40 PDT)
[AMBER] analysising trajectory
(Wed Jul 07 2010 - 19:05:30 PDT)
[AMBER] create a prmtop file without water & ions,
(Thu Jul 01 2010 - 20:13:52 PDT)
Re: [AMBER] vlimit exceeded for step
(Wed Jun 30 2010 - 22:22:04 PDT)
hong-bin Xie
Re: [AMBER] TIP4P question
(Wed Jul 14 2010 - 10:53:17 PDT)
[AMBER] TIP4P question
(Wed Jul 14 2010 - 10:16:33 PDT)
Hoshin Kim
[AMBER] RDF analysis of glucose made by GLYCAM problem
(Tue Jul 13 2010 - 18:10:30 PDT)
[AMBER] Solvation in water
(Thu Jul 01 2010 - 19:39:42 PDT)
InSuk Joung
Re: [AMBER] NAB problem with a metallic atom
(Wed Jul 28 2010 - 16:16:46 PDT)
Re: [AMBER] NAB problem with a metallic atom
(Wed Jul 28 2010 - 14:59:15 PDT)
[AMBER] NAB problem with a metallic atom
(Wed Jul 28 2010 - 14:34:19 PDT)
Jagdeesh C
Re: [AMBER] segmentation fault
(Thu Jul 22 2010 - 02:51:15 PDT)
Re: [AMBER] Segmentation fault
(Mon Jul 05 2010 - 20:10:11 PDT)
James Maier
Re: [AMBER] file format
(Thu Jul 22 2010 - 12:31:06 PDT)
Re: [AMBER] simulation runs very slow..
(Mon Jul 12 2010 - 08:11:47 PDT)
Re: [AMBER] How to find the angle bond etc parameters used for practicular atom type used in AMBER?
(Fri Jul 09 2010 - 07:21:55 PDT)
Re: [AMBER] step 0 of minimization ?
(Mon Jul 05 2010 - 17:55:37 PDT)
Jason Swails
Re: [AMBER] obtain a .pdb file from a .prepin/.frcmod file
(Sat Jul 31 2010 - 13:45:57 PDT)
Re: [AMBER] Constant pH simulation at pH 7
(Sat Jul 31 2010 - 07:39:55 PDT)
Re: [AMBER] fix CM
(Fri Jul 30 2010 - 13:14:28 PDT)
Re: [AMBER] very high and unstable RMSD
(Wed Jul 28 2010 - 13:56:51 PDT)
Re: [AMBER] about dielectric constant..
(Wed Jul 28 2010 - 04:59:16 PDT)
Re: [AMBER] mpi with openmpi - with input files
(Tue Jul 27 2010 - 10:57:32 PDT)
Re: [AMBER] very high and unstable RMSD
(Tue Jul 27 2010 - 09:07:41 PDT)
Re: [AMBER] question about bond command
(Sat Jul 24 2010 - 22:13:51 PDT)
Re: [AMBER] question about bond command
(Sat Jul 24 2010 - 22:04:18 PDT)
Re: [AMBER] PM6 in Amber 11
(Fri Jul 23 2010 - 07:05:54 PDT)
Re: [AMBER] PM6 in Amber 11
(Fri Jul 23 2010 - 06:39:45 PDT)
Re: [AMBER] mandatory command lines in MMPBSA.PY
(Fri Jul 23 2010 - 05:06:24 PDT)
Re: [AMBER] file format
(Thu Jul 22 2010 - 16:00:46 PDT)
Re: [AMBER] pmemd amber10 compilation error
(Thu Jul 22 2010 - 07:55:40 PDT)
Re: [AMBER] pmemd amber10 compilation error
(Thu Jul 22 2010 - 07:54:21 PDT)
Re: [AMBER] minimization segmentation fault
(Thu Jul 22 2010 - 07:42:00 PDT)
Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md
(Thu Jul 22 2010 - 07:26:56 PDT)
Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md
(Thu Jul 22 2010 - 05:06:00 PDT)
Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md
(Wed Jul 21 2010 - 09:33:03 PDT)
Re: [AMBER] FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type.
(Wed Jul 21 2010 - 08:10:56 PDT)
Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3
(Wed Jul 21 2010 - 07:59:52 PDT)
Re: [AMBER] L and D peptides
(Wed Jul 21 2010 - 07:51:15 PDT)
Re: [AMBER] L and D peptides
(Tue Jul 20 2010 - 12:51:41 PDT)
Re: [AMBER] adding ion concentration
(Tue Jul 20 2010 - 05:36:04 PDT)
Re: [AMBER] problem with the total charge
(Mon Jul 19 2010 - 21:27:08 PDT)
Re: [AMBER] Parameters missing after changing topology
(Mon Jul 19 2010 - 18:36:05 PDT)
Re: [AMBER] Head-Tail covalently bound substrate and
(Mon Jul 19 2010 - 11:20:34 PDT)
Re: [AMBER] Can I calculate the interaction energy between two connected domains of a protein using mmpbsa.py?
(Mon Jul 19 2010 - 10:54:32 PDT)
Re: [AMBER] Can I calculate the interaction energy between two connected domains of a protein?
(Mon Jul 19 2010 - 08:12:43 PDT)
Re: [AMBER] How to remove PBC effects?
(Mon Jul 19 2010 - 08:08:07 PDT)
Re: [AMBER] MMPBSA.PY with two parts receptor
(Mon Jul 19 2010 - 07:57:29 PDT)
Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2
(Thu Jul 15 2010 - 08:56:31 PDT)
Re: [AMBER] problems with NAB and SHIFTS
(Thu Jul 15 2010 - 08:54:49 PDT)
Re: [AMBER] About RAMD
(Thu Jul 15 2010 - 04:41:12 PDT)
Re: [AMBER] amber tool installing problem
(Thu Jul 15 2010 - 04:37:35 PDT)
Re: [AMBER] entropy from mass weighted covariance matrix
(Wed Jul 14 2010 - 12:30:32 PDT)
Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2
(Wed Jul 14 2010 - 12:18:53 PDT)
Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2
(Wed Jul 14 2010 - 08:24:27 PDT)
Re: [AMBER] problem with tleap and xleap
(Wed Jul 14 2010 - 08:22:32 PDT)
Re: [AMBER] Query regarding Abscissa and their corresponding weights in Thermodynamic Integration
(Wed Jul 14 2010 - 08:18:23 PDT)
Re: [AMBER] general enquiry
(Wed Jul 14 2010 - 03:56:34 PDT)
Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2
(Wed Jul 14 2010 - 03:47:36 PDT)
Re: [AMBER] Units for mass weighted covariance matrix in ptraj
(Mon Jul 12 2010 - 19:56:23 PDT)
Re: [AMBER] compile ambertools on mac
(Mon Jul 12 2010 - 14:03:17 PDT)
[AMBER] AmberTools citation
(Mon Jul 12 2010 - 13:00:05 PDT)
Re: [AMBER] mm_pbsa.pl in PARALLEL does not finish
(Mon Jul 12 2010 - 10:32:57 PDT)
Re: [AMBER] simulation runs very slow..
(Mon Jul 12 2010 - 08:22:09 PDT)
Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md
(Mon Jul 12 2010 - 07:04:30 PDT)
Re: [AMBER] residue wise rmsd, not getting expected results
(Mon Jul 12 2010 - 06:59:39 PDT)
Re: [AMBER] compiling amber 10 with mpi
(Fri Jul 09 2010 - 13:13:12 PDT)
Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions
(Fri Jul 09 2010 - 08:09:00 PDT)
Re: [AMBER] No solvent overlap
(Fri Jul 09 2010 - 07:58:36 PDT)
Re: [AMBER] counterions placings
(Fri Jul 09 2010 - 07:48:22 PDT)
Re: [AMBER] MMPBSA using counterions
(Fri Jul 09 2010 - 07:44:04 PDT)
Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions
(Thu Jul 08 2010 - 20:26:08 PDT)
Re: [AMBER] atom-type cz ???
(Thu Jul 08 2010 - 15:25:56 PDT)
Re: [AMBER] atom-type cz ???
(Thu Jul 08 2010 - 13:13:32 PDT)
Re: [AMBER] compile ambertools on mac
(Thu Jul 08 2010 - 05:52:07 PDT)
Re: [AMBER] rms command
(Thu Jul 08 2010 - 04:18:46 PDT)
Re: [AMBER] compile ambertools on mac
(Thu Jul 08 2010 - 04:14:26 PDT)
Re: [AMBER] Is It Possible to Prevent Center-of-Mass Rotation During MD?
(Wed Jul 07 2010 - 21:15:03 PDT)
Re: [AMBER] compile ambertools on mac
(Wed Jul 07 2010 - 17:58:22 PDT)
Re: [AMBER] mmgbsa for ternary system
(Wed Jul 07 2010 - 07:15:08 PDT)
Re: [AMBER] mmgbsa tricky output: PART 2
(Wed Jul 07 2010 - 07:04:56 PDT)
Re: [AMBER] mmgbsa tricky output: PART 2
(Tue Jul 06 2010 - 06:00:59 PDT)
Re: [AMBER] error massage in constant pH simulation
(Tue Jul 06 2010 - 05:53:07 PDT)
Re: [AMBER] Should I define drug intercalation site of a DNA as internal (DT/DA) or terminal (DT3/DA5) unit ?
(Mon Jul 05 2010 - 07:15:51 PDT)
Re: [AMBER] No potential terms in sander output! Check out put files - MMPBSA.py.MPI
(Sun Jul 04 2010 - 20:04:45 PDT)
Re: [AMBER] Steered MD calc
(Sun Jul 04 2010 - 16:16:27 PDT)
Re: [AMBER] RESP charges outside Gaussian
(Sun Jul 04 2010 - 09:01:22 PDT)
Re: [AMBER] MMPBSA.py install error
(Sat Jul 03 2010 - 07:44:41 PDT)
Re: [AMBER] Checking multiple production run
(Sat Jul 03 2010 - 04:22:04 PDT)
Re: [AMBER] Adding Ions.
(Fri Jul 02 2010 - 09:00:47 PDT)
Re: [AMBER] Solvation in water
(Fri Jul 02 2010 - 08:57:37 PDT)
Re: [AMBER] Any parameters for Mg2+?
(Fri Jul 02 2010 - 07:28:41 PDT)
Re: [AMBER] About the ptraj problem
(Fri Jul 02 2010 - 07:24:59 PDT)
Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o
(Fri Jul 02 2010 - 07:19:51 PDT)
Re: [AMBER] About the ptraj problem
(Thu Jul 01 2010 - 22:48:06 PDT)
Re: [AMBER] create a prmtop file without water & ions,
(Thu Jul 01 2010 - 22:46:17 PDT)
Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o
(Thu Jul 01 2010 - 20:55:20 PDT)
Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o
(Thu Jul 01 2010 - 08:00:16 PDT)
Re: [AMBER] results calculated by mmpbsa.pl and mmpbsa.py
(Thu Jul 01 2010 - 07:55:50 PDT)
Re: [AMBER] File MAKE_CRD is not found
(Thu Jul 01 2010 - 06:41:31 PDT)
Re: [AMBER] maintaining temperature scheme
(Wed Jun 30 2010 - 23:11:16 PDT)
Re: [AMBER] AmberTools installation in Cygwin
(Wed Jun 30 2010 - 22:59:45 PDT)
Re: [AMBER] adding counterions
(Wed Jun 30 2010 - 22:49:33 PDT)
Jia Xu
[AMBER] how to generate porcupine plot
(Thu Jul 29 2010 - 09:31:36 PDT)
Jianyin Shao
Re: [AMBER] ptraj-clustering
(Tue Jul 27 2010 - 12:37:22 PDT)
Jio M
Re: [AMBER] counterions placings
(Sat Jul 10 2010 - 03:23:00 PDT)
Re: [AMBER] counterions placings
(Fri Jul 09 2010 - 21:45:52 PDT)
[AMBER] counterions placings
(Thu Jul 08 2010 - 23:46:48 PDT)
Jorgen Simonsen
Re: [AMBER] minimization segmentation fault
(Fri Jul 30 2010 - 04:11:31 PDT)
Re: [AMBER] minimization segmentation fault
(Tue Jul 27 2010 - 11:37:24 PDT)
Re: [AMBER] regarding remd
(Mon Jul 26 2010 - 12:44:46 PDT)
[AMBER] regarding remd
(Mon Jul 26 2010 - 06:29:31 PDT)
Re: [AMBER] radius of K+ ions
(Mon Jul 26 2010 - 03:19:36 PDT)
Re: [AMBER] For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+
(Sun Jul 25 2010 - 11:27:38 PDT)
[AMBER] For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+
(Sun Jul 25 2010 - 10:45:27 PDT)
[AMBER] minimization segmentation fault
(Thu Jul 22 2010 - 06:16:02 PDT)
Re: [AMBER] L and D peptides
(Tue Jul 20 2010 - 14:20:05 PDT)
[AMBER] L and D peptides
(Tue Jul 20 2010 - 09:52:30 PDT)
[AMBER] residues lacking connect
(Sat Jul 17 2010 - 11:54:06 PDT)
Re: [AMBER] compile ambertools on mac
(Tue Jul 13 2010 - 05:22:49 PDT)
Re: [AMBER] compile ambertools on mac
(Mon Jul 12 2010 - 14:34:39 PDT)
Re: [AMBER] compile ambertools on mac
(Mon Jul 12 2010 - 13:50:13 PDT)
Re: [AMBER] compile ambertools on mac
(Mon Jul 12 2010 - 05:57:58 PDT)
Re: [AMBER] compile ambertools on mac
(Sun Jul 11 2010 - 13:56:46 PDT)
Re: [AMBER] compiling amber 10 with mpi
(Fri Jul 09 2010 - 12:53:57 PDT)
[AMBER] compiling amber 10 with mpi
(Fri Jul 09 2010 - 10:13:37 PDT)
Re: [AMBER] compile ambertools on mac
(Thu Jul 08 2010 - 05:41:04 PDT)
Re: [AMBER] compile ambertools on mac
(Thu Jul 08 2010 - 03:42:16 PDT)
[AMBER] compile ambertools on mac
(Wed Jul 07 2010 - 16:21:28 PDT)
Jose Borreguero
Re: [AMBER] please, units of LENNARD_JONES_ACOEF in prmptop?
(Wed Jul 14 2010 - 07:56:08 PDT)
[AMBER] please, units of LENNARD_JONES_ACOEF in prmptop?
(Tue Jul 13 2010 - 16:45:07 PDT)
Josh Berryman
Re: [AMBER] NAB: pbc calculations available after all?
(Mon Jul 26 2010 - 07:24:57 PDT)
[AMBER] NAB: pbc calculations available after all?
(Mon Jul 26 2010 - 05:06:20 PDT)
Re: [AMBER] NAB rdparm seg fault
(Mon Jul 26 2010 - 04:54:47 PDT)
Re: [AMBER] NAB rdparm seg fault
(Thu Jul 15 2010 - 04:49:13 PDT)
[AMBER] NAB rdparm seg fault
(Wed Jul 14 2010 - 05:03:41 PDT)
Justine Shaw
Re: [AMBER] RESP "too many charge-group constraints" error
(Thu Jul 29 2010 - 09:37:38 PDT)
Re: [AMBER] RESP "too many charge-group constraints" error
(Wed Jul 28 2010 - 14:18:19 PDT)
Re: [AMBER] RESP "too many charge-group constraints" error
(Wed Jul 28 2010 - 13:51:57 PDT)
[AMBER] RESP "too many charge-group constraints" error
(Wed Jul 28 2010 - 13:24:05 PDT)
kamlesh sahu
Re: [AMBER] FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type.
(Wed Jul 21 2010 - 20:06:36 PDT)
[AMBER] FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type.
(Wed Jul 21 2010 - 05:11:34 PDT)
Re: [AMBER] No potential terms in sander output! Check out put files - MMPBSA.py.MPI
(Sun Jul 04 2010 - 23:08:08 PDT)
[AMBER] No potential terms in sander output! Check out put files - MMPBSA.py.MPI
(Sun Jul 04 2010 - 18:56:21 PDT)
Karl N. Kirschner
Re: [AMBER] L and D peptides
(Wed Jul 21 2010 - 03:26:21 PDT)
Keith Van Nostrand
Re: [AMBER] random number seed - range
(Tue Jul 27 2010 - 07:25:19 PDT)
Kevin Hauser
Re: [AMBER] very high and unstable RMSD
(Wed Jul 28 2010 - 21:34:36 PDT)
Re: [AMBER] very high and unstable RMSD
(Wed Jul 28 2010 - 21:32:21 PDT)
kirsten
[AMBER] WARNING: Local coordinate 382 differs from partner coordinate 382 !
(Sun Jul 04 2010 - 05:07:08 PDT)
kurisaki ikuo
Re: [AMBER] Reference of ion parameters employed in parm99
(Tue Jul 27 2010 - 22:22:00 PDT)
Re: [AMBER] Reference of ion parameters employed in parm99
(Tue Jul 27 2010 - 22:13:44 PDT)
Re: [AMBER] Reference of ion parameters employed in parm99
(Tue Jul 27 2010 - 21:33:54 PDT)
[AMBER] Reference of ion parameters employed in parm99
(Tue Jul 27 2010 - 20:21:09 PDT)
Re: [AMBER] Mutation of DNA
(Sun Jul 25 2010 - 17:57:42 PDT)
Lachele Foley (Lists)
Re: [AMBER] RDF analysis of glucose made by GLYCAM problem
(Wed Jul 14 2010 - 07:53:54 PDT)
Lekpa Duukori
Re: [AMBER] entropy from mass weighted covariance matrix
(Wed Jul 14 2010 - 14:29:18 PDT)
[AMBER] entropy from mass weighted covariance matrix
(Wed Jul 14 2010 - 09:50:41 PDT)
Re: [AMBER] Units for mass weighted covariance matrix in ptraj
(Tue Jul 13 2010 - 11:16:54 PDT)
Re: [AMBER] Units for mass weighted covariance matrix in ptraj
(Tue Jul 13 2010 - 08:27:36 PDT)
[AMBER] Units for mass weighted covariance matrix in ptraj
(Mon Jul 12 2010 - 18:34:38 PDT)
Levi Pierce
Re: [AMBER] Issue with preparing pdb, top and crd files via leap for a non-standard residue
(Wed Jul 21 2010 - 14:40:11 PDT)
Re: [AMBER] problem about cyclic peptide
(Tue Jul 20 2010 - 09:37:32 PDT)
Re: [AMBER] Problem with pmemd.cuda
(Mon Jul 19 2010 - 12:49:19 PDT)
lidansa.mail.ustc.edu.cn
[AMBER] results calculated by mmpbsa.pl and mmpbsa.py
(Thu Jul 01 2010 - 07:18:09 PDT)
llduan.itcs.ecnu.edu.cn
Re: [AMBER] amber02pol: sequence: Illegal UNIT named: NHE
(Wed Jul 14 2010 - 00:19:09 PDT)
[AMBER] amber02pol: sequence: Illegal UNIT named: NHE
(Tue Jul 13 2010 - 07:49:05 PDT)
[AMBER] (no subject)
(Sat Jul 10 2010 - 00:04:33 PDT)
Logan Ahlstrom
[AMBER] Periodic Neighbor Distance
(Tue Jul 13 2010 - 16:23:58 PDT)
[AMBER] Is It Possible to Prevent Center-of-Mass Rotation During MD?
(Wed Jul 07 2010 - 19:41:47 PDT)
Lorenzo Gontrani
[AMBER] Simulation cell reduction
(Thu Jul 15 2010 - 03:15:47 PDT)
M. Reza Ganjalikhany
[AMBER] about grid & radial distribution function
(Sun Jul 25 2010 - 03:59:36 PDT)
Re: [AMBER] PMEMD installation error
(Sun Jul 04 2010 - 01:26:14 PDT)
[AMBER] PMEMD installation error
(Sat Jul 03 2010 - 01:51:14 PDT)
M. Shahid
Re: [AMBER] atom-type cz ???
(Thu Jul 08 2010 - 15:02:31 PDT)
Re: [AMBER] atom-type cz ???
(Thu Jul 08 2010 - 06:43:39 PDT)
Mahmoud A. A. Ibrahim
Re: [AMBER] Do I have to keep the Na+ counterions in prmtop and snapshot generation when I do mmGBSA/PBSA calculation?
(Fri Jul 09 2010 - 04:29:37 PDT)
Mannan
Re: [AMBER] mmgbsa tricky output
(Wed Jul 07 2010 - 20:08:01 PDT)
manoj singh
[AMBER] MM-PBSA per residue decompostion
(Tue Jul 27 2010 - 08:39:08 PDT)
Marc Moreau
[AMBER] Minor Typo bug.
(Thu Jul 29 2010 - 10:20:22 PDT)
Re: [AMBER] Parallel test times
(Wed Jul 28 2010 - 10:08:17 PDT)
[AMBER] Parallel test times
(Wed Jul 28 2010 - 10:03:42 PDT)
Re: [AMBER] Permission to post Admin processes?
(Mon Jul 26 2010 - 13:33:32 PDT)
[AMBER] Permission to post Admin processes?
(Mon Jul 26 2010 - 12:31:05 PDT)
Re: [AMBER] Workaround for gfortran-4.1.2?
(Wed Jul 21 2010 - 18:38:38 PDT)
Re: [AMBER] Workaround for gfortran-4.1.2?
(Tue Jul 20 2010 - 18:39:11 PDT)
[AMBER] Workaround for gfortran-4.1.2?
(Tue Jul 20 2010 - 16:19:53 PDT)
Re: [AMBER] OpenMP programs
(Thu Jul 08 2010 - 14:10:49 PDT)
[AMBER] OpenMP programs
(Thu Jul 08 2010 - 10:46:21 PDT)
Marcela Madrid
[AMBER] pmemd amber10 compilation error
(Thu Jul 22 2010 - 07:49:00 PDT)
Marek Maly
Re: [AMBER] The system size limitations for Tesla C2050 ?
(Tue Jul 13 2010 - 16:04:01 PDT)
Re: [AMBER] The system size limitations for Tesla C2050 ?
(Tue Jul 13 2010 - 14:47:17 PDT)
Re: [AMBER] The system size limitations for Tesla C2050 ?
(Tue Jul 13 2010 - 09:45:37 PDT)
Re: [AMBER] The system size limitations for Tesla C2050 ?
(Mon Jul 12 2010 - 09:49:55 PDT)
Re: [AMBER] The system size limitations for Tesla C2050 ?
(Mon Jul 12 2010 - 06:59:10 PDT)
[AMBER] The system size limitations for Tesla C2050 ?
(Mon Jul 12 2010 - 01:37:43 PDT)
Mark Williamson
Re: [AMBER] Workaround for gfortran-4.1.2?
(Tue Jul 20 2010 - 16:51:43 PDT)
Markus Knauth
[AMBER] Getting missing force constants for Amber from Gaussian?
(Wed Jul 21 2010 - 01:00:02 PDT)
Mengjuei Hsieh
Re: [AMBER] Minor Typo bug.
(Thu Jul 29 2010 - 11:59:04 PDT)
Re: [AMBER] compile ambertools on mac
(Mon Jul 26 2010 - 14:32:53 PDT)
Re: [AMBER] compile ambertools on mac
(Mon Jul 26 2010 - 14:17:09 PDT)
Re: [AMBER] compile ambertools on mac
(Sun Jul 25 2010 - 04:54:38 PDT)
Re: [AMBER] compile ambertools on mac
(Thu Jul 15 2010 - 16:11:19 PDT)
Re: [AMBER] compile ambertools on mac
(Thu Jul 15 2010 - 11:22:33 PDT)
Re: [AMBER] compile ambertools on mac
(Tue Jul 13 2010 - 11:55:05 PDT)
Mirko Cestari
Re: [AMBER] installing AmberTools 1.4 on AIX
(Wed Jul 07 2010 - 05:52:27 PDT)
Re: [AMBER] installing AmberTools 1.4 on AIX
(Thu Jul 01 2010 - 00:44:23 PDT)
missing_grace.sina.com
[AMBER] maintaining temperature scheme
(Wed Jun 30 2010 - 21:05:21 PDT)
moacyr comar
[AMBER] Problem with sander.MPI
(Sat Jul 17 2010 - 12:15:42 PDT)
[AMBER] problem with tleap and xleap
(Wed Jul 14 2010 - 07:05:38 PDT)
moitrayee.mbu.iisc.ernet.in
[AMBER] [Fwd: Re: ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption]
(Sat Jul 10 2010 - 05:45:54 PDT)
Re: [AMBER] ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption
(Fri Jul 09 2010 - 11:14:31 PDT)
[AMBER] ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption
(Fri Jul 09 2010 - 05:12:18 PDT)
[AMBER] problem with 2d-rmsd based clustering
(Wed Jul 07 2010 - 12:37:06 PDT)
monica.imtech.res.in
[AMBER] file format
(Thu Jul 22 2010 - 08:12:37 PDT)
[AMBER] general enquiry
(Wed Jul 14 2010 - 00:40:40 PDT)
[AMBER] simulations in urea
(Sat Jul 03 2010 - 05:14:38 PDT)
Necmettin Pirinccioglu
Re: [AMBER] ptraj-clustering
(Sun Jul 25 2010 - 23:46:12 PDT)
[AMBER] ptraj-clustering
(Fri Jul 23 2010 - 00:28:30 PDT)
Neha Gandhi
[AMBER] adding ion concentration
(Tue Jul 20 2010 - 02:08:05 PDT)
nicholus bhattacharjee
[AMBER] Constant pH simulation at pH 7
(Sat Jul 31 2010 - 07:19:00 PDT)
Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md
(Thu Jul 22 2010 - 06:42:39 PDT)
Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md
(Thu Jul 22 2010 - 04:41:31 PDT)
Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md
(Thu Jul 22 2010 - 02:37:35 PDT)
Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md
(Wed Jul 21 2010 - 06:37:26 PDT)
[AMBER] problem in converting cprestrt to cpin2 file in constant pH md
(Sun Jul 11 2010 - 21:23:25 PDT)
[AMBER] error massage in constant pH simulation
(Tue Jul 06 2010 - 02:16:35 PDT)
[AMBER] Checking multiple production run
(Sat Jul 03 2010 - 01:41:11 PDT)
Re: [AMBER] Questions with input file in constant pH MD
(Wed Jun 30 2010 - 23:53:26 PDT)
Oliver Grant
Re: [AMBER] mandatory command lines in MMPBSA.PY
(Fri Jul 23 2010 - 03:55:56 PDT)
Re: [AMBER] Segmentation fault in MMPBSA.PY with two parts receptor
(Tue Jul 20 2010 - 03:30:45 PDT)
Re: [AMBER] Do I have to keep the Na+ counterions in prmtop and snapshot generation when I do mmGBSA/PBSA calculation?
(Fri Jul 09 2010 - 04:42:32 PDT)
Re: [AMBER] Do I have to keep the Na+ counterions in prmtop and snapshot generation when I do mmGBSA/PBSA calculation?
(Fri Jul 09 2010 - 04:24:38 PDT)
Re: [AMBER] What is the way to change from MMPBSA+GBSA to MMGBSA only input file.
(Fri Jul 09 2010 - 03:57:02 PDT)
Oliver Kuhn
Re: [AMBER] How to remove PBC effects?
(Tue Jul 20 2010 - 01:36:10 PDT)
Re: [AMBER] How to remove PBC effects?
(Mon Jul 19 2010 - 06:55:31 PDT)
[AMBER] How to remove PBC effects?
(Mon Jul 19 2010 - 05:04:23 PDT)
Paul S. Nerenberg
Re: [AMBER] Reference of ion parameters employed in parm99
(Tue Jul 27 2010 - 21:45:38 PDT)
Re: [AMBER] Reference of ion parameters employed in parm99
(Tue Jul 27 2010 - 21:04:12 PDT)
Re: [AMBER] random number seed - range
(Tue Jul 27 2010 - 07:44:38 PDT)
Re: [AMBER] compile ambertools on mac
(Mon Jul 26 2010 - 09:57:57 PDT)
Re: [AMBER] atomic radii of ions
(Sun Jul 25 2010 - 08:46:30 PDT)
Re: [AMBER] random number seed - range
(Sat Jul 24 2010 - 18:11:00 PDT)
Re: [AMBER] Relax command for tleap
(Fri Jul 23 2010 - 10:32:42 PDT)
Re: [AMBER] Relax command for tleap
(Fri Jul 23 2010 - 09:33:04 PDT)
Re: [AMBER] sign me off please~
(Wed Jul 14 2010 - 09:47:48 PDT)
Re: [AMBER] amber02pol: sequence: Illegal UNIT named: NHE
(Wed Jul 14 2010 - 07:53:54 PDT)
Re: [AMBER] please, units of LENNARD_JONES_ACOEF in prmptop?
(Tue Jul 13 2010 - 17:31:13 PDT)
Re: [AMBER] Periodic Neighbor Distance
(Tue Jul 13 2010 - 16:49:00 PDT)
Re: [AMBER] amber02pol: sequence: Illegal UNIT named: NHE
(Tue Jul 13 2010 - 07:52:40 PDT)
Re: [AMBER] adding counterions
(Thu Jul 01 2010 - 11:39:44 PDT)
Philippe Pinard
Re: [AMBER] RDF 3 files and 3 columns
(Sat Jul 31 2010 - 17:03:39 PDT)
Re: [AMBER] RDF 3 files and 3 columns
(Thu Jul 29 2010 - 12:50:55 PDT)
Re: [AMBER] RDF 3 files and 3 columns
(Tue Jul 27 2010 - 09:48:19 PDT)
Re: [AMBER] RDF 3 files and 3 columns
(Tue Jul 27 2010 - 06:37:37 PDT)
[AMBER] RDF 3 files and 3 columns
(Mon Jul 26 2010 - 15:19:33 PDT)
[AMBER] RDF 3 files and 3 columns
(Mon Jul 26 2010 - 14:43:12 PDT)
Re: [AMBER] question about bond command
(Sun Jul 25 2010 - 20:52:21 PDT)
Re: [AMBER] question about bond command
(Sat Jul 24 2010 - 19:38:39 PDT)
Re: [AMBER] question about bond command
(Sat Jul 24 2010 - 17:13:45 PDT)
Re: [AMBER] question about bond command
(Sat Jul 24 2010 - 09:34:19 PDT)
Re: [AMBER] question about bond command
(Thu Jul 22 2010 - 19:38:33 PDT)
Re: [AMBER] question about bond command
(Thu Jul 22 2010 - 14:41:26 PDT)
Re: [AMBER] question about bond command
(Thu Jul 22 2010 - 12:16:38 PDT)
Re: [AMBER] question about bond command
(Thu Jul 22 2010 - 11:34:11 PDT)
[AMBER] question about bond command
(Thu Jul 22 2010 - 10:36:38 PDT)
Ping
Re: [AMBER] adding counterions
(Thu Jul 01 2010 - 11:37:47 PDT)
Re: [AMBER] adding counterions
(Thu Jul 01 2010 - 11:12:24 PDT)
Purisima, Enrico
Re: [AMBER] Can I calculate the interaction energy between two connected domains of a protein?
(Mon Jul 19 2010 - 08:56:39 PDT)
Qian Wang
Re: [AMBER] source code to calculate electrostatic interaction in amber6
(Mon Jul 12 2010 - 13:48:32 PDT)
[AMBER] source code to calculate electrostatic interaction in amber6
(Mon Jul 12 2010 - 13:37:51 PDT)
Qiuting Hong
[AMBER] sign me off please~
(Wed Jul 14 2010 - 09:35:00 PDT)
rameshwar prajapati
[AMBER] Invitation to connect on LinkedIn
(Wed Jul 28 2010 - 09:39:52 PDT)
RANAJIT SHINDE
[AMBER] nmode problem with mm_pbsa.pl
(Fri Jul 02 2010 - 11:51:12 PDT)
Ray Luo
Re: [AMBER] mmgbsa tricky output
(Thu Jul 01 2010 - 15:46:37 PDT)
Rebeca García Fandiño
Re: [AMBER] problem about cyclic peptide
(Tue Jul 20 2010 - 09:43:59 PDT)
[AMBER] problem about cyclic peptide
(Tue Jul 20 2010 - 08:33:15 PDT)
REENU KHATTRI
[AMBER] h bond analysis
(Sat Jul 03 2010 - 20:45:25 PDT)
riya david
[AMBER] fix CM
(Fri Jul 30 2010 - 12:43:16 PDT)
Robert Duke
Re: [AMBER] about dielectric constant..
(Wed Jul 28 2010 - 06:09:59 PDT)
Re: [AMBER] random number seed - range
(Tue Jul 27 2010 - 12:13:00 PDT)
Roman Osman
Re: [AMBER] L and D peptides
(Wed Jul 21 2010 - 08:13:00 PDT)
ros
[AMBER] antechamber vs. REDDB
(Fri Jul 23 2010 - 11:19:16 PDT)
Re: [AMBER] question about bond command
(Thu Jul 22 2010 - 11:06:19 PDT)
Re: [AMBER] Problem with pmemd.cuda
(Mon Jul 19 2010 - 23:30:02 PDT)
Re: [AMBER] Problem with pmemd.cuda
(Mon Jul 19 2010 - 22:53:36 PDT)
Re: [AMBER] Problem with pmemd.cuda
(Mon Jul 19 2010 - 22:16:45 PDT)
Re: [AMBER] Problem with pmemd.cuda
(Mon Jul 19 2010 - 14:42:58 PDT)
Re: [AMBER] Problem with pmemd.cuda
(Mon Jul 19 2010 - 13:55:26 PDT)
Re: [AMBER] Problem with pmemd.cuda
(Mon Jul 19 2010 - 13:14:18 PDT)
Re: [AMBER] Problem with pmemd.cuda
(Mon Jul 19 2010 - 11:34:02 PDT)
[AMBER] Problem with pmemd.cuda
(Mon Jul 19 2010 - 09:11:12 PDT)
Re: [AMBER] compiling amber 10 with mpi
(Fri Jul 09 2010 - 11:54:33 PDT)
[AMBER] AMBER purchase
(Mon Jul 05 2010 - 10:40:07 PDT)
Re: [AMBER] Should I define drug intercalation site of a DNA as internal (DT/DA) or terminal (DT3/DA5) unit ?
(Mon Jul 05 2010 - 06:27:01 PDT)
Ross Walker
Re: [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests?
(Thu Jul 29 2010 - 19:09:20 PDT)
Re: [AMBER] random number seed - range
(Sat Jul 24 2010 - 16:12:15 PDT)
Re: [AMBER] pmemd amber10 compilation error
(Thu Jul 22 2010 - 07:57:51 PDT)
Re: [AMBER] Performance from pmemd.cuda
(Tue Jul 20 2010 - 11:01:33 PDT)
Re: [AMBER] Problem with sander.MPI
(Sun Jul 18 2010 - 02:21:16 PDT)
Re: [AMBER] reference structure
(Mon Jul 12 2010 - 23:54:39 PDT)
Re: [AMBER] The system size limitations for Tesla C2050 ?
(Mon Jul 12 2010 - 11:02:19 PDT)
Re: [AMBER] Are there any GPU clusters that offer compute time?
(Fri Jul 09 2010 - 19:08:40 PDT)
Re: [AMBER] OpenMP programs
(Thu Jul 08 2010 - 12:23:04 PDT)
Re: [AMBER] Restrain with PMEMD
(Tue Jul 06 2010 - 09:19:30 PDT)
Re: [AMBER] License
(Tue Jul 06 2010 - 08:06:26 PDT)
Rubben Torella
Re: [AMBER] Can I calculate the interaction energy between two connected domains of a protein?
(Mon Jul 19 2010 - 00:45:08 PDT)
Sangita Kachhap
Re: [AMBER] very high and unstable RMSD
(Wed Jul 28 2010 - 21:44:49 PDT)
Re: [AMBER] very high and unstable RMSD
(Wed Jul 28 2010 - 21:17:24 PDT)
Re: [AMBER] very high and unstable RMSD
(Wed Jul 28 2010 - 12:06:12 PDT)
[AMBER] very high and unstable RMSD
(Tue Jul 27 2010 - 03:15:20 PDT)
Sasha Buzko
[AMBER] Parallel pmemd.cuda: any preliminary cross-node tests?
(Thu Jul 29 2010 - 16:52:01 PDT)
Re: [AMBER] Are there any GPU clusters that offer compute time?
(Fri Jul 09 2010 - 17:33:49 PDT)
[AMBER] Are there any GPU clusters that offer compute time?
(Fri Jul 09 2010 - 17:09:52 PDT)
Scott Le Grand
Re: [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests?
(Sat Jul 31 2010 - 10:12:29 PDT)
Re: [AMBER] The system size limitations for Tesla C2050 ?
(Tue Jul 13 2010 - 15:13:14 PDT)
Re: [AMBER] The system size limitations for Tesla C2050 ?
(Tue Jul 13 2010 - 14:37:19 PDT)
Re: [AMBER] The system size limitations for Tesla C2050 ?
(Mon Jul 12 2010 - 11:27:35 PDT)
Re: [AMBER] The system size limitations for Tesla C2050 ?
(Mon Jul 12 2010 - 10:23:53 PDT)
Re: [AMBER] The system size limitations for Tesla C2050 ?
(Mon Jul 12 2010 - 09:13:05 PDT)
Re: [AMBER] The system size limitations for Tesla C2050 ?
(Mon Jul 12 2010 - 09:11:27 PDT)
setyanto tri wahyudi
Re: [AMBER] how to prepare a system with solvent of ethanol + water ?
(Fri Jul 30 2010 - 04:00:30 PDT)
Re: [AMBER] How to make hexane parameter using antechamber ?
(Sun Jul 25 2010 - 18:21:24 PDT)
[AMBER] How to make hexane parameter using antechamber ?
(Fri Jul 23 2010 - 03:42:05 PDT)
Re: [AMBER] how to create a mixture solvent of hexane and water
(Fri Jul 23 2010 - 03:21:41 PDT)
[AMBER] how to create a mixture solvent of hexane and water
(Wed Jul 14 2010 - 20:43:24 PDT)
Shubhra Gupta
Re: [AMBER] Fwd: Error report please fix it
(Wed Jul 28 2010 - 00:28:34 PDT)
[AMBER] Fwd: Error report please fix it
(Tue Jul 27 2010 - 21:25:24 PDT)
Re: [AMBER] Error report please fix it
(Mon Jul 26 2010 - 22:45:54 PDT)
Re: [AMBER] Error report please fix it
(Mon Jul 26 2010 - 22:42:13 PDT)
[AMBER] Error report please fix it
(Mon Jul 26 2010 - 00:25:42 PDT)
Shulin Zhuang
[AMBER] how to develop parameter for organotin
(Wed Jul 28 2010 - 00:04:31 PDT)
Siddharth Rastogi
[AMBER] vlimit exceeded after 10ns MD
(Mon Jul 26 2010 - 14:37:36 PDT)
[AMBER] How to make oligo-peptides using AMBER ?
(Wed Jul 21 2010 - 15:51:02 PDT)
[AMBER] radial distribution function
(Tue Jul 20 2010 - 06:06:20 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)
(Tue Jul 20 2010 - 04:48:14 PDT)
[AMBER] distance between two residues from their center of mass
(Fri Jul 09 2010 - 02:28:10 PDT)
Sidney Elmer
[AMBER] website down
(Thu Jul 15 2010 - 18:17:57 PDT)
sonali dhindwal
Re: [AMBER] License
(Tue Jul 06 2010 - 09:37:24 PDT)
[AMBER] License
(Tue Jul 06 2010 - 07:01:38 PDT)
Re: [AMBER] Regarding Antechamber Tutorial
(Thu Jul 01 2010 - 01:43:05 PDT)
[AMBER] Regarding Antechamber Tutorial
(Thu Jul 01 2010 - 00:23:09 PDT)
sophie fourtanier
[AMBER] ANALYSES LIGAND EXIT TRAJECTORIES
(Tue Jul 20 2010 - 05:49:16 PDT)
steinbrt.rci.rutgers.edu
Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 !
(Fri Jul 09 2010 - 05:43:47 PDT)
Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration
(Thu Jul 08 2010 - 01:53:53 PDT)
Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 !
(Thu Jul 08 2010 - 01:49:49 PDT)
Re: [AMBER] WARNING: Local coordinate 382 differs from partner coordinate 382 !
(Sun Jul 04 2010 - 07:53:00 PDT)
Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 !
(Fri Jul 02 2010 - 03:43:09 PDT)
Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 !
(Fri Jul 02 2010 - 01:33:19 PDT)
Steve Seibold
[AMBER] ptraj
(Mon Jul 12 2010 - 09:52:07 PDT)
Re: [AMBER] xleap error
(Fri Jul 09 2010 - 10:26:13 PDT)
Re: [AMBER] xleap error
(Fri Jul 09 2010 - 10:05:23 PDT)
Re: [AMBER] xleap error
(Fri Jul 09 2010 - 09:21:33 PDT)
[AMBER] xleap error
(Fri Jul 09 2010 - 08:38:31 PDT)
Re: [AMBER] Combine trajectory files error
(Fri Jul 09 2010 - 05:32:45 PDT)
Sudha Mani Karra
Re: [AMBER] Calculation of Intramolecular hydrogen bonding using ptraj
(Tue Jul 27 2010 - 09:51:55 PDT)
[AMBER] Calculation of Intramolecular hydrogen bonding using ptraj
(Tue Jul 27 2010 - 07:20:05 PDT)
sudipta
[AMBER] Mutation of DNA
(Sun Jul 25 2010 - 05:15:03 PDT)
sunita gupta
[AMBER] Query regarding Abscissa and their corresponding weights in Thermodynamic Integration
(Wed Jul 14 2010 - 05:16:05 PDT)
Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 !
(Fri Jul 09 2010 - 05:11:40 PDT)
Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 !
(Thu Jul 08 2010 - 01:10:27 PDT)
Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 !
(Fri Jul 02 2010 - 02:01:51 PDT)
[AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 !
(Fri Jul 02 2010 - 00:43:25 PDT)
Sushil Mishra
[AMBER] Warning: Input error! "nmode_igb=1" is an invalid option.
(Tue Jul 20 2010 - 08:24:08 PDT)
Syed Tarique Moin
[AMBER] b-factor
(Fri Jul 23 2010 - 06:42:41 PDT)
Thomas Cheatham
Re: [AMBER] about grid & radial distribution function
(Thu Jul 29 2010 - 19:03:07 PDT)
Re: [AMBER] RDF 3 files and 3 columns
(Thu Jul 29 2010 - 18:44:56 PDT)
Thomas Cheatham III
Re: [AMBER] Calculation of Intramolecular hydrogen bonding using ptraj
(Tue Jul 27 2010 - 10:15:43 PDT)
Re: [AMBER] RDF 3 files and 3 columns
(Tue Jul 27 2010 - 10:11:15 PDT)
Re: [AMBER] Calculation of Intramolecular hydrogen bonding using ptraj
(Tue Jul 27 2010 - 08:46:12 PDT)
Re: [AMBER] RDF 3 files and 3 columns
(Tue Jul 27 2010 - 08:41:30 PDT)
Re: [AMBER] RDF 3 files and 3 columns
(Tue Jul 27 2010 - 08:39:29 PDT)
Re: [AMBER] RDF 3 files and 3 columns
(Mon Jul 26 2010 - 15:49:24 PDT)
Re: [AMBER] clustering analysis changes my coordinates
(Fri Jul 23 2010 - 08:51:43 PDT)
Thomas Exner
Re: [AMBER] No solvent overlap
(Sat Jul 10 2010 - 00:23:01 PDT)
[AMBER] No solvent overlap
(Fri Jul 09 2010 - 07:13:31 PDT)
Thomas Zeiser
[AMBER] cumulative patch with two bugfixes for threaded mm_pbsa.pl
(Tue Jul 27 2010 - 09:13:57 PDT)
Re: [AMBER] mm_pbsa.pl in PARALLEL does not finish
(Thu Jul 22 2010 - 07:22:38 PDT)
Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3
(Thu Jul 22 2010 - 05:13:08 PDT)
Timothy J Giese
Re: [AMBER] Coulson vs. Mulliken, CM1, etc. in antechamber + mopac
(Mon Jul 26 2010 - 08:22:50 PDT)
Tom Joseph
Re: [AMBER] random number seed - range
(Sat Jul 24 2010 - 15:27:14 PDT)
Tyler Luchko
Re: [AMBER] 1D-RISM in AmberTools: the reference for ion parameters and LJ parameters
(Fri Jul 09 2010 - 08:21:27 PDT)
Re: [AMBER] 1D-RISM in AmberTools: atom order in output, a bug?
(Fri Jul 09 2010 - 08:06:30 PDT)
Re: [AMBER] 3D-RISM in NAB AmberTools: 2) what is tolerance
(Fri Jul 02 2010 - 07:08:41 PDT)
Re: [AMBER] 3D-RISM in NAB AmberTools: what is tolerance and initial guess
(Fri Jul 02 2010 - 06:39:18 PDT)
v.satish.iitg.ernet.in
Re: [AMBER] distance between two residues from their center of mass
(Fri Jul 09 2010 - 05:13:19 PDT)
vaibhav dixit
Re: [AMBER] residue wise rmsd, not getting expected results
(Mon Jul 12 2010 - 09:19:45 PDT)
Re: [AMBER] residue wise rmsd, not getting expected results
(Mon Jul 12 2010 - 06:57:16 PDT)
[AMBER] residue wise rmsd, not getting expected results
(Mon Jul 12 2010 - 01:30:55 PDT)
Re: [AMBER] Regarding Antechamber Tutorial
(Thu Jul 01 2010 - 00:49:30 PDT)
Vaibhav Jain
[AMBER] rfree: Error decoding variable 2 2
(Wed Jul 07 2010 - 11:43:28 PDT)
Valerie Fako
[AMBER] Relax command for tleap
(Fri Jul 23 2010 - 09:11:43 PDT)
[AMBER] Issue with preparing pdb, top and crd files via leap for a non-standard residue
(Wed Jul 21 2010 - 14:29:54 PDT)
Vasillis Myrianthopoulos
[AMBER] POPC parameters
(Thu Jul 22 2010 - 04:57:27 PDT)
vasu mathi
Re: [AMBER] how to prepare a system with solvent of ethanol + water ?
(Sat Jul 31 2010 - 09:57:31 PDT)
[AMBER] how to prepare a system with solvent of ethanol + water ?
(Fri Jul 30 2010 - 03:06:37 PDT)
Vijay Manickam Achari
[AMBER] vlimit exceeding situtaion with ntt option
(Thu Jul 15 2010 - 01:30:20 PDT)
[AMBER] simulation runs very slow..
(Mon Jul 12 2010 - 01:54:24 PDT)
Vlad Cojocaru
Re: [AMBER] test of parallel NAB and PTRAJ
(Fri Jul 23 2010 - 03:09:08 PDT)
[AMBER] test of parallel NAB and PTRAJ
(Fri Jul 23 2010 - 02:52:25 PDT)
William Flak
[AMBER] Which one, ESP calculation?
(Thu Jul 29 2010 - 20:41:50 PDT)
Wong, Sergio E.
[AMBER] external electric field?
(Wed Jul 21 2010 - 11:42:08 PDT)
Wookyung Yu
[AMBER] about dielectric constant..
(Tue Jul 27 2010 - 20:18:19 PDT)
Xinfu Xia
Re: [AMBER] problems with NAB and SHIFTS
(Thu Jul 15 2010 - 10:31:08 PDT)
Re: [AMBER] problems with NAB and SHIFTS
(Thu Jul 15 2010 - 08:30:41 PDT)
Xioling Chuang
[AMBER] AmberTools1.3 with amber9
(Sun Jul 25 2010 - 20:47:31 PDT)
[AMBER] MM-PBSA/MM-GBSA: mono valent salt
(Sun Jul 25 2010 - 08:45:38 PDT)
Re: [AMBER] atomic radii of ions
(Sun Jul 25 2010 - 08:27:52 PDT)
[AMBER] atomic radii of ions
(Fri Jul 23 2010 - 01:04:41 PDT)
Re: [AMBER] same dihedral with different parameter in FRCMOD file
(Sun Jul 11 2010 - 06:57:59 PDT)
[AMBER] same dihedral with different parameter in FRCMOD file
(Sat Jul 10 2010 - 05:39:14 PDT)
Yan Gao
Re: [AMBER] mpi with openmpi - SGE error
(Tue Jul 27 2010 - 19:47:05 PDT)
Re: [AMBER] mpi with openmpi - with input files
(Tue Jul 27 2010 - 12:15:00 PDT)
Re: [AMBER] Segmentation fault with translate command
(Tue Jul 27 2010 - 08:43:05 PDT)
Re: [AMBER] mpi with openmpi
(Mon Jul 26 2010 - 19:38:35 PDT)
Re: [AMBER] mpi with openmpi - with input files
(Mon Jul 26 2010 - 18:45:25 PDT)
[AMBER] mpi with openmpi
(Mon Jul 26 2010 - 18:26:55 PDT)
Re: [AMBER] simulate large molecules with implicit water model (GB)
(Mon Jul 26 2010 - 11:28:23 PDT)
[AMBER] Segmentation fault with translate command
(Mon Jul 26 2010 - 11:28:30 PDT)
[AMBER] simulate large molecules with implicit water model (GB)
(Mon Jul 26 2010 - 10:42:59 PDT)
Re: [AMBER] problem with the total charge
(Tue Jul 20 2010 - 09:48:44 PDT)
[AMBER] problem with the total charge
(Mon Jul 19 2010 - 20:25:37 PDT)
Re: [AMBER] website down
(Thu Jul 15 2010 - 19:17:11 PDT)
Re: [AMBER] The atom number exceeds the MAXATOM, reallocate memory Segmentation fault (core dumped) --- thank you and more questions!
(Wed Jul 14 2010 - 12:12:42 PDT)
[AMBER] The atom number exceeds the MAXATOM, reallocate memory Segmentation fault (core dumped)
(Wed Jul 14 2010 - 11:02:12 PDT)
Re: [AMBER] error 126 when install AmberTool1.4
(Tue Jul 13 2010 - 09:09:23 PDT)
Re: [AMBER] error 126 when install AmberTool1.4
(Tue Jul 13 2010 - 09:07:01 PDT)
[AMBER] error 126 when install AmberTool1.4
(Mon Jul 12 2010 - 22:42:31 PDT)
Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions
(Fri Jul 09 2010 - 08:57:00 PDT)
Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions
(Fri Jul 09 2010 - 06:45:41 PDT)
Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions
(Thu Jul 08 2010 - 21:51:24 PDT)
Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions
(Thu Jul 08 2010 - 21:41:23 PDT)
Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions
(Thu Jul 08 2010 - 16:26:55 PDT)
[AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes
(Thu Jul 08 2010 - 13:57:34 PDT)
[AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes
(Thu Jul 08 2010 - 10:21:21 PDT)
[AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes
(Thu Jul 08 2010 - 10:20:35 PDT)
Re: [AMBER] AmberTools installation in Cygwin
(Thu Jul 01 2010 - 14:11:33 PDT)
Re: [AMBER] AmberTools installation in Cygwin --- thanks and new errors
(Thu Jul 01 2010 - 11:53:34 PDT)
Re: [AMBER] AmberTools installation in Cygwin
(Thu Jul 01 2010 - 11:52:51 PDT)
Re: [AMBER] AmberTools installation in Cygwin
(Thu Jul 01 2010 - 10:22:02 PDT)
Yu Chen
Re: [AMBER] dyld: lazy symbol binding failed: Symbol not found: _iconv_open
(Tue Jul 06 2010 - 13:26:42 PDT)
[AMBER] dyld: lazy symbol binding failed: Symbol not found: _iconv_open
(Tue Jul 06 2010 - 11:17:51 PDT)
Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o
(Fri Jul 02 2010 - 06:50:24 PDT)
Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o
(Fri Jul 02 2010 - 06:31:44 PDT)
Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o
(Thu Jul 01 2010 - 14:16:04 PDT)
Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o
(Thu Jul 01 2010 - 08:37:46 PDT)
Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o
(Thu Jul 01 2010 - 08:24:09 PDT)
Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o
(Thu Jul 01 2010 - 06:58:33 PDT)
Yubo Fan
Re: [AMBER] Compiling failure of Amber 9
(Fri Jul 23 2010 - 07:17:08 PDT)
Re: [AMBER] Compiling failure of Amber 9
(Thu Jul 22 2010 - 08:43:18 PDT)
[AMBER] Align two ligands
(Fri Jul 09 2010 - 10:43:10 PDT)
Yuqin Cai
[AMBER] Conformation capture in molecular dynamics
(Thu Jul 01 2010 - 18:46:01 PDT)
Zora Strelcova
Re: [AMBER] PM6 in Amber 11
(Mon Jul 26 2010 - 00:32:27 PDT)
Re: [AMBER] PM6 in Amber 11
(Fri Jul 23 2010 - 06:54:58 PDT)
[AMBER] PM6 in Amber 11
(Fri Jul 23 2010 - 06:13:34 PDT)
冉挺
Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration
(Fri Jul 09 2010 - 19:52:33 PDT)
池田輝彦
[AMBER] make test trouble with Amber11
(Tue Jul 27 2010 - 05:46:46 PDT)
강지영
[AMBER] H3O+ force field file
(Mon Jul 05 2010 - 17:52:17 PDT)
Last message date
:
Sat Jul 31 2010 - 17:30:03 PDT
Archived on
: Fri Dec 20 2024 - 05:54:08 PST
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