Amber Archive May 2015 by thread
454 messages
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Starting
Fri May 01 2015 - 06:30:02 PDT,
Ending
Sun May 31 2015 - 06:30:02 PDT
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[AMBER] Implicit water for MD studies
Shreeramesh
(Fri May 01 2015 - 06:17:10 PDT)
Re: [AMBER] Implicit water for MD studies
Jason Swails
(Fri May 01 2015 - 07:20:52 PDT)
Re: [AMBER] Implicit water for MD studies
Carlos Simmerling
(Fri May 01 2015 - 09:13:38 PDT)
Re: [AMBER] Implicit water for MD studies
Shreeramesh
(Mon May 04 2015 - 01:44:21 PDT)
Re: [AMBER] Implicit water for MD studies
Debayan Chakraborty
(Mon May 04 2015 - 02:58:08 PDT)
Re: [AMBER] Implicit water for MD studies
Jason Swails
(Mon May 04 2015 - 05:41:59 PDT)
Re: [AMBER] Implicit water for MD studies
Shreeramesh
(Thu May 07 2015 - 03:45:58 PDT)
[AMBER] CPPTRAJ V12.1 principal axis different to V13.22 and V14.25
CHAMI F.
(Fri May 01 2015 - 07:34:43 PDT)
Re: [AMBER] CPPTRAJ V12.1 principal axis different to V13.22 and V14.25
Daniel Roe
(Fri May 01 2015 - 09:06:13 PDT)
Re: [AMBER] CPPTRAJ V12.1 principal axis different to V13.22 and V14.25
CHAMI F.
(Fri May 01 2015 - 09:29:39 PDT)
[AMBER] Solvation of a long protein
Steven Ramsey
(Fri May 01 2015 - 07:39:38 PDT)
Re: [AMBER] Solvation of a long protein
amin.imtech.res.in
(Fri May 01 2015 - 08:00:08 PDT)
Re: [AMBER] Solvation of a long protein
Jason Swails
(Fri May 01 2015 - 08:48:03 PDT)
Re: [AMBER] Solvation of a long protein
Daniel Roe
(Fri May 01 2015 - 09:09:27 PDT)
Re: [AMBER] Solvation of a long protein
Steven Ramsey
(Fri May 01 2015 - 09:31:20 PDT)
[AMBER] cpptraj: Per residue rmsd
George Tzotzos
(Sat May 02 2015 - 11:37:51 PDT)
Re: [AMBER] cpptraj: Per residue rmsd
Daniel Roe
(Sat May 02 2015 - 15:32:24 PDT)
Re: [AMBER] cpptraj: Per residue rmsd
George Tzotzos
(Sun May 03 2015 - 02:27:44 PDT)
Re: [AMBER] error in amber installation
Atila Petrosian
(Sun May 03 2015 - 04:23:27 PDT)
Re: [AMBER] error in amber installation
David A Case
(Sun May 03 2015 - 04:52:04 PDT)
Re: [AMBER] error in amber installation
Atila Petrosian
(Sun May 03 2015 - 07:21:30 PDT)
Re: [AMBER] error in amber installation
David A Case
(Sun May 03 2015 - 09:10:28 PDT)
Re: [AMBER] error in amber installation
Jason Swails
(Sun May 03 2015 - 17:26:59 PDT)
Re: [AMBER] error in amber installation
Atila Petrosian
(Mon May 04 2015 - 10:51:14 PDT)
Re: [AMBER] error in amber installation
Jason Swails
(Mon May 04 2015 - 11:03:05 PDT)
Re: [AMBER] error in amber installation
Atila Petrosian
(Mon May 04 2015 - 23:08:11 PDT)
Re: [AMBER] error in amber installation
David A Case
(Tue May 05 2015 - 04:41:49 PDT)
[AMBER] Problem Regarding PMF Graph
Shubhadip Das
(Mon May 04 2015 - 04:27:27 PDT)
[AMBER] Fw: Problem Regarding PMF Graph
Shubhadip Das
(Mon May 04 2015 - 04:34:01 PDT)
Re: [AMBER] Fw: Problem Regarding PMF Graph
Adrian Roitberg
(Mon May 04 2015 - 06:34:52 PDT)
Re: [AMBER] Fw: Problem Regarding PMF Graph
Shubhadip Das
(Thu May 14 2015 - 21:47:22 PDT)
Re: [AMBER] Fw: Problem Regarding PMF Graph
Jason Swails
(Fri May 15 2015 - 02:27:19 PDT)
[AMBER] Problem regarding PMF curve
Shubhadip Das
(Mon May 04 2015 - 04:35:51 PDT)
[AMBER] Announcement: Release of AmberTools15
David A Case
(Mon May 04 2015 - 06:28:43 PDT)
[AMBER] amber tools 15 upgrade problem
Michael Shokhen
(Mon May 04 2015 - 07:54:32 PDT)
Re: [AMBER] amber tools 15 upgrade problem
Daniel Roe
(Mon May 04 2015 - 08:10:37 PDT)
Re: [AMBER] amber tools 15 upgrade problem
Kenneth Huang
(Mon May 04 2015 - 08:12:41 PDT)
Re: [AMBER] amber tools 15 upgrade problem
Michael Shokhen
(Mon May 04 2015 - 08:53:48 PDT)
Re: [AMBER] amber tools 15 upgrade problem
Jason Swails
(Mon May 04 2015 - 08:59:16 PDT)
Re: [AMBER] amber tools 15 upgrade problem
Kenneth Huang
(Mon May 04 2015 - 09:09:44 PDT)
Re: [AMBER] amber tools 15 upgrade problem
David A Case
(Mon May 04 2015 - 09:04:54 PDT)
Re: [AMBER] amber tools 15 upgrade problem
David A Case
(Mon May 04 2015 - 09:57:30 PDT)
Re: [AMBER] amber tools 15 upgrade problem
Michael Shokhen
(Thu May 07 2015 - 03:57:24 PDT)
[AMBER] representing structure from equilibrium
newamber list
(Mon May 04 2015 - 09:35:25 PDT)
Re: [AMBER] representing structure from equilibrium
Daniel Roe
(Mon May 11 2015 - 13:09:46 PDT)
Re: [AMBER] representing structure from equilibrium
newamber list
(Mon May 11 2015 - 13:45:55 PDT)
[AMBER] MM_PBSA analysis
Ramin Ekhteiari
(Mon May 04 2015 - 11:06:47 PDT)
Re: [AMBER] MM_PBSA analysis
Jason Swails
(Mon May 04 2015 - 17:38:55 PDT)
Re: [AMBER] MM_PBSA analysis
Hai Nguyen
(Fri May 08 2015 - 19:16:48 PDT)
Re: [AMBER] MM_PBSA analysis
Ramin Ekhteiari
(Sat May 09 2015 - 03:09:47 PDT)
Re: [AMBER] MM_PBSA analysis
Vlad Cojocaru
(Sat May 09 2015 - 03:23:17 PDT)
Re: [AMBER] MM_PBSA analysis
Ramin Ekhteiari
(Sat May 09 2015 - 04:18:10 PDT)
Re: [AMBER] MM_PBSA analysis
Vlad Cojocaru
(Sat May 09 2015 - 04:42:36 PDT)
[AMBER] Difference between EXTDIEL and EPSOUT?
Chinh Su Tran To
(Mon May 04 2015 - 23:54:53 PDT)
Re: [AMBER] Difference between EXTDIEL and EPSOUT?
Jason Swails
(Tue May 05 2015 - 05:21:50 PDT)
[AMBER] Is it necessary to cap the N and C terminal using ACE and NHE in tleap?
Wang Moye
(Tue May 05 2015 - 00:09:28 PDT)
Re: [AMBER] Is it necessary to cap the N and C terminal using ACE and NHE in tleap?
Carlos Simmerling
(Tue May 05 2015 - 03:19:01 PDT)
Re: [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)
[AMBER] forcefield for DNA
王珍
(Tue May 05 2015 - 01:52:23 PDT)
Re: [AMBER] forcefield for DNA
David A Case
(Tue May 05 2015 - 04:44:09 PDT)
Re: [AMBER] forcefield for DNA
王珍
(Tue May 05 2015 - 06:22:54 PDT)
Re: [AMBER] forcefield for DNA
Thomas C. Bishop
(Tue May 05 2015 - 06:37:48 PDT)
Re: [AMBER] forcefield for DNA
Christina Bergonzo
(Tue May 05 2015 - 06:53:40 PDT)
[AMBER] IRED
Sylvester Tumusiime
(Tue May 05 2015 - 08:40:05 PDT)
Re: [AMBER] IRED
Christina Bergonzo
(Tue May 05 2015 - 08:52:06 PDT)
Re: [AMBER] IRED
Sylvester Tumusiime
(Tue May 05 2015 - 09:12:36 PDT)
Re: [AMBER] IRED
Christina Bergonzo
(Tue May 05 2015 - 09:22:52 PDT)
Re: [AMBER] IRED
Sylvester Tumusiime
(Tue May 05 2015 - 09:49:44 PDT)
[AMBER] Computational Chemical Biology Conference - Abstract Deadline May 15th
Ross Walker
(Tue May 05 2015 - 10:32:34 PDT)
[AMBER] GPCR-MM_PBSA
Ramin Ekhteiari
(Tue May 05 2015 - 10:56:23 PDT)
[AMBER] GPCR-MM_PBSA
Ramin Ekhteiari
(Tue May 05 2015 - 10:59:41 PDT)
[AMBER] GPCR-MM_PBSA
Ramin Ekhteiari
(Tue May 05 2015 - 11:02:10 PDT)
Re: [AMBER] GPCR-MM_PBSA
Holger Gohlke
(Tue May 05 2015 - 11:55:15 PDT)
[AMBER] Atome type fatal error
Pierre Bertin
(Wed May 06 2015 - 01:20:34 PDT)
Re: [AMBER] Atome type fatal error
Hannes Loeffler
(Wed May 06 2015 - 01:28:18 PDT)
Re: [AMBER] Atome type fatal error
David A Case
(Wed May 06 2015 - 06:12:53 PDT)
Re: [AMBER] Atome type fatal error
Pierre Bertin
(Thu May 07 2015 - 12:52:19 PDT)
[AMBER] Query on how to simulate bulk no.of molecules in AMBER
srilaxmi reddy
(Wed May 06 2015 - 02:39:12 PDT)
Re: [AMBER] Query on how to simulate bulk no.of molecules in AMBER
Ashutosh Shandilya
(Wed May 06 2015 - 03:37:30 PDT)
Re: [AMBER] Query on how to simulate bulk no.of molecules in AMBER
Jason Swails
(Wed May 06 2015 - 06:15:07 PDT)
[AMBER] Error when compile ambertools15
amber amber
(Wed May 06 2015 - 04:32:24 PDT)
Re: [AMBER] Error when compile ambertools15
Jason Swails
(Wed May 06 2015 - 06:11:57 PDT)
[AMBER] CUDA compiling of Amber tools 14
anu chandra
(Wed May 06 2015 - 04:49:35 PDT)
Re: [AMBER] CUDA compiling of Amber tools 14
Jason Swails
(Wed May 06 2015 - 06:08:46 PDT)
Re: [AMBER] Nmode analysis calculation problem for Implicit simulation.
Bajarang Kumbhar
(Wed May 06 2015 - 07:25:38 PDT)
Re: [AMBER] Nmode analysis calculation problem for Implicit simulation.
David A Case
(Wed May 06 2015 - 08:25:52 PDT)
[AMBER] MMPBSA.py
Ramin Ekhteiari
(Wed May 06 2015 - 07:18:49 PDT)
Re: [AMBER] MMPBSA.py
David A Case
(Wed May 06 2015 - 08:16:45 PDT)
Re: [AMBER] MMPBSA.py
Ramin Ekhteiari
(Wed May 06 2015 - 11:14:02 PDT)
Re: [AMBER] MMPBSA.py
David A Case
(Wed May 06 2015 - 12:45:45 PDT)
Re: [AMBER] MMPBSA.py
Ramin Ekhteiari
(Wed May 06 2015 - 14:06:58 PDT)
Re: [AMBER] MMPBSA.py
Jason Swails
(Wed May 06 2015 - 18:46:52 PDT)
Re: [AMBER] MMPBSA.py
Ramin Ekhteiari
(Wed May 06 2015 - 23:32:34 PDT)
Re: [AMBER] MMPBSA.py
Jason Swails
(Thu May 07 2015 - 05:41:31 PDT)
Re: [AMBER] MMPBSA.py
Jason Swails
(Thu May 07 2015 - 06:12:52 PDT)
Re: [AMBER] MMPBSA.py
Ramin Ekhteiari
(Thu May 07 2015 - 10:02:14 PDT)
[AMBER] MCPB error
Takeshi Baba
(Fri May 08 2015 - 03:33:46 PDT)
Re: [AMBER] MCPB error
Pengfei Li
(Fri May 08 2015 - 07:32:51 PDT)
[AMBER] cpptraj checkoverlap
Aronica, Pietro
(Fri May 08 2015 - 09:12:36 PDT)
Re: [AMBER] cpptraj checkoverlap
Jason Swails
(Fri May 08 2015 - 09:28:26 PDT)
Re: [AMBER] cpptraj checkoverlap
Aronica, Pietro
(Fri May 08 2015 - 09:39:42 PDT)
Re: [AMBER] cpptraj checkoverlap
Daniel Roe
(Fri May 08 2015 - 09:51:00 PDT)
Re: [AMBER] cpptraj checkoverlap
Daniel Roe
(Fri May 08 2015 - 09:44:26 PDT)
Re: [AMBER] cpptraj checkoverlap
Daniel Roe
(Wed May 13 2015 - 14:51:51 PDT)
Re: [AMBER] MCPB error
Takeshi Baba
(Fri May 08 2015 - 23:54:26 PDT)
[AMBER] Trouble understanding DBSCAN clustering algorithm
Juan Eiros Zamora
(Wed May 06 2015 - 09:22:04 PDT)
Re: [AMBER] Trouble understanding DBSCAN clustering algorithm
Christina Bergonzo
(Wed May 06 2015 - 09:47:01 PDT)
Re: [AMBER] Trouble understanding DBSCAN clustering algorithm
Daniel Roe
(Wed May 06 2015 - 09:49:29 PDT)
Re: [AMBER] Trouble understanding DBSCAN clustering algorithm
Juan Eiros Zamora
(Thu May 07 2015 - 02:29:34 PDT)
Re: [AMBER] Trouble understanding DBSCAN clustering algorithm
Daniel Roe
(Thu May 07 2015 - 09:12:11 PDT)
Re: [AMBER] Trouble understanding DBSCAN clustering algorithm
Juan Eiros Zamora
(Fri May 08 2015 - 07:06:30 PDT)
Re: [AMBER] Trouble understanding DBSCAN clustering algorithm
Daniel Roe
(Fri May 08 2015 - 07:24:49 PDT)
[AMBER] Error with running ParmEd
Yinglong Miao
(Wed May 06 2015 - 09:42:31 PDT)
Re: [AMBER] Error with running ParmEd
Jason Swails
(Wed May 06 2015 - 18:59:27 PDT)
Re: [AMBER] Error with running ParmEd
Yinglong Miao
(Thu May 07 2015 - 09:58:25 PDT)
Re: [AMBER] Error with running ParmEd
Jason Swails
(Thu May 07 2015 - 12:16:44 PDT)
[AMBER] Replica-exchange molecular dynamics
新生大侠
(Wed May 06 2015 - 23:15:09 PDT)
Re: [AMBER] Replica-exchange molecular dynamics
Carlos Simmerling
(Thu May 07 2015 - 03:24:13 PDT)
[AMBER] leap: adding a residue to a unit
Hannes Loeffler
(Thu May 07 2015 - 02:24:41 PDT)
Re: [AMBER] leap: adding a residue to a unit
David A Case
(Fri May 08 2015 - 05:19:37 PDT)
[AMBER] CpHMD for Ser residue?
Michael Shokhen
(Thu May 07 2015 - 03:39:18 PDT)
Re: [AMBER] CpHMD for Ser residue?
Jason Swails
(Thu May 07 2015 - 04:17:29 PDT)
Re: [AMBER] CpHMD for Ser residue?
Carlos Simmerling
(Thu May 07 2015 - 04:19:48 PDT)
[AMBER] bad atom type: Ng (*.prmtop files from tleap)
Carlos Modenutti
(Thu May 07 2015 - 05:04:20 PDT)
Re: [AMBER] bad atom type: Ng (*.prmtop files from tleap)
Jason Swails
(Thu May 07 2015 - 06:49:24 PDT)
Re: [AMBER] bad atom type: Ng (*.prmtop files from tleap)
Daniel Roe
(Thu May 07 2015 - 09:17:31 PDT)
Re: [AMBER] bad atom type: Ng (*.prmtop files from tleap)
Carlos Modenutti
(Thu May 07 2015 - 09:55:37 PDT)
[AMBER] Error when compile ambertools15
amber amber
(Thu May 07 2015 - 05:11:43 PDT)
Re: [AMBER] Error when compile ambertools15
Jason Swails
(Thu May 07 2015 - 06:43:15 PDT)
Re: [AMBER] Error when compile ambertools15
Yu Chen
(Thu May 07 2015 - 14:14:03 PDT)
Re: [AMBER] Error when compile ambertools15
Jason Swails
(Thu May 07 2015 - 14:20:08 PDT)
Re: [AMBER] Error when compile ambertools15
Yu Chen
(Thu May 07 2015 - 18:21:46 PDT)
Re: [AMBER] Error when compile ambertools15
Jason Swails
(Fri May 08 2015 - 04:30:45 PDT)
[AMBER] query parameter files for mercuric ions
Ya Gao
(Thu May 07 2015 - 06:18:01 PDT)
Re: [AMBER] query parameter files for mercuric ions
Pengfei Li
(Thu May 07 2015 - 06:52:21 PDT)
[AMBER] box's information
Fatemeh Sadat Alavi
(Thu May 07 2015 - 06:45:44 PDT)
Re: [AMBER] box's information
Jason Swails
(Thu May 07 2015 - 07:23:27 PDT)
Re: [AMBER] box's information
Fatemeh Sadat Alavi
(Fri May 08 2015 - 00:42:57 PDT)
Re: [AMBER] box's information
Jason Swails
(Fri May 08 2015 - 04:34:20 PDT)
Re: [AMBER] box's information
David A Case
(Fri May 08 2015 - 05:07:49 PDT)
[AMBER] problem with prepgen in an organic molecule parameterization
Rebeca García Fandiño
(Thu May 07 2015 - 07:37:14 PDT)
Re: [AMBER] problem with prepgen in an organic molecule parameterization
Daniel Roe
(Thu May 07 2015 - 07:51:09 PDT)
Re: [AMBER] problem with prepgen in an organic molecule parameterization
Rebeca García Fandiño
(Thu May 07 2015 - 08:12:31 PDT)
Re: [AMBER] problem with prepgen in an organic molecule parameterization
Daniel Roe
(Thu May 07 2015 - 09:31:01 PDT)
Re: [AMBER] problem with prepgen in an organic molecule parameterization
Rebeca García Fandiño
(Thu May 07 2015 - 10:05:32 PDT)
Re: [AMBER] problem with prepgen in an organic molecule parameterization
Daniel Roe
(Thu May 07 2015 - 10:54:20 PDT)
Re: [AMBER] problem with prepgen in an organic molecule parameterization
Rebeca García Fandiño
(Fri May 08 2015 - 02:11:00 PDT)
[AMBER] Assistance required installing amber in cuda
Bala Subramani
(Thu May 07 2015 - 09:14:29 PDT)
Re: [AMBER] Assistance required installing amber in cuda
Daniel Roe
(Thu May 07 2015 - 09:33:05 PDT)
Re: [AMBER] Assistance required installing amber in cuda
Bala Subramani
(Thu May 07 2015 - 10:52:08 PDT)
Re: [AMBER] Assistance required installing amber in cuda
Bala Subramani
(Thu May 07 2015 - 10:54:14 PDT)
Re: [AMBER] Assistance required installing amber in cuda
Jason Swails
(Thu May 07 2015 - 12:15:02 PDT)
Re: [AMBER] MMPBSA problem with calcium
Francesco Gentile
(Thu May 07 2015 - 14:02:44 PDT)
[AMBER] Error when compile ambertools15
amber amber
(Fri May 08 2015 - 01:37:29 PDT)
[AMBER] Faulty_atom_connection error
nibedita jana
(Fri May 08 2015 - 03:06:02 PDT)
Re: [AMBER] Faulty_atom_connection error
David A Case
(Fri May 08 2015 - 05:03:38 PDT)
[AMBER] MMPBSA.py.MPI
George Tzotzos
(Fri May 08 2015 - 12:24:20 PDT)
Re: [AMBER] MMPBSA.py.MPI
Jason Swails
(Sat May 09 2015 - 05:02:31 PDT)
Re: [AMBER] MMPBSA.py.MPI
George Tzotzos
(Fri May 15 2015 - 13:22:18 PDT)
Re: [AMBER] MMPBSA.py.MPI
Jason Swails
(Fri May 15 2015 - 17:47:42 PDT)
Re: [AMBER] MMPBSA.py.MPI
George Tzotzos
(Sat May 16 2015 - 06:05:26 PDT)
Re: [AMBER] MMPBSA.py.MPI
Jason Swails
(Sat May 16 2015 - 09:30:17 PDT)
Re: [AMBER] MMPBSA.py.MPI
George Tzotzos
(Sat May 16 2015 - 11:31:56 PDT)
[AMBER] The output file about SMD
wjli
(Sat May 09 2015 - 06:24:05 PDT)
Re: [AMBER] The output file about SMD
Jason Swails
(Sat May 09 2015 - 08:37:57 PDT)
[AMBER] Problem with Configuring NetCDF
Alaa Mohye El-din Soliman
(Sat May 09 2015 - 06:42:18 PDT)
Re: [AMBER] Problem with Configuring NetCDF
Jason Swails
(Sat May 09 2015 - 07:25:08 PDT)
Re: [AMBER] Problem with Configuring NetCDF
Alaa Mohye El-din Soliman
(Sat May 09 2015 - 12:19:29 PDT)
Re: [AMBER] Problem with Configuring NetCDF
Jason Swails
(Sat May 09 2015 - 12:43:58 PDT)
Re: [AMBER] Problem with Configuring NetCDF
Alaa Mohye El-din Soliman
(Sun May 10 2015 - 16:05:22 PDT)
Re: [AMBER] Problem with Configuring NetCDF
Jason Swails
(Sun May 10 2015 - 17:18:44 PDT)
[AMBER] question regarding SMD simulation
Asmita Gupta
(Sat May 09 2015 - 07:38:39 PDT)
[AMBER] Selection of chain
muhammad tahir ayub
(Sat May 09 2015 - 11:54:01 PDT)
Re: [AMBER] Selection of chain
David A Case
(Sat May 09 2015 - 19:37:29 PDT)
[AMBER] Fwd: Selection of chain
muhammad tahir ayub
(Sun May 10 2015 - 07:57:03 PDT)
Re: [AMBER] Fwd: Selection of chain
Kenneth Huang
(Sun May 10 2015 - 08:47:58 PDT)
[AMBER] QM/MM Protein-Ligand interaction w/cofactor
William Martin
(Sat May 09 2015 - 12:35:30 PDT)
Re: [AMBER] QM/MM Protein-Ligand interaction w/cofactor
Gustavo Seabra
(Sat May 09 2015 - 13:04:03 PDT)
Re: [AMBER] QM/MM Protein-Ligand interaction w/cofactor
David A Case
(Sat May 09 2015 - 19:43:01 PDT)
Re: [AMBER] QM/MM Protein-Ligand interaction w/cofactor
William Martin
(Sat May 09 2015 - 22:27:30 PDT)
[AMBER] parameters for type: Cl-
Michael Shokhen
(Sun May 10 2015 - 11:08:20 PDT)
Re: [AMBER] parameters for type: Cl-
Kenneth Huang
(Sun May 10 2015 - 11:35:59 PDT)
Re: [AMBER] parameters for type: Cl-
Michael Shokhen
(Sun May 10 2015 - 11:57:49 PDT)
Re: [AMBER] parameters for type: Cl-
Marc van der Kamp
(Sun May 10 2015 - 12:28:04 PDT)
Re: [AMBER] parameters for type: Cl-
David A Case
(Sun May 10 2015 - 14:08:53 PDT)
[AMBER] Algorithms for integrating the equations of motion
gepaula.web.de
(Sun May 10 2015 - 16:15:40 PDT)
Re: [AMBER] Algorithms for integrating the equations of motion
Hai Nguyen
(Sun May 10 2015 - 16:37:10 PDT)
[AMBER] qmcut in Amber14 Manual
Robert Molt
(Sun May 10 2015 - 23:13:18 PDT)
Re: [AMBER] qmcut in Amber14 Manual
Marc van der Kamp
(Mon May 11 2015 - 01:43:32 PDT)
Re: [AMBER] qmcut in Amber14 Manual
Jason Swails
(Mon May 11 2015 - 05:05:52 PDT)
[AMBER] restart an SMD run
Asmita Gupta
(Sun May 10 2015 - 23:31:21 PDT)
Re: [AMBER] restart an SMD run
Jason Swails
(Mon May 11 2015 - 05:44:35 PDT)
Re: [AMBER] restart an SMD run
Asmita Gupta
(Tue May 12 2015 - 04:42:08 PDT)
Re: [AMBER] restart an SMD run
Jason Swails
(Tue May 12 2015 - 04:51:26 PDT)
Re: [AMBER] restart an SMD run
Asmita Gupta
(Tue May 12 2015 - 05:07:39 PDT)
Re: [AMBER] restart an SMD run
Jason Swails
(Tue May 12 2015 - 05:15:29 PDT)
[AMBER] Error while running tleap for protein-RNA complex
Shreeramesh
(Mon May 11 2015 - 01:59:30 PDT)
Re: [AMBER] Error while running tleap for protein-RNA complex
Hector A. Baldoni
(Mon May 11 2015 - 04:10:37 PDT)
Re: [AMBER] Error while running tleap for protein-RNA complex
David A Case
(Mon May 11 2015 - 04:55:17 PDT)
Re: [AMBER] Error while running tleap for protein-RNA complex
Shreeramesh
(Tue May 12 2015 - 02:48:47 PDT)
Re: [AMBER] Error while running tleap for protein-RNA complex
Jason Swails
(Tue May 12 2015 - 05:12:39 PDT)
[AMBER] principal component analysis
abdennour braka
(Mon May 11 2015 - 02:27:13 PDT)
Re: [AMBER] principal component analysis
Daniel Roe
(Mon May 11 2015 - 12:55:38 PDT)
[AMBER] AMD with restrained molecule.
Binwu Zhao
(Mon May 11 2015 - 11:09:21 PDT)
[AMBER] mmpbsa.py error
George Tzotzos
(Mon May 11 2015 - 11:52:04 PDT)
Re: [AMBER] mmpbsa.py error
Jason Swails
(Mon May 11 2015 - 12:00:11 PDT)
Re: [AMBER] mmpbsa.py error
George Tzotzos
(Mon May 11 2015 - 12:11:23 PDT)
[AMBER] parallel installation of ambertools14 on centOS-rocks system
Andrew Bostick
(Mon May 11 2015 - 12:17:29 PDT)
Re: [AMBER] parallel installation of ambertools14 on centOS-rocks system
Jason Swails
(Mon May 11 2015 - 12:31:52 PDT)
[AMBER] experimental coulomb and van der Waals cutoffs
Ahmet yıldırım
(Tue May 12 2015 - 01:52:16 PDT)
Re: [AMBER] experimental coulomb and van der Waals cutoffs
Carlos Simmerling
(Tue May 12 2015 - 03:28:06 PDT)
Re: [AMBER] experimental coulomb and van der Waals cutoffs
Ahmet yıldırım
(Tue May 12 2015 - 04:03:29 PDT)
Re: [AMBER] experimental coulomb and van der Waals cutoffs
Jason Swails
(Tue May 12 2015 - 05:03:13 PDT)
[AMBER] How to fix missing residues
Shreeramesh
(Tue May 12 2015 - 03:48:18 PDT)
Re: [AMBER] How to fix missing residues
Sajeewa Pemasinghe
(Tue May 12 2015 - 04:21:03 PDT)
[AMBER] mmpbsa.py: new error message
George Tzotzos
(Tue May 12 2015 - 07:15:46 PDT)
[AMBER] mmpbsa.py: new error message
Kenneth Huang
(Tue May 12 2015 - 07:27:38 PDT)
Re: [AMBER] mmpbsa.py: new error message
Jason Swails
(Tue May 12 2015 - 10:03:03 PDT)
Re: [AMBER] mmpbsa.py: new error message
George Tzotzos
(Tue May 12 2015 - 10:40:24 PDT)
Re: [AMBER] mmpbsa.py: new error message
Jason Swails
(Tue May 12 2015 - 10:58:13 PDT)
[AMBER] pmemd performance on GTX Titan Z
Kenneth Huang
(Tue May 12 2015 - 09:22:13 PDT)
Re: [AMBER] pmemd performance on GTX Titan Z
Ross Walker
(Tue May 12 2015 - 20:42:17 PDT)
[AMBER] pmemd performance on GTX Titan Z
Kenneth Huang
(Wed May 13 2015 - 18:05:29 PDT)
[AMBER] Atoms overlapped in vacuum minimization
anu chandra
(Wed May 13 2015 - 04:08:54 PDT)
Re: [AMBER] Atoms overlapped in vacuum minimization
Carlos Simmerling
(Wed May 13 2015 - 04:58:34 PDT)
Re: [AMBER] Atoms overlapped in vacuum minimization
David A Case
(Wed May 13 2015 - 05:53:35 PDT)
Re: [AMBER] Atoms overlapped in vacuum minimization
anu chandra
(Wed May 13 2015 - 06:21:31 PDT)
Re: [AMBER] Atoms overlapped in vacuum minimization
Carlos Simmerling
(Wed May 13 2015 - 07:08:50 PDT)
[AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
James Starlight
(Wed May 13 2015 - 06:55:04 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
Vlad Cojocaru
(Wed May 13 2015 - 07:04:36 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
James Starlight
(Wed May 13 2015 - 08:26:24 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
Vlad Cojocaru
(Wed May 13 2015 - 08:47:28 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
James Starlight
(Fri May 15 2015 - 04:30:32 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
James Starlight
(Mon May 18 2015 - 04:38:00 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
Vlad Cojocaru
(Mon May 18 2015 - 05:37:58 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
James Starlight
(Mon May 18 2015 - 06:15:03 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
Vlad Cojocaru
(Mon May 18 2015 - 06:53:51 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
James Starlight
(Mon May 18 2015 - 07:16:21 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
James Starlight
(Mon May 18 2015 - 07:23:53 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
Vlad Cojocaru
(Mon May 18 2015 - 07:31:54 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
Vlad Cojocaru
(Mon May 18 2015 - 07:57:12 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
James Starlight
(Mon May 18 2015 - 08:37:31 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
Vlad Cojocaru
(Mon May 18 2015 - 10:27:00 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
James Starlight
(Tue May 19 2015 - 05:23:11 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
James Starlight
(Tue May 19 2015 - 05:32:42 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
Vlad Cojocaru
(Tue May 19 2015 - 06:04:03 PDT)
Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py"
Vlad Cojocaru
(Mon May 18 2015 - 07:25:55 PDT)
[AMBER] Principal moments of inertia
Sylvester Tumusiime
(Wed May 13 2015 - 07:18:31 PDT)
Re: [AMBER] Principal moments of inertia
Daniel Roe
(Thu May 14 2015 - 06:49:38 PDT)
[AMBER] site down?
Gerald Monard
(Wed May 13 2015 - 08:00:58 PDT)
Re: [AMBER] site down?
Akash Deep Biswas
(Wed May 13 2015 - 08:10:36 PDT)
Re: [AMBER] site down?
Marc van der Kamp
(Wed May 13 2015 - 08:13:35 PDT)
Re: [AMBER] site down?
Gerald Monard
(Wed May 13 2015 - 08:19:39 PDT)
Re: [AMBER] site down?
Ross Walker
(Wed May 13 2015 - 08:23:43 PDT)
Re: [AMBER] site down?
Gerald Monard
(Wed May 13 2015 - 08:31:15 PDT)
Re: [AMBER] site down?
Jason Swails
(Wed May 13 2015 - 09:23:24 PDT)
Re: [AMBER] site down?
Jonathan Gough
(Wed May 13 2015 - 08:19:54 PDT)
Re: [AMBER] site down?
Ross Walker
(Wed May 13 2015 - 08:21:35 PDT)
Re: [AMBER] site down?
Wang Moye
(Wed May 13 2015 - 18:26:25 PDT)
Re: [AMBER] site down?
Gerald Monard
(Thu May 14 2015 - 05:11:28 PDT)
Re: [AMBER] site down?
David A Case
(Thu May 14 2015 - 04:57:38 PDT)
[AMBER] adp amber parameters
Carlos Romero
(Wed May 13 2015 - 08:36:44 PDT)
Re: [AMBER] adp amber parameters
David A Case
(Wed May 13 2015 - 10:09:14 PDT)
Re: [AMBER] adp amber parameters
Carlos Romero
(Wed May 13 2015 - 10:14:39 PDT)
[AMBER] error using the lipidorder command
Sylvester Tumusiime
(Wed May 13 2015 - 08:49:34 PDT)
Re: [AMBER] error using the lipidorder command
Daniel Roe
(Thu May 14 2015 - 06:51:46 PDT)
[AMBER] Amber website down
Crystal VanderZanden
(Wed May 13 2015 - 09:04:14 PDT)
Re: [AMBER] Amber website down
James Maier
(Wed May 13 2015 - 09:07:54 PDT)
Re: [AMBER] Amber website down
Wang Moye
(Wed May 13 2015 - 19:02:00 PDT)
[AMBER] DOPC lipid bilayer in Amber using lipid14 force field.
Him Shweta
(Wed May 13 2015 - 10:26:26 PDT)
Re: [AMBER] DOPC lipid bilayer in Amber using lipid14 force field.
Ross Walker
(Wed May 13 2015 - 11:03:23 PDT)
[AMBER] Question about lipid simulation
Victor Ma
(Wed May 13 2015 - 10:51:48 PDT)
Re: [AMBER] Question about lipid simulation
Ross Walker
(Wed May 13 2015 - 10:59:52 PDT)
[AMBER] ante-mmpbsa.py: troubleshooting
George Tzotzos
(Wed May 13 2015 - 11:26:36 PDT)
Re: [AMBER] ante-mmpbsa.py: troubleshooting
Jason Swails
(Wed May 13 2015 - 12:19:10 PDT)
Re: [AMBER] ante-mmpbsa.py: troubleshooting
George Tzotzos
(Wed May 13 2015 - 12:28:37 PDT)
Re: [AMBER] ante-mmpbsa.py: troubleshooting
Jason Swails
(Wed May 13 2015 - 12:41:26 PDT)
Re: [AMBER] ante-mmpbsa.py: troubleshooting
George Tzotzos
(Wed May 13 2015 - 13:33:15 PDT)
[AMBER] Error selecting compatible GPU all CUDA-capable devices are busy or unavailable
Jagga Soorma
(Wed May 13 2015 - 15:02:10 PDT)
Re: [AMBER] Error selecting compatible GPU all CUDA-capable devices are busy or unavailable
Jason Swails
(Thu May 14 2015 - 07:14:08 PDT)
[AMBER] Praise
Dr. Robert Molt Jr.
(Wed May 13 2015 - 15:10:11 PDT)
[AMBER] minimization error
Carlos Romero
(Thu May 14 2015 - 07:26:36 PDT)
Re: [AMBER] minimization error
Jason Swails
(Thu May 14 2015 - 10:16:44 PDT)
Re: [AMBER] minimization error
Carlos Romero
(Thu May 14 2015 - 11:32:20 PDT)
[AMBER] Warning when trying to get RMS
Mohammad Salem
(Thu May 14 2015 - 11:56:15 PDT)
Re: [AMBER] Warning when trying to get RMS
Daniel Roe
(Thu May 14 2015 - 12:14:49 PDT)
[AMBER] Announcement: GLYCAM/GLYCAM-Web mailing list
Lachele Foley
(Thu May 14 2015 - 15:25:33 PDT)
[AMBER] How to run GBSA in MD and binding energy calculation (MMPBSA.py)?
Huang
(Thu May 14 2015 - 20:46:35 PDT)
Re: [AMBER] How to run GBSA in MD and binding energy calculation (MMPBSA.py)?
Jason Swails
(Fri May 15 2015 - 02:07:51 PDT)
Re: [AMBER] How to run GBSA in MD and binding energy calculation (MMPBSA.py)?
Carlos Simmerling
(Fri May 15 2015 - 03:15:10 PDT)
[AMBER] Arsenic force field parametrization
Sushi Shilpa
(Fri May 15 2015 - 00:03:56 PDT)
Re: [AMBER] Arsenic force field parametrization
Andrew Schaub
(Sat May 16 2015 - 22:55:13 PDT)
Re: [AMBER] Arsenic force field parametrization
Pengfei Li
(Mon May 18 2015 - 14:18:14 PDT)
Re: [AMBER] Arsenic force field parametrization
Pengfei Li
(Wed May 27 2015 - 08:28:07 PDT)
Re: [AMBER] Arsenic force field parametrization
Jason Swails
(Wed May 27 2015 - 08:47:08 PDT)
Re: [AMBER] Arsenic force field parametrization
Pengfei Li
(Fri May 29 2015 - 12:31:38 PDT)
[AMBER] ESURF in MMPBSA.py results
Huang
(Fri May 15 2015 - 01:26:22 PDT)
Re: [AMBER] ESURF in MMPBSA.py results
Jason Swails
(Fri May 15 2015 - 02:15:40 PDT)
[AMBER] the energy between two ligand molecules
chemjxn
(Fri May 15 2015 - 02:10:02 PDT)
Re: [AMBER] the energy between two ligand molecules
Jason Swails
(Fri May 15 2015 - 02:18:54 PDT)
[AMBER] Biligand, trimetal subtrate simulation
Julio Dominguez
(Fri May 15 2015 - 12:47:23 PDT)
[AMBER] disable minimization in nmode MMPBSA.py
Carlos Modenutti
(Fri May 15 2015 - 14:02:22 PDT)
Re: [AMBER] disable minimization in nmode MMPBSA.py
Jason Swails
(Fri May 15 2015 - 15:07:03 PDT)
[AMBER] Help needed on MMPBSA for a system with different protonation states in free & bound forms, using multiple trajectory protocol
Shailesh Pandey
(Sat May 16 2015 - 04:18:42 PDT)
Re: [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)
[AMBER] Regarding - "Help needed on MMPBSA for a system with different protonation states in free & bound forms"
Shailesh Pandey
(Sun May 17 2015 - 03:05:28 PDT)
Re: [AMBER] Regarding - "Help needed on MMPBSA for a system with different protonation states in free & bound forms"
Jason Swails
(Mon May 18 2015 - 06:06:59 PDT)
Re: [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)
[AMBER] Polymorphism study using Amber
jacob wick
(Sun May 17 2015 - 23:53:29 PDT)
Re: [AMBER] Polymorphism study using Amber
David A Case
(Mon May 18 2015 - 05:10:03 PDT)
[AMBER] Changing two conditions simultaneously in pmemd
Juan Eiros Zamora
(Mon May 18 2015 - 05:06:56 PDT)
Re: [AMBER] Changing two conditions simultaneously in pmemd
Hannes Loeffler
(Mon May 18 2015 - 05:13:10 PDT)
Re: [AMBER] Changing two conditions simultaneously in pmemd
Juan Eiros Zamora
(Mon May 18 2015 - 06:37:13 PDT)
Re: [AMBER] Changing two conditions simultaneously in pmemd
Hannes Loeffler
(Mon May 18 2015 - 06:55:01 PDT)
Re: [AMBER] Changing two conditions simultaneously in pmemd
Vlad Cojocaru
(Mon May 18 2015 - 06:56:11 PDT)
Re: [AMBER] Changing two conditions simultaneously in pmemd
Vlad Cojocaru
(Mon May 18 2015 - 07:00:48 PDT)
Re: [AMBER] Changing two conditions simultaneously in pmemd
Juan Eiros Zamora
(Mon May 18 2015 - 07:13:14 PDT)
Re: [AMBER] Changing two conditions simultaneously in pmemd
Hannes Loeffler
(Mon May 18 2015 - 07:18:38 PDT)
Re: [AMBER] Changing two conditions simultaneously in pmemd
Jason Swails
(Mon May 18 2015 - 07:29:16 PDT)
Re: [AMBER] Changing two conditions simultaneously in pmemd
Vlad Cojocaru
(Mon May 18 2015 - 07:39:24 PDT)
Re: [AMBER] Changing two conditions simultaneously in pmemd
Ross Walker
(Mon May 18 2015 - 09:07:07 PDT)
Re: [AMBER] Changing two conditions simultaneously in pmemd
Vlad Cojocaru
(Mon May 18 2015 - 10:30:00 PDT)
Re: [AMBER] Changing two conditions simultaneously in pmemd
Christina Bergonzo
(Mon May 18 2015 - 08:05:09 PDT)
Re: [AMBER] Changing two conditions simultaneously in pmemd
Hannes Loeffler
(Mon May 18 2015 - 08:44:28 PDT)
[AMBER] WEBSITE not opening
Elvis Martis
(Mon May 18 2015 - 05:57:30 PDT)
Re: [AMBER] WEBSITE not opening
Jason Swails
(Mon May 18 2015 - 06:00:03 PDT)
Re: [AMBER] WEBSITE not opening
Elvis Martis
(Mon May 18 2015 - 20:06:08 PDT)
Re: [AMBER] WEBSITE not opening
Ross Walker
(Mon May 18 2015 - 20:18:05 PDT)
Re: [AMBER] DNS manipulations
David A Case
(Tue May 19 2015 - 05:06:00 PDT)
Re: [AMBER] DNS manipulations
Ross Walker
(Tue May 19 2015 - 10:10:31 PDT)
Re: [AMBER] DNS manipulations
Bill Ross
(Tue May 19 2015 - 17:19:21 PDT)
Re: [AMBER] WEBSITE not opening
Ye Mei
(Mon May 18 2015 - 20:46:08 PDT)
Re: [AMBER] WEBSITE not opening
Elvis Martis
(Tue May 19 2015 - 20:12:05 PDT)
[AMBER] Problem with amb2gmx in AmberTools 15
Soumendranath Bhakat
(Tue May 19 2015 - 04:01:50 PDT)
Re: [AMBER] Problem with amb2gmx in AmberTools 15
David A Case
(Tue May 19 2015 - 05:03:30 PDT)
Re: [AMBER] Problem with amb2gmx in AmberTools 15
Soumendranath Bhakat
(Wed May 20 2015 - 02:52:02 PDT)
Re: [AMBER] Problem with amb2gmx in AmberTools 15
Hannes Loeffler
(Wed May 20 2015 - 03:04:46 PDT)
Re: [AMBER] Problem with amb2gmx in AmberTools 15
Soumendranath Bhakat
(Wed May 20 2015 - 03:13:11 PDT)
Re: [AMBER] Problem with amb2gmx in AmberTools 15
Soumendranath Bhakat
(Wed May 20 2015 - 03:15:18 PDT)
Re: [AMBER] Problem with amb2gmx in AmberTools 15
Hannes Loeffler
(Wed May 20 2015 - 03:25:25 PDT)
Re: [AMBER] Problem with amb2gmx in AmberTools 15
David A Case
(Wed May 20 2015 - 04:33:46 PDT)
Re: [AMBER] Problem with amb2gmx in AmberTools 15
Soumendranath Bhakat
(Wed May 20 2015 - 05:14:10 PDT)
Re: [AMBER] Problem with amb2gmx in AmberTools 15
Soumendranath Bhakat
(Wed May 20 2015 - 09:45:13 PDT)
[AMBER] Sander QMMM Bomb Problem
Gulsevin,Alican
(Thu May 14 2015 - 12:56:59 PDT)
Re: [AMBER] Sander QMMM Bomb Problem
Gustavo Seabra
(Tue May 19 2015 - 10:13:42 PDT)
[AMBER] Computational Chemical Biology Conference - TALK DEADLINE EXTENDED
Ross Walker
(Tue May 19 2015 - 09:46:43 PDT)
[AMBER] MCPB.py issues
David Poole
(Tue May 19 2015 - 10:46:15 PDT)
Re: [AMBER] MCPB.py issues
David A Case
(Wed May 20 2015 - 04:48:18 PDT)
Re: [AMBER] MCPB.py issues
Pengfei Li
(Wed May 20 2015 - 07:24:02 PDT)
Re: [AMBER] MCPB.py issues
David Poole
(Fri May 22 2015 - 17:11:08 PDT)
Re: [AMBER] MCPB.py issues
Pengfei Li
(Tue May 26 2015 - 09:30:06 PDT)
[AMBER] Computational Chemical Biology Conference - Abstract Deadline Extended to June 1st
Ross Walker
(Tue May 19 2015 - 13:00:14 PDT)
[AMBER] problems with "explicit solvent"
Investigador Química
(Tue May 19 2015 - 17:20:16 PDT)
Re: [AMBER] problems with "explicit solvent"
David A Case
(Tue May 19 2015 - 18:19:17 PDT)
[AMBER] MC-simulation-MM-PBSA
Ramin Ekhteiari
(Tue May 19 2015 - 23:51:30 PDT)
[AMBER] MMGBSA: interpretation of results
George Tzotzos
(Wed May 20 2015 - 05:09:19 PDT)
Re: [AMBER] MMGBSA: interpretation of results
George Tzotzos
(Wed May 20 2015 - 11:37:02 PDT)
Re: [AMBER] MMGBSA: interpretation of results
Kenneth Huang
(Wed May 20 2015 - 12:13:13 PDT)
[AMBER] Amber12 + GTX 980
Robinson, Roger
(Wed May 20 2015 - 06:09:54 PDT)
[AMBER] Amber 12 + GTX 980
Robinson, Roger
(Wed May 20 2015 - 06:14:03 PDT)
Re: [AMBER] Amber 12 + GTX 980
Ross Walker
(Wed May 20 2015 - 09:13:18 PDT)
Re: [AMBER] Amber 12 + GTX 980
Robinson, Roger
(Wed May 20 2015 - 23:31:44 PDT)
Re: [AMBER] Amber 12 + GTX 980
Scott Le Grand
(Thu May 21 2015 - 15:29:45 PDT)
[AMBER] AMBERHOME environment variable setting problem
Gustavo Avelar Molina
(Wed May 20 2015 - 08:15:16 PDT)
Re: [AMBER] AMBERHOME environment variable setting problem
Jason Swails
(Wed May 20 2015 - 08:20:37 PDT)
Re: [AMBER] AMBERHOME environment variable setting problem
MOHD HOMAIDUR RAHMAN
(Wed May 20 2015 - 10:25:24 PDT)
[AMBER] Bad Contact from lack of QM/MM Heating?
Dr. Robert Molt Jr.
(Wed May 20 2015 - 20:43:07 PDT)
[AMBER] MC-MM-PBSA
Ramin Ekhteiari
(Wed May 20 2015 - 22:46:09 PDT)
Re: [AMBER] MC-MM-PBSA
Jason Swails
(Thu May 21 2015 - 05:37:53 PDT)
[AMBER] Question about Extra Point
zhouhaibin2008.ok
(Fri May 22 2015 - 00:14:07 PDT)
Re: [AMBER] Question about Extra Point
David A Case
(Fri May 22 2015 - 04:47:16 PDT)
[AMBER] Regarding AMD simulation
Aditya Sarkar
(Fri May 22 2015 - 04:08:44 PDT)
Re: [AMBER] Regarding AMD simulation
Daniel Roe
(Fri May 22 2015 - 07:27:24 PDT)
[AMBER] Does GLYCAM only can deal with Oligosaccharides or Polysaccharides BUT NOT Monosaccharide？？？
Chris
(Fri May 22 2015 - 07:02:18 PDT)
Re: [AMBER] Does GLYCAM only can deal with Oligosaccharides or Polysaccharides BUT NOT Monosaccharide？？？
Lachele Foley
(Fri May 22 2015 - 09:55:14 PDT)
[AMBER] Developing Parameters using tleap
Brittany Boykin
(Fri May 22 2015 - 12:44:55 PDT)
Re: [AMBER] Developing Parameters using tleap
David A Case
(Sat May 23 2015 - 09:29:33 PDT)
[AMBER] Determining number of molecules from a point by integration using xmgrace
Sylvester Tumusiime
(Fri May 22 2015 - 12:48:26 PDT)
Re: [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)
[AMBER] Regarding high temp simulation of DNA and amber MD module
MOHD HOMAIDUR RAHMAN
(Fri May 22 2015 - 14:23:29 PDT)
Re: [AMBER] Regarding high temp simulation of DNA and amber MD module
Carlos Simmerling
(Sat May 23 2015 - 02:33:58 PDT)
Re: [AMBER] Regarding high temp simulation of DNA and amber MD module
David A Case
(Sat May 23 2015 - 09:38:54 PDT)
[AMBER] Problem with covalently bonded ligand parametrization
Gustavo Avelar Molina
(Fri May 22 2015 - 19:07:43 PDT)
Re: [AMBER] Problem with covalently bonded ligand parametrization
David A Case
(Sat May 23 2015 - 09:45:27 PDT)
Re: [AMBER] Problem with covalently bonded ligand parametrization
Gustavo Avelar Molina
(Sat May 23 2015 - 16:59:03 PDT)
[AMBER] tleap maintainer
Matt Harvey
(Sat May 23 2015 - 05:13:29 PDT)
Re: [AMBER] tleap maintainer
David A Case
(Sat May 23 2015 - 09:48:44 PDT)
[AMBER] Doubt about ligand binding in proteins
Gustavo Avelar Molina
(Sat May 23 2015 - 18:05:28 PDT)
Re: [AMBER] Doubt about ligand binding in proteins
Kenneth Huang
(Sun May 24 2015 - 10:51:22 PDT)
[AMBER] cpptraj: lie
George Tzotzos
(Sun May 24 2015 - 04:18:49 PDT)
Re: [AMBER] cpptraj: lie
Jason Swails
(Sun May 24 2015 - 08:31:46 PDT)
Re: [AMBER] cpptraj: lie
Daniel Roe
(Sun May 24 2015 - 10:30:53 PDT)
[AMBER] NTX Keyword
Robert Molt
(Sun May 24 2015 - 10:10:23 PDT)
Re: [AMBER] NTX Keyword
Kenneth Huang
(Sun May 24 2015 - 11:13:35 PDT)
Re: [AMBER] NTX Keyword
Jason Swails
(Sun May 24 2015 - 15:38:01 PDT)
[AMBER] help me to understand using GLYCAM!!!
Chris
(Mon May 25 2015 - 06:52:37 PDT)
Re: [AMBER] help me to understand using GLYCAM!!!
Lachele Foley
(Mon May 25 2015 - 18:02:55 PDT)
Re: [AMBER] help me to understand using GLYCAM!!!
Chris
(Mon May 25 2015 - 19:22:39 PDT)
Re: [AMBER] help me to understand using GLYCAM!!!
David A Case
(Tue May 26 2015 - 04:35:48 PDT)
Re: [AMBER] help me to understand using GLYCAM!!!
Lachele Foley
(Tue May 26 2015 - 10:25:28 PDT)
[AMBER] Extracting temperature-based potential energies from REMD
Lee-Ping Wang
(Mon May 25 2015 - 09:44:10 PDT)
Re: [AMBER] Extracting temperature-based potential energies from REMD
Jason Swails
(Mon May 25 2015 - 12:12:03 PDT)
Re: [AMBER] Extracting temperature-based potential energies from REMD
Lee-Ping Wang
(Mon May 25 2015 - 13:43:32 PDT)
Re: [AMBER] Extracting temperature-based potential energies from REMD
Hai Nguyen
(Mon May 25 2015 - 18:29:07 PDT)
Re: [AMBER] Extracting temperature-based potential energies from REMD
Lee-Ping Wang
(Mon May 25 2015 - 20:04:55 PDT)
Re: [AMBER] Extracting temperature-based potential energies from REMD
Lee-Ping Wang
(Sun May 31 2015 - 05:09:00 PDT)
Re: [AMBER] Extracting temperature-based potential energies from REMD
Hai Nguyen
(Sun May 31 2015 - 06:02:35 PDT)
[AMBER] Protein-Membrane assembly
Ofir Tal
(Tue May 26 2015 - 00:44:01 PDT)
[AMBER] partition error in shake
Evgenia Dueva
(Tue May 26 2015 - 06:37:44 PDT)
Re: [AMBER] partition error in shake
David A Case
(Tue May 26 2015 - 08:11:50 PDT)
[AMBER] MMGBSA: pairwise decomposition
George Tzotzos
(Tue May 26 2015 - 10:53:39 PDT)
Re: [AMBER] MMGBSA: pairwise decomposition
Jason Swails
(Tue May 26 2015 - 12:19:58 PDT)
[AMBER] membrane protein simulation
Victor Ma
(Tue May 26 2015 - 14:13:48 PDT)
Re: [AMBER] membrane protein simulation
Ross Walker
(Tue May 26 2015 - 18:16:22 PDT)
Re: [AMBER] membrane protein simulation
Victor Ma
(Wed May 27 2015 - 08:35:53 PDT)
Re: [AMBER] membrane protein simulation
Ross Walker
(Wed May 27 2015 - 08:43:34 PDT)
Re: [AMBER] membrane protein simulation
Victor Ma
(Wed May 27 2015 - 09:55:06 PDT)
[AMBER] Next AMBER release?
Mohd Farid Ismail
(Tue May 26 2015 - 17:20:35 PDT)
Re: [AMBER] Next AMBER release?
Ross Walker
(Tue May 26 2015 - 18:18:26 PDT)
[AMBER] RNA unfolding studies..
Asmita Gupta
(Wed May 27 2015 - 03:54:40 PDT)
Re: [AMBER] RNA unfolding studies..
David A Case
(Wed May 27 2015 - 05:14:49 PDT)
[AMBER] loading molecule in leap
jacob wick
(Wed May 27 2015 - 04:23:46 PDT)
Re: [AMBER] loading molecule in leap
David A Case
(Wed May 27 2015 - 05:30:15 PDT)
[AMBER] WARNING: SGFT, instead of TEMPSG, should be set for SGMDfp/SGLDfp!
barbara rossi
(Wed May 27 2015 - 06:22:22 PDT)
[AMBER] Fwd: Using the CHARMM force field to run simulations with AMBER
Shalini Gupta
(Wed May 27 2015 - 12:22:13 PDT)
Re: [AMBER] Fwd: Using the CHARMM force field to run simulations with AMBER
Jason Swails
(Wed May 27 2015 - 13:50:46 PDT)
Re: [AMBER] Fwd: Using the CHARMM force field to run simulations with AMBER
Brian Radak
(Wed May 27 2015 - 14:27:58 PDT)
Re: [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)
[AMBER] Bug in LIE action command of cpptraj?
Samuel Bowerman
(Wed May 27 2015 - 12:25:27 PDT)
Re: [AMBER] Bug in LIE action command of cpptraj?
Jason Swails
(Wed May 27 2015 - 12:34:20 PDT)
Re: [AMBER] Bug in LIE action command of cpptraj?
Samuel Bowerman
(Wed May 27 2015 - 13:07:21 PDT)
Re: [AMBER] Bug in LIE action command of cpptraj?
Jason Swails
(Wed May 27 2015 - 13:44:30 PDT)
Re: [AMBER] Bug in LIE action command of cpptraj?
Samuel Bowerman
(Wed May 27 2015 - 14:49:54 PDT)
[AMBER] AMBER 15 ERROR
汪盛
(Wed May 27 2015 - 20:45:23 PDT)
Re: [AMBER] AMBER 15 ERROR
Hai Nguyen
(Wed May 27 2015 - 21:24:29 PDT)
Re: [AMBER] AMBER 15 ERROR
Ye Mei
(Wed May 27 2015 - 22:04:56 PDT)
[AMBER] Torsion restraints with pmemd.amoeba
Karl Debiec
(Thu May 28 2015 - 09:17:07 PDT)
Re: [AMBER] Torsion restraints with pmemd.amoeba
David A Case
(Thu May 28 2015 - 09:44:35 PDT)
[AMBER] mmpbsa.py.MPI: patching
George Tzotzos
(Thu May 28 2015 - 11:33:11 PDT)
Re: [AMBER] mmpbsa.py.MPI: patching
Kenneth Huang
(Thu May 28 2015 - 11:55:09 PDT)
[AMBER] MMPBSA.py API AttributeError: 'MMPBSA_App' object has no attribute ‘using_chamber'
D.J. Pattinson
(Fri May 29 2015 - 03:46:44 PDT)
Re: [AMBER] MMPBSA.py API AttributeError: 'MMPBSA_App' object has no attribute ‘using_chamber'
Jason Swails
(Fri May 29 2015 - 06:28:27 PDT)
Re: [AMBER] MMPBSA.py API AttributeError: 'MMPBSA_App' object has no attribute ‘using_chamber'
D.J. Pattinson
(Fri May 29 2015 - 06:58:08 PDT)
[AMBER] Ambertools 12 Download
xy21hb
(Fri May 29 2015 - 06:43:06 PDT)
Re: [AMBER] Ambertools 12 Download
Jason Swails
(Fri May 29 2015 - 06:45:47 PDT)
Re: [AMBER] Ambertools 12 Download
Jason Swails
(Fri May 29 2015 - 06:46:34 PDT)
Re: [AMBER] Ambertools 12 Download
xy21hb
(Fri May 29 2015 - 06:53:57 PDT)
Re: [AMBER] Ambertools 12 Download
Jason Swails
(Fri May 29 2015 - 07:13:15 PDT)
[AMBER] Umbrella Sampling and wham
MOHD HOMAIDUR RAHMAN
(Fri May 29 2015 - 07:46:58 PDT)
Re: [AMBER] Umbrella Sampling and wham
Brian Radak
(Sat May 30 2015 - 11:13:37 PDT)
[AMBER] Fwd: MPI Runtime Error
Kusum Mehla
(Fri May 29 2015 - 21:38:42 PDT)
Re: [AMBER] Fwd: MPI Runtime Error
David A Case
(Sat May 30 2015 - 09:18:40 PDT)
[AMBER] water bridges
Hector A. Baldoni
(Sat May 30 2015 - 09:43:48 PDT)
Re: [AMBER] water bridges
Sylvester Tumusiime
(Sat May 30 2015 - 14:44:31 PDT)
Last message date
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Sun May 31 2015 - 06:30:02 PDT
Archived on
: Fri Apr 19 2024 - 05:54:56 PDT
454 messages
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