Amber Archive May 2015: by subject

[AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
- Vlad Cojocaru (Tue May 19 2015 - 06:04:03 PDT)
- James Starlight (Tue May 19 2015 - 05:32:42 PDT)
- James Starlight (Tue May 19 2015 - 05:23:11 PDT)
- Vlad Cojocaru (Mon May 18 2015 - 10:27:00 PDT)
- James Starlight (Mon May 18 2015 - 08:37:31 PDT)
- Vlad Cojocaru (Mon May 18 2015 - 07:57:12 PDT)
- Vlad Cojocaru (Mon May 18 2015 - 07:31:54 PDT)
- Vlad Cojocaru (Mon May 18 2015 - 07:25:55 PDT)
- James Starlight (Mon May 18 2015 - 07:23:53 PDT)
- James Starlight (Mon May 18 2015 - 07:16:21 PDT)
- Vlad Cojocaru (Mon May 18 2015 - 06:53:51 PDT)
- James Starlight (Mon May 18 2015 - 06:15:03 PDT)
- Vlad Cojocaru (Mon May 18 2015 - 05:37:58 PDT)
- James Starlight (Mon May 18 2015 - 04:38:00 PDT)
- James Starlight (Fri May 15 2015 - 04:30:32 PDT)
- Vlad Cojocaru (Wed May 13 2015 - 08:47:28 PDT)
- James Starlight (Wed May 13 2015 - 08:26:24 PDT)
- Vlad Cojocaru (Wed May 13 2015 - 07:04:36 PDT)
- James Starlight (Wed May 13 2015 - 06:55:04 PDT)
[AMBER] adp amber parameters
- Carlos Romero (Wed May 13 2015 - 10:14:39 PDT)
- David A Case (Wed May 13 2015 - 10:09:14 PDT)
- Carlos Romero (Wed May 13 2015 - 08:36:44 PDT)
[AMBER] Algorithms for integrating the equations of motion
- Hai Nguyen (Sun May 10 2015 - 16:37:10 PDT)
- gepaula.web.de (Sun May 10 2015 - 16:15:40 PDT)
[AMBER] Amber 12 + GTX 980
- Scott Le Grand (Thu May 21 2015 - 15:29:45 PDT)
- Robinson, Roger (Wed May 20 2015 - 23:31:44 PDT)
- Ross Walker (Wed May 20 2015 - 09:13:18 PDT)
- Robinson, Roger (Wed May 20 2015 - 06:14:03 PDT)
[AMBER] AMBER 15 ERROR
- Ye Mei (Wed May 27 2015 - 22:04:56 PDT)
- Hai Nguyen (Wed May 27 2015 - 21:24:29 PDT)
- 汪盛 (Wed May 27 2015 - 20:45:23 PDT)
[AMBER] amber tools 15 upgrade problem
- Michael Shokhen (Thu May 07 2015 - 03:57:24 PDT)
- David A Case (Mon May 04 2015 - 09:57:30 PDT)
- Kenneth Huang (Mon May 04 2015 - 09:09:44 PDT)
- David A Case (Mon May 04 2015 - 09:04:54 PDT)
- Jason Swails (Mon May 04 2015 - 08:59:16 PDT)
- Michael Shokhen (Mon May 04 2015 - 08:53:48 PDT)
- Kenneth Huang (Mon May 04 2015 - 08:12:41 PDT)
- Daniel Roe (Mon May 04 2015 - 08:10:37 PDT)
- Michael Shokhen (Mon May 04 2015 - 07:54:32 PDT)
[AMBER] Amber website down
- Wang Moye (Wed May 13 2015 - 19:02:00 PDT)
- James Maier (Wed May 13 2015 - 09:07:54 PDT)
- Crystal VanderZanden (Wed May 13 2015 - 09:04:14 PDT)
[AMBER] Amber12 + GTX 980
- Robinson, Roger (Wed May 20 2015 - 06:09:54 PDT)
[AMBER] AMBERHOME environment variable setting problem
- MOHD HOMAIDUR RAHMAN (Wed May 20 2015 - 10:25:24 PDT)
- Jason Swails (Wed May 20 2015 - 08:20:37 PDT)
- Gustavo Avelar Molina (Wed May 20 2015 - 08:15:16 PDT)
[AMBER] Ambertools 12 Download
- Jason Swails (Fri May 29 2015 - 07:13:15 PDT)
- xy21hb (Fri May 29 2015 - 06:53:57 PDT)
- Jason Swails (Fri May 29 2015 - 06:46:34 PDT)
- Jason Swails (Fri May 29 2015 - 06:45:47 PDT)
- xy21hb (Fri May 29 2015 - 06:43:06 PDT)
[AMBER] AMD with restrained molecule.
- Binwu Zhao (Mon May 11 2015 - 11:09:21 PDT)
[AMBER] Announcement: GLYCAM/GLYCAM-Web mailing list
- Lachele Foley (Thu May 14 2015 - 15:25:33 PDT)
[AMBER] Announcement: Release of AmberTools15
- David A Case (Mon May 04 2015 - 06:28:43 PDT)
[AMBER] ante-mmpbsa.py: troubleshooting
- George Tzotzos (Wed May 13 2015 - 13:33:15 PDT)
- Jason Swails (Wed May 13 2015 - 12:41:26 PDT)
- George Tzotzos (Wed May 13 2015 - 12:28:37 PDT)
- Jason Swails (Wed May 13 2015 - 12:19:10 PDT)
- George Tzotzos (Wed May 13 2015 - 11:26:36 PDT)
[AMBER] Arsenic force field parametrization
- Pengfei Li (Fri May 29 2015 - 12:31:38 PDT)
- Jason Swails (Wed May 27 2015 - 08:47:08 PDT)
- Pengfei Li (Wed May 27 2015 - 08:28:07 PDT)
- Pengfei Li (Mon May 18 2015 - 14:18:14 PDT)
- Andrew Schaub (Sat May 16 2015 - 22:55:13 PDT)
- Sushi Shilpa (Fri May 15 2015 - 00:03:56 PDT)
[AMBER] Assistance required installing amber in cuda
- Jason Swails (Thu May 07 2015 - 12:15:02 PDT)
- Bala Subramani (Thu May 07 2015 - 10:54:14 PDT)
- Bala Subramani (Thu May 07 2015 - 10:52:08 PDT)
- Daniel Roe (Thu May 07 2015 - 09:33:05 PDT)
- Bala Subramani (Thu May 07 2015 - 09:14:29 PDT)
[AMBER] Atome type fatal error
- Pierre Bertin (Thu May 07 2015 - 12:52:19 PDT)
- David A Case (Wed May 06 2015 - 06:12:53 PDT)
- Hannes Loeffler (Wed May 06 2015 - 01:28:18 PDT)
- Pierre Bertin (Wed May 06 2015 - 01:20:34 PDT)
[AMBER] Atoms overlapped in vacuum minimization
- Carlos Simmerling (Wed May 13 2015 - 07:08:50 PDT)
- anu chandra (Wed May 13 2015 - 06:21:31 PDT)
- David A Case (Wed May 13 2015 - 05:53:35 PDT)
- Carlos Simmerling (Wed May 13 2015 - 04:58:34 PDT)
- anu chandra (Wed May 13 2015 - 04:08:54 PDT)
[AMBER] bad atom type: Ng (*.prmtop files from tleap)
- Carlos Modenutti (Thu May 07 2015 - 09:55:37 PDT)
- Daniel Roe (Thu May 07 2015 - 09:17:31 PDT)
- Jason Swails (Thu May 07 2015 - 06:49:24 PDT)
- Carlos Modenutti (Thu May 07 2015 - 05:04:20 PDT)
[AMBER] Bad Contact from lack of QM/MM Heating?
- Dr. Robert Molt Jr. (Wed May 20 2015 - 20:43:07 PDT)
[AMBER] Biligand, trimetal subtrate simulation
- Julio Dominguez (Fri May 15 2015 - 12:47:23 PDT)
[AMBER] box's information
- David A Case (Fri May 08 2015 - 05:07:49 PDT)
- Jason Swails (Fri May 08 2015 - 04:34:20 PDT)
- Fatemeh Sadat Alavi (Fri May 08 2015 - 00:42:57 PDT)
- Jason Swails (Thu May 07 2015 - 07:23:27 PDT)
- Fatemeh Sadat Alavi (Thu May 07 2015 - 06:45:44 PDT)
[AMBER] Bug in LIE action command of cpptraj?
- Samuel Bowerman (Wed May 27 2015 - 14:49:54 PDT)
- Jason Swails (Wed May 27 2015 - 13:44:30 PDT)
- Samuel Bowerman (Wed May 27 2015 - 13:07:21 PDT)
- Jason Swails (Wed May 27 2015 - 12:34:20 PDT)
- Samuel Bowerman (Wed May 27 2015 - 12:25:27 PDT)
[AMBER] Changing two conditions simultaneously in pmemd
- Vlad Cojocaru (Mon May 18 2015 - 10:30:00 PDT)
- Ross Walker (Mon May 18 2015 - 09:07:07 PDT)
- Hannes Loeffler (Mon May 18 2015 - 08:44:28 PDT)
- Christina Bergonzo (Mon May 18 2015 - 08:05:09 PDT)
- Vlad Cojocaru (Mon May 18 2015 - 07:39:24 PDT)
- Jason Swails (Mon May 18 2015 - 07:29:16 PDT)
- Hannes Loeffler (Mon May 18 2015 - 07:18:38 PDT)
- Juan Eiros Zamora (Mon May 18 2015 - 07:13:14 PDT)
- Vlad Cojocaru (Mon May 18 2015 - 07:00:48 PDT)
- Vlad Cojocaru (Mon May 18 2015 - 06:56:11 PDT)
- Hannes Loeffler (Mon May 18 2015 - 06:55:01 PDT)
- Juan Eiros Zamora (Mon May 18 2015 - 06:37:13 PDT)
- Hannes Loeffler (Mon May 18 2015 - 05:13:10 PDT)
- Juan Eiros Zamora (Mon May 18 2015 - 05:06:56 PDT)
[AMBER] Computational Chemical Biology Conference - Abstract Deadline Extended to June 1st
- Ross Walker (Tue May 19 2015 - 13:00:14 PDT)
[AMBER] Computational Chemical Biology Conference - Abstract Deadline May 15th
- Ross Walker (Tue May 05 2015 - 10:32:34 PDT)
[AMBER] Computational Chemical Biology Conference - TALK DEADLINE EXTENDED
- Ross Walker (Tue May 19 2015 - 09:46:43 PDT)
[AMBER] CpHMD for Ser residue?
- Carlos Simmerling (Thu May 07 2015 - 04:19:48 PDT)
- Jason Swails (Thu May 07 2015 - 04:17:29 PDT)
- Michael Shokhen (Thu May 07 2015 - 03:39:18 PDT)
[AMBER] cpptraj checkoverlap
- Daniel Roe (Wed May 13 2015 - 14:51:51 PDT)
- Daniel Roe (Fri May 08 2015 - 09:51:00 PDT)
- Daniel Roe (Fri May 08 2015 - 09:44:26 PDT)
- Aronica, Pietro (Fri May 08 2015 - 09:39:42 PDT)
- Jason Swails (Fri May 08 2015 - 09:28:26 PDT)
- Aronica, Pietro (Fri May 08 2015 - 09:12:36 PDT)
[AMBER] CPPTRAJ V12.1 principal axis different to V13.22 and V14.25
- CHAMI F. (Fri May 01 2015 - 09:29:39 PDT)
- Daniel Roe (Fri May 01 2015 - 09:06:13 PDT)
- CHAMI F. (Fri May 01 2015 - 07:34:43 PDT)
[AMBER] cpptraj: lie
- Daniel Roe (Sun May 24 2015 - 10:30:53 PDT)
- Jason Swails (Sun May 24 2015 - 08:31:46 PDT)
- George Tzotzos (Sun May 24 2015 - 04:18:49 PDT)
[AMBER] cpptraj: Per residue rmsd
- George Tzotzos (Sun May 03 2015 - 02:27:44 PDT)
- Daniel Roe (Sat May 02 2015 - 15:32:24 PDT)
- George Tzotzos (Sat May 02 2015 - 11:37:51 PDT)
[AMBER] CUDA compiling of Amber tools 14
- Jason Swails (Wed May 06 2015 - 06:08:46 PDT)
- anu chandra (Wed May 06 2015 - 04:49:35 PDT)
[AMBER] Determining number of molecules from a point by integration using xmgrace
- hannes.loeffler.stfc.ac.uk (Fri May 22 2015 - 12:59:56 PDT)
- Sylvester Tumusiime (Fri May 22 2015 - 12:48:26 PDT)
[AMBER] Developing Parameters using tleap
- David A Case (Sat May 23 2015 - 09:29:33 PDT)
- Brittany Boykin (Fri May 22 2015 - 12:44:55 PDT)
[AMBER] Difference between EXTDIEL and EPSOUT?
- Jason Swails (Tue May 05 2015 - 05:21:50 PDT)
- Chinh Su Tran To (Mon May 04 2015 - 23:54:53 PDT)
[AMBER] disable minimization in nmode MMPBSA.py
- Jason Swails (Fri May 15 2015 - 15:07:03 PDT)
- Carlos Modenutti (Fri May 15 2015 - 14:02:22 PDT)
[AMBER] DNS manipulations
- Bill Ross (Tue May 19 2015 - 17:19:21 PDT)
- Ross Walker (Tue May 19 2015 - 10:10:31 PDT)
- David A Case (Tue May 19 2015 - 05:06:00 PDT)
[AMBER] Does GLYCAM only can deal with Oligosaccharides or Polysaccharides BUT NOT Monosaccharide？？？
- Lachele Foley (Fri May 22 2015 - 09:55:14 PDT)
- Chris (Fri May 22 2015 - 07:02:18 PDT)
[AMBER] DOPC lipid bilayer in Amber using lipid14 force field.
- Ross Walker (Wed May 13 2015 - 11:03:23 PDT)
- Him Shweta (Wed May 13 2015 - 10:26:26 PDT)
[AMBER] Doubt about ligand binding in proteins
- Kenneth Huang (Sun May 24 2015 - 10:51:22 PDT)
- Gustavo Avelar Molina (Sat May 23 2015 - 18:05:28 PDT)
[AMBER] error in amber installation
- David A Case (Tue May 05 2015 - 04:41:49 PDT)
- Atila Petrosian (Mon May 04 2015 - 23:08:11 PDT)
- Jason Swails (Mon May 04 2015 - 11:03:05 PDT)
- Atila Petrosian (Mon May 04 2015 - 10:51:14 PDT)
- Jason Swails (Sun May 03 2015 - 17:26:59 PDT)
- David A Case (Sun May 03 2015 - 09:10:28 PDT)
- Atila Petrosian (Sun May 03 2015 - 07:21:30 PDT)
- David A Case (Sun May 03 2015 - 04:52:04 PDT)
- Atila Petrosian (Sun May 03 2015 - 04:23:27 PDT)
[AMBER] Error selecting compatible GPU all CUDA-capable devices are busy or unavailable
- Jason Swails (Thu May 14 2015 - 07:14:08 PDT)
- Jagga Soorma (Wed May 13 2015 - 15:02:10 PDT)
[AMBER] error using the lipidorder command
- Daniel Roe (Thu May 14 2015 - 06:51:46 PDT)
- Sylvester Tumusiime (Wed May 13 2015 - 08:49:34 PDT)
[AMBER] Error when compile ambertools15
- Jason Swails (Fri May 08 2015 - 04:30:45 PDT)
- amber amber (Fri May 08 2015 - 01:37:29 PDT)
- Yu Chen (Thu May 07 2015 - 18:21:46 PDT)
- Jason Swails (Thu May 07 2015 - 14:20:08 PDT)
- Yu Chen (Thu May 07 2015 - 14:14:03 PDT)
- Jason Swails (Thu May 07 2015 - 06:43:15 PDT)
- amber amber (Thu May 07 2015 - 05:11:43 PDT)
- Jason Swails (Wed May 06 2015 - 06:11:57 PDT)
- amber amber (Wed May 06 2015 - 04:32:24 PDT)
[AMBER] Error while running tleap for protein-RNA complex
- Jason Swails (Tue May 12 2015 - 05:12:39 PDT)
- Shreeramesh (Tue May 12 2015 - 02:48:47 PDT)
- David A Case (Mon May 11 2015 - 04:55:17 PDT)
- Hector A. Baldoni (Mon May 11 2015 - 04:10:37 PDT)
- Shreeramesh (Mon May 11 2015 - 01:59:30 PDT)
[AMBER] Error with running ParmEd
- Jason Swails (Thu May 07 2015 - 12:16:44 PDT)
- Yinglong Miao (Thu May 07 2015 - 09:58:25 PDT)
- Jason Swails (Wed May 06 2015 - 18:59:27 PDT)
- Yinglong Miao (Wed May 06 2015 - 09:42:31 PDT)
[AMBER] ESURF in MMPBSA.py results
- Jason Swails (Fri May 15 2015 - 02:15:40 PDT)
- Huang (Fri May 15 2015 - 01:26:22 PDT)
[AMBER] experimental coulomb and van der Waals cutoffs
- Jason Swails (Tue May 12 2015 - 05:03:13 PDT)
- Ahmet yıldırım (Tue May 12 2015 - 04:03:29 PDT)
- Carlos Simmerling (Tue May 12 2015 - 03:28:06 PDT)
- Ahmet yıldırım (Tue May 12 2015 - 01:52:16 PDT)
[AMBER] Extracting temperature-based potential energies from REMD
- Hai Nguyen (Sun May 31 2015 - 06:02:35 PDT)
- Lee-Ping Wang (Sun May 31 2015 - 05:09:00 PDT)
- Lee-Ping Wang (Mon May 25 2015 - 20:04:55 PDT)
- Hai Nguyen (Mon May 25 2015 - 18:29:07 PDT)
- Lee-Ping Wang (Mon May 25 2015 - 13:43:32 PDT)
- Jason Swails (Mon May 25 2015 - 12:12:03 PDT)
- Lee-Ping Wang (Mon May 25 2015 - 09:44:10 PDT)
[AMBER] Faulty_atom_connection error
- David A Case (Fri May 08 2015 - 05:03:38 PDT)
- nibedita jana (Fri May 08 2015 - 03:06:02 PDT)
[AMBER] forcefield for DNA
- Christina Bergonzo (Tue May 05 2015 - 06:53:40 PDT)
- Thomas C. Bishop (Tue May 05 2015 - 06:37:48 PDT)
- 王珍 (Tue May 05 2015 - 06:22:54 PDT)
- David A Case (Tue May 05 2015 - 04:44:09 PDT)
- 王珍 (Tue May 05 2015 - 01:52:23 PDT)
[AMBER] Fwd: MPI Runtime Error
- David A Case (Sat May 30 2015 - 09:18:40 PDT)
- Kusum Mehla (Fri May 29 2015 - 21:38:42 PDT)
[AMBER] Fwd: Selection of chain
- Kenneth Huang (Sun May 10 2015 - 08:47:58 PDT)
- muhammad tahir ayub (Sun May 10 2015 - 07:57:03 PDT)
[AMBER] Fwd: Using the CHARMM force field to run simulations with AMBER
- hannes.loeffler.stfc.ac.uk (Wed May 27 2015 - 23:36:39 PDT)
- Brian Radak (Wed May 27 2015 - 14:27:58 PDT)
- Jason Swails (Wed May 27 2015 - 13:50:46 PDT)
- Shalini Gupta (Wed May 27 2015 - 12:22:13 PDT)
[AMBER] GPCR-MM_PBSA
- Holger Gohlke (Tue May 05 2015 - 11:55:15 PDT)
- Ramin Ekhteiari (Tue May 05 2015 - 11:02:10 PDT)
- Ramin Ekhteiari (Tue May 05 2015 - 10:59:41 PDT)
- Ramin Ekhteiari (Tue May 05 2015 - 10:56:23 PDT)
[AMBER] help me to understand using GLYCAM!!!
- Lachele Foley (Tue May 26 2015 - 10:25:28 PDT)
- David A Case (Tue May 26 2015 - 04:35:48 PDT)
- Chris (Mon May 25 2015 - 19:22:39 PDT)
- Lachele Foley (Mon May 25 2015 - 18:02:55 PDT)
- Chris (Mon May 25 2015 - 06:52:37 PDT)
[AMBER] Help needed on MMPBSA for a system with different protonation states in free & bound forms, using multiple trajectory protocol
- Jason Swails (Sat May 16 2015 - 09:59:21 PDT)
- Shailesh Pandey (Sat May 16 2015 - 04:18:42 PDT)
[AMBER] How to fix missing residues
- Sajeewa Pemasinghe (Tue May 12 2015 - 04:21:03 PDT)
- Shreeramesh (Tue May 12 2015 - 03:48:18 PDT)
[AMBER] How to run GBSA in MD and binding energy calculation (MMPBSA.py)?
- Carlos Simmerling (Fri May 15 2015 - 03:15:10 PDT)
- Jason Swails (Fri May 15 2015 - 02:07:51 PDT)
- Huang (Thu May 14 2015 - 20:46:35 PDT)
[AMBER] Implicit water for MD studies
- Shreeramesh (Thu May 07 2015 - 03:45:58 PDT)
- Jason Swails (Mon May 04 2015 - 05:41:59 PDT)
- Debayan Chakraborty (Mon May 04 2015 - 02:58:08 PDT)
- Shreeramesh (Mon May 04 2015 - 01:44:21 PDT)
- Carlos Simmerling (Fri May 01 2015 - 09:13:38 PDT)
- Jason Swails (Fri May 01 2015 - 07:20:52 PDT)
- Shreeramesh (Fri May 01 2015 - 06:17:10 PDT)
[AMBER] IRED
- Sylvester Tumusiime (Tue May 05 2015 - 09:49:44 PDT)
- Christina Bergonzo (Tue May 05 2015 - 09:22:52 PDT)
- Sylvester Tumusiime (Tue May 05 2015 - 09:12:36 PDT)
- Christina Bergonzo (Tue May 05 2015 - 08:52:06 PDT)
- Sylvester Tumusiime (Tue May 05 2015 - 08:40:05 PDT)
[AMBER] Is it necessary to cap the N and C terminal using ACE and NHE in tleap?
- Wang Moye (Tue May 05 2015 - 18:15:46 PDT)
- Carlos Simmerling (Tue May 05 2015 - 03:19:01 PDT)
- Wang Moye (Tue May 05 2015 - 00:09:28 PDT)
[AMBER] leap: adding a residue to a unit
- David A Case (Fri May 08 2015 - 05:19:37 PDT)
- Hannes Loeffler (Thu May 07 2015 - 02:24:41 PDT)
[AMBER] loading molecule in leap
- David A Case (Wed May 27 2015 - 05:30:15 PDT)
- jacob wick (Wed May 27 2015 - 04:23:46 PDT)
[AMBER] MC-MM-PBSA
- Jason Swails (Thu May 21 2015 - 05:37:53 PDT)
- Ramin Ekhteiari (Wed May 20 2015 - 22:46:09 PDT)
[AMBER] MC-simulation-MM-PBSA
- Ramin Ekhteiari (Tue May 19 2015 - 23:51:30 PDT)
[AMBER] MCPB error
- Takeshi Baba (Fri May 08 2015 - 23:54:26 PDT)
- Pengfei Li (Fri May 08 2015 - 07:32:51 PDT)
- Takeshi Baba (Fri May 08 2015 - 03:33:46 PDT)
[AMBER] MCPB.py issues
- Pengfei Li (Tue May 26 2015 - 09:30:06 PDT)
- David Poole (Fri May 22 2015 - 17:11:08 PDT)
- Pengfei Li (Wed May 20 2015 - 07:24:02 PDT)
- David A Case (Wed May 20 2015 - 04:48:18 PDT)
- David Poole (Tue May 19 2015 - 10:46:15 PDT)
[AMBER] membrane protein simulation
- Victor Ma (Wed May 27 2015 - 09:55:06 PDT)
- Ross Walker (Wed May 27 2015 - 08:43:34 PDT)
- Victor Ma (Wed May 27 2015 - 08:35:53 PDT)
- Ross Walker (Tue May 26 2015 - 18:16:22 PDT)
- Victor Ma (Tue May 26 2015 - 14:13:48 PDT)
[AMBER] minimization error
- Carlos Romero (Thu May 14 2015 - 11:32:20 PDT)
- Jason Swails (Thu May 14 2015 - 10:16:44 PDT)
- Carlos Romero (Thu May 14 2015 - 07:26:36 PDT)
[AMBER] MM_PBSA analysis
- Vlad Cojocaru (Sat May 09 2015 - 04:42:36 PDT)
- Ramin Ekhteiari (Sat May 09 2015 - 04:18:10 PDT)
- Vlad Cojocaru (Sat May 09 2015 - 03:23:17 PDT)
- Ramin Ekhteiari (Sat May 09 2015 - 03:09:47 PDT)
- Hai Nguyen (Fri May 08 2015 - 19:16:48 PDT)
- Jason Swails (Mon May 04 2015 - 17:38:55 PDT)
- Ramin Ekhteiari (Mon May 04 2015 - 11:06:47 PDT)
[AMBER] MMGBSA: interpretation of results
- Kenneth Huang (Wed May 20 2015 - 12:13:13 PDT)
- George Tzotzos (Wed May 20 2015 - 11:37:02 PDT)
- George Tzotzos (Wed May 20 2015 - 05:09:19 PDT)
[AMBER] MMGBSA: pairwise decomposition
- Jason Swails (Tue May 26 2015 - 12:19:58 PDT)
- George Tzotzos (Tue May 26 2015 - 10:53:39 PDT)
[AMBER] MMPBSA problem with calcium
- Francesco Gentile (Thu May 07 2015 - 14:02:44 PDT)
[AMBER] MMPBSA.py
- Ramin Ekhteiari (Thu May 07 2015 - 10:02:14 PDT)
- Jason Swails (Thu May 07 2015 - 06:12:52 PDT)
- Jason Swails (Thu May 07 2015 - 05:41:31 PDT)
- Ramin Ekhteiari (Wed May 06 2015 - 23:32:34 PDT)
- Jason Swails (Wed May 06 2015 - 18:46:52 PDT)
- Ramin Ekhteiari (Wed May 06 2015 - 14:06:58 PDT)
- David A Case (Wed May 06 2015 - 12:45:45 PDT)
- Ramin Ekhteiari (Wed May 06 2015 - 11:14:02 PDT)
- David A Case (Wed May 06 2015 - 08:16:45 PDT)
- Ramin Ekhteiari (Wed May 06 2015 - 07:18:49 PDT)
[AMBER] MMPBSA.py API AttributeError: 'MMPBSA_App' object has no attribute ‘using_chamber'
- D.J. Pattinson (Fri May 29 2015 - 06:58:08 PDT)
- Jason Swails (Fri May 29 2015 - 06:28:27 PDT)
- D.J. Pattinson (Fri May 29 2015 - 03:46:44 PDT)
[AMBER] mmpbsa.py error
- George Tzotzos (Mon May 11 2015 - 12:11:23 PDT)
- Jason Swails (Mon May 11 2015 - 12:00:11 PDT)
- George Tzotzos (Mon May 11 2015 - 11:52:04 PDT)
[AMBER] MMPBSA.py.MPI
- George Tzotzos (Sat May 16 2015 - 11:31:56 PDT)
- Jason Swails (Sat May 16 2015 - 09:30:17 PDT)
- George Tzotzos (Sat May 16 2015 - 06:05:26 PDT)
- Jason Swails (Fri May 15 2015 - 17:47:42 PDT)
- George Tzotzos (Fri May 15 2015 - 13:22:18 PDT)
- Jason Swails (Sat May 09 2015 - 05:02:31 PDT)
- George Tzotzos (Fri May 08 2015 - 12:24:20 PDT)
[AMBER] mmpbsa.py.MPI: patching
- Kenneth Huang (Thu May 28 2015 - 11:55:09 PDT)
- George Tzotzos (Thu May 28 2015 - 11:33:11 PDT)
[AMBER] mmpbsa.py: new error message
- Jason Swails (Tue May 12 2015 - 10:58:13 PDT)
- George Tzotzos (Tue May 12 2015 - 10:40:24 PDT)
- Jason Swails (Tue May 12 2015 - 10:03:03 PDT)
- Kenneth Huang (Tue May 12 2015 - 07:27:38 PDT)
- George Tzotzos (Tue May 12 2015 - 07:15:46 PDT)
[AMBER] Next AMBER release?
- Ross Walker (Tue May 26 2015 - 18:18:26 PDT)
- Mohd Farid Ismail (Tue May 26 2015 - 17:20:35 PDT)
[AMBER] Nmode analysis calculation problem for Implicit simulation.
- David A Case (Wed May 06 2015 - 08:25:52 PDT)
- Bajarang Kumbhar (Wed May 06 2015 - 07:25:38 PDT)
[AMBER] NTX Keyword
- Jason Swails (Sun May 24 2015 - 15:38:01 PDT)
- Kenneth Huang (Sun May 24 2015 - 11:13:35 PDT)
- Robert Molt (Sun May 24 2015 - 10:10:23 PDT)
[AMBER] parallel installation of ambertools14 on centOS-rocks system
- Jason Swails (Mon May 11 2015 - 12:31:52 PDT)
- Andrew Bostick (Mon May 11 2015 - 12:17:29 PDT)
[AMBER] parameters for type: Cl-
- David A Case (Sun May 10 2015 - 14:08:53 PDT)
- Marc van der Kamp (Sun May 10 2015 - 12:28:04 PDT)
- Michael Shokhen (Sun May 10 2015 - 11:57:49 PDT)
- Kenneth Huang (Sun May 10 2015 - 11:35:59 PDT)
- Michael Shokhen (Sun May 10 2015 - 11:08:20 PDT)
[AMBER] partition error in shake
- David A Case (Tue May 26 2015 - 08:11:50 PDT)
- Evgenia Dueva (Tue May 26 2015 - 06:37:44 PDT)
[AMBER] pmemd performance on GTX Titan Z
- Kenneth Huang (Wed May 13 2015 - 18:05:29 PDT)
- Ross Walker (Tue May 12 2015 - 20:42:17 PDT)
- Kenneth Huang (Tue May 12 2015 - 09:22:13 PDT)
[AMBER] Polymorphism study using Amber
- David A Case (Mon May 18 2015 - 05:10:03 PDT)
- jacob wick (Sun May 17 2015 - 23:53:29 PDT)
[AMBER] Praise
- Dr. Robert Molt Jr. (Wed May 13 2015 - 15:10:11 PDT)
[AMBER] principal component analysis
- Daniel Roe (Mon May 11 2015 - 12:55:38 PDT)
- abdennour braka (Mon May 11 2015 - 02:27:13 PDT)
[AMBER] Principal moments of inertia
- Daniel Roe (Thu May 14 2015 - 06:49:38 PDT)
- Sylvester Tumusiime (Wed May 13 2015 - 07:18:31 PDT)
[AMBER] Problem regarding PMF curve
- Shubhadip Das (Mon May 04 2015 - 04:35:51 PDT)
[AMBER] Problem Regarding PMF Graph
- Shubhadip Das (Mon May 04 2015 - 04:27:27 PDT)
[AMBER] Problem with amb2gmx in AmberTools 15
- Soumendranath Bhakat (Wed May 20 2015 - 09:45:13 PDT)
- Soumendranath Bhakat (Wed May 20 2015 - 05:14:10 PDT)
- David A Case (Wed May 20 2015 - 04:33:46 PDT)
- Hannes Loeffler (Wed May 20 2015 - 03:25:25 PDT)
- Soumendranath Bhakat (Wed May 20 2015 - 03:15:18 PDT)
- Soumendranath Bhakat (Wed May 20 2015 - 03:13:11 PDT)
- Hannes Loeffler (Wed May 20 2015 - 03:04:46 PDT)
- Soumendranath Bhakat (Wed May 20 2015 - 02:52:02 PDT)
- David A Case (Tue May 19 2015 - 05:03:30 PDT)
- Soumendranath Bhakat (Tue May 19 2015 - 04:01:50 PDT)
[AMBER] Problem with Configuring NetCDF
- Jason Swails (Sun May 10 2015 - 17:18:44 PDT)
- Alaa Mohye El-din Soliman (Sun May 10 2015 - 16:05:22 PDT)
- Jason Swails (Sat May 09 2015 - 12:43:58 PDT)
- Alaa Mohye El-din Soliman (Sat May 09 2015 - 12:19:29 PDT)
- Jason Swails (Sat May 09 2015 - 07:25:08 PDT)
- Alaa Mohye El-din Soliman (Sat May 09 2015 - 06:42:18 PDT)
[AMBER] Problem with covalently bonded ligand parametrization
- Gustavo Avelar Molina (Sat May 23 2015 - 16:59:03 PDT)
- David A Case (Sat May 23 2015 - 09:45:27 PDT)
- Gustavo Avelar Molina (Fri May 22 2015 - 19:07:43 PDT)
[AMBER] problem with prepgen in an organic molecule parameterization
- Rebeca García Fandiño (Fri May 08 2015 - 02:11:00 PDT)
- Daniel Roe (Thu May 07 2015 - 10:54:20 PDT)
- Rebeca García Fandiño (Thu May 07 2015 - 10:05:32 PDT)
- Daniel Roe (Thu May 07 2015 - 09:31:01 PDT)
- Rebeca García Fandiño (Thu May 07 2015 - 08:12:31 PDT)
- Daniel Roe (Thu May 07 2015 - 07:51:09 PDT)
- Rebeca García Fandiño (Thu May 07 2015 - 07:37:14 PDT)
[AMBER] problems with "explicit solvent"
- David A Case (Tue May 19 2015 - 18:19:17 PDT)
- Investigador Química (Tue May 19 2015 - 17:20:16 PDT)
[AMBER] Protein-Membrane assembly
- Ofir Tal (Tue May 26 2015 - 00:44:01 PDT)
[AMBER] QM/MM Protein-Ligand interaction w/cofactor
- William Martin (Sat May 09 2015 - 22:27:30 PDT)
- David A Case (Sat May 09 2015 - 19:43:01 PDT)
- Gustavo Seabra (Sat May 09 2015 - 13:04:03 PDT)
- William Martin (Sat May 09 2015 - 12:35:30 PDT)
[AMBER] qmcut in Amber14 Manual
- Jason Swails (Mon May 11 2015 - 05:05:52 PDT)
- Marc van der Kamp (Mon May 11 2015 - 01:43:32 PDT)
- Robert Molt (Sun May 10 2015 - 23:13:18 PDT)
[AMBER] Query on how to simulate bulk no.of molecules in AMBER
- Jason Swails (Wed May 06 2015 - 06:15:07 PDT)
- Ashutosh Shandilya (Wed May 06 2015 - 03:37:30 PDT)
- srilaxmi reddy (Wed May 06 2015 - 02:39:12 PDT)
[AMBER] query parameter files for mercuric ions
- Pengfei Li (Thu May 07 2015 - 06:52:21 PDT)
- Ya Gao (Thu May 07 2015 - 06:18:01 PDT)
[AMBER] Question about Extra Point
- David A Case (Fri May 22 2015 - 04:47:16 PDT)
- zhouhaibin2008.ok (Fri May 22 2015 - 00:14:07 PDT)
[AMBER] Question about lipid simulation
- Ross Walker (Wed May 13 2015 - 10:59:52 PDT)
- Victor Ma (Wed May 13 2015 - 10:51:48 PDT)
[AMBER] question regarding SMD simulation
- Asmita Gupta (Sat May 09 2015 - 07:38:39 PDT)
[AMBER] Regarding - "Help needed on MMPBSA for a system with different protonation states in free & bound forms"
- Shailesh Pandey (Mon May 18 2015 - 08:54:22 PDT)
- Jason Swails (Mon May 18 2015 - 06:06:59 PDT)
- Shailesh Pandey (Sun May 17 2015 - 03:05:28 PDT)
[AMBER] Regarding AMD simulation
- Daniel Roe (Fri May 22 2015 - 07:27:24 PDT)
- Aditya Sarkar (Fri May 22 2015 - 04:08:44 PDT)
[AMBER] Regarding high temp simulation of DNA and amber MD module
- David A Case (Sat May 23 2015 - 09:38:54 PDT)
- Carlos Simmerling (Sat May 23 2015 - 02:33:58 PDT)
- MOHD HOMAIDUR RAHMAN (Fri May 22 2015 - 14:23:29 PDT)
[AMBER] Replica-exchange molecular dynamics
- Carlos Simmerling (Thu May 07 2015 - 03:24:13 PDT)
- 新生大侠 (Wed May 06 2015 - 23:15:09 PDT)
[AMBER] representing structure from equilibrium
- newamber list (Mon May 11 2015 - 13:45:55 PDT)
- Daniel Roe (Mon May 11 2015 - 13:09:46 PDT)
- newamber list (Mon May 04 2015 - 09:35:25 PDT)
[AMBER] restart an SMD run
- Jason Swails (Tue May 12 2015 - 05:15:29 PDT)
- Asmita Gupta (Tue May 12 2015 - 05:07:39 PDT)
- Jason Swails (Tue May 12 2015 - 04:51:26 PDT)
- Asmita Gupta (Tue May 12 2015 - 04:42:08 PDT)
- Jason Swails (Mon May 11 2015 - 05:44:35 PDT)
- Asmita Gupta (Sun May 10 2015 - 23:31:21 PDT)
[AMBER] RNA unfolding studies..
- David A Case (Wed May 27 2015 - 05:14:49 PDT)
- Asmita Gupta (Wed May 27 2015 - 03:54:40 PDT)
[AMBER] Sander QMMM Bomb Problem
- Gustavo Seabra (Tue May 19 2015 - 10:13:42 PDT)
- Gulsevin,Alican (Thu May 14 2015 - 12:56:59 PDT)
[AMBER] Selection of chain
- David A Case (Sat May 09 2015 - 19:37:29 PDT)
- muhammad tahir ayub (Sat May 09 2015 - 11:54:01 PDT)
[AMBER] site down?
- David A Case (Thu May 14 2015 - 04:57:38 PDT)
- Gerald Monard (Thu May 14 2015 - 05:11:28 PDT)
- Wang Moye (Wed May 13 2015 - 18:26:25 PDT)
- Jason Swails (Wed May 13 2015 - 09:23:24 PDT)
- Gerald Monard (Wed May 13 2015 - 08:31:15 PDT)
- Ross Walker (Wed May 13 2015 - 08:23:43 PDT)
- Ross Walker (Wed May 13 2015 - 08:21:35 PDT)
- Jonathan Gough (Wed May 13 2015 - 08:19:54 PDT)
- Gerald Monard (Wed May 13 2015 - 08:19:39 PDT)
- Marc van der Kamp (Wed May 13 2015 - 08:13:35 PDT)
- Akash Deep Biswas (Wed May 13 2015 - 08:10:36 PDT)
- Gerald Monard (Wed May 13 2015 - 08:00:58 PDT)
[AMBER] Solvation of a long protein
- Steven Ramsey (Fri May 01 2015 - 09:31:20 PDT)
- Daniel Roe (Fri May 01 2015 - 09:09:27 PDT)
- Jason Swails (Fri May 01 2015 - 08:48:03 PDT)
- amin.imtech.res.in (Fri May 01 2015 - 08:00:08 PDT)
- Steven Ramsey (Fri May 01 2015 - 07:39:38 PDT)
[AMBER] the energy between two ligand molecules
- Jason Swails (Fri May 15 2015 - 02:18:54 PDT)
- chemjxn (Fri May 15 2015 - 02:10:02 PDT)
[AMBER] The output file about SMD
- Jason Swails (Sat May 09 2015 - 08:37:57 PDT)
- wjli (Sat May 09 2015 - 06:24:05 PDT)
[AMBER] tleap maintainer
- David A Case (Sat May 23 2015 - 09:48:44 PDT)
- Matt Harvey (Sat May 23 2015 - 05:13:29 PDT)
[AMBER] Torsion restraints with pmemd.amoeba
- David A Case (Thu May 28 2015 - 09:44:35 PDT)
- Karl Debiec (Thu May 28 2015 - 09:17:07 PDT)
[AMBER] Trouble understanding DBSCAN clustering algorithm
- Daniel Roe (Fri May 08 2015 - 07:24:49 PDT)
- Juan Eiros Zamora (Fri May 08 2015 - 07:06:30 PDT)
- Daniel Roe (Thu May 07 2015 - 09:12:11 PDT)
- Juan Eiros Zamora (Thu May 07 2015 - 02:29:34 PDT)
- Daniel Roe (Wed May 06 2015 - 09:49:29 PDT)
- Christina Bergonzo (Wed May 06 2015 - 09:47:01 PDT)
- Juan Eiros Zamora (Wed May 06 2015 - 09:22:04 PDT)
[AMBER] Umbrella Sampling and wham
- Brian Radak (Sat May 30 2015 - 11:13:37 PDT)
- MOHD HOMAIDUR RAHMAN (Fri May 29 2015 - 07:46:58 PDT)
[AMBER] Warning when trying to get RMS
- Daniel Roe (Thu May 14 2015 - 12:14:49 PDT)
- Mohammad Salem (Thu May 14 2015 - 11:56:15 PDT)
[AMBER] WARNING: SGFT, instead of TEMPSG, should be set for SGMDfp/SGLDfp!
- barbara rossi (Wed May 27 2015 - 06:22:22 PDT)
[AMBER] water bridges
- Sylvester Tumusiime (Sat May 30 2015 - 14:44:31 PDT)
- Hector A. Baldoni (Sat May 30 2015 - 09:43:48 PDT)
[AMBER] WEBSITE not opening
- Elvis Martis (Tue May 19 2015 - 20:12:05 PDT)
- Ye Mei (Mon May 18 2015 - 20:46:08 PDT)
- Ross Walker (Mon May 18 2015 - 20:18:05 PDT)
- Elvis Martis (Mon May 18 2015 - 20:06:08 PDT)
- Jason Swails (Mon May 18 2015 - 06:00:03 PDT)
- Elvis Martis (Mon May 18 2015 - 05:57:30 PDT)
Problem Regarding PMF Graph
- Jason Swails (Fri May 15 2015 - 02:27:19 PDT)
- Shubhadip Das (Thu May 14 2015 - 21:47:22 PDT)
- Adrian Roitberg (Mon May 04 2015 - 06:34:52 PDT)
- Shubhadip Das (Mon May 04 2015 - 04:34:01 PDT)

Amber Archive May 2015 by subject