Amber Archive Jan 2009: by date

Thursday, 1 January 2009
- AMBER: energy jumps during molecule minimization Paul Ledbetter
Friday, 2 January 2009
- Re: AMBER: energy jumps during molecule minimization David A. Case
- Re: AMBER: SMD-related questions Gustavo Seabra
- Re: AMBER: RMS plot Carlos Simmerling
- Re: AMBER: a question about ff03ua oguz gurbulak
- AMBER: apparent error in closest function in ptraj 10 Roman Osman
- Re: AMBER: apparent error in closest function in ptraj 10 D.J. Cole
- Re: AMBER: a question about ff03ua David A. Case
- Re: AMBER: apparent error in closest function in ptraj 10 Roman Osman
- Re: AMBER: a question about ff03ua FyD
Saturday, 3 January 2009
- AMBER: Dielectric constant musa özboyacı
- AMBER: IMPORTANT INFORMATION: Notice regarding transition of AMBER mailing list to new address. Ross Walker
Sunday, 4 January 2009
- AMBER: CHCl3 solvent box WJ Ding
- AMBER: reg sander crashing on more than 32 cores over IB Amit Bajaj
Monday, 5 January 2009
- Re: AMBER: reg sander crashing on more than 32 cores over IB David A. Case
- Re: AMBER: CHCl3 solvent box David A. Case
- AMBER: bug of the mm_pbsa module in ambertools 1.2 Ye Mei
- Re: AMBER: CHCl3 solvent box WJ Ding
- AMBER: ligand parameter Bo Baker
- RE: AMBER: ligand parameter Ross Walker
- AMBER: error in amber 10 archana sonawani
Tuesday, 6 January 2009
- AMBER: questions about equilibram wei zhang
- Re: AMBER: error in amber 10 David A. Case
- Re: AMBER: error in amber 10 David A. Case
- AMBER: Re: nmode error: bad nonbon (amber 10) Jeremy Harris
- Re: AMBER: Re: nmode error: bad nonbon (amber 10) David A. Case
- AMBER: install amber10 wl2290.columbia.edu
- AMBER: problem with ptraj image command in Amber 10? Ryan Pavlovicz
- Re: AMBER: problem with ptraj image command in Amber 10? Carlos Simmerling
- Re: AMBER: bug of the mm_pbsa module in ambertools 1.2 Scott Brozell
- AMBER: xleap problem Bala subramanian
- Re: AMBER: xleap problem Carlos Simmerling
- Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) Scott Brozell
- Re: AMBER: install amber10 Scott Brozell
- RE: AMBER: RMS plot Duggan, Brendan M.
- Re: AMBER: RMS plot Carlos Simmerling
- AMBER: IMPORTANT Information regarding AMBER Mailing List - please read. Ross Walker
- Re: AMBER: xleap problem Bala subramanian
- AMBER: mail list Mark M Huntress
- [AMBER] amber.ambermd.org open for business Ross Walker
- [AMBER] RE: AMBER: mail list Ross Walker
- [AMBER] TEST Message - please ignore. Ross Walker
- Re: [AMBER] RE: AMBER: mail list James W. Caldwell
- [AMBER] RE: AMBER: xleap problem Ross Walker
- [AMBER] Re: AMBER: ligand parameter Bo Baker
- RE: [AMBER] Re: AMBER: ligand parameter Ross Walker
- Re: [AMBER] Re: AMBER: ligand parameter Bo Baker
Wednesday, 7 January 2009
- Re: [AMBER] RE: AMBER: xleap problem Bala subramanian
- [AMBER] Re: AMBER: questions about equilibram David A. Case
- Re: [AMBER] RE: AMBER: xleap problem David A. Case
- Re: [AMBER] Re: AMBER: ligand parameter David A. Case
- Re: [AMBER] RE: AMBER: xleap problem Bala subramanian
- [AMBER] AMBER: Problems in solvation with xleap vallespardojl.chem.leidenuniv.nl
- Re: [AMBER] RE: AMBER: xleap problem David A. Case
- [AMBER] MD Beale, John
- [AMBER] four prepin/frcmod files be read simultaneously by leap Yi Mao
- Re: [AMBER] RE: AMBER: xleap problem Bala subramanian
- [AMBER] PBSA: PB bomb in pb_setgrd() Larry Layne
- Re: [AMBER] RE: AMBER: mail list M. L. Dodson
- Re: [AMBER] four prepin/frcmod files be read simultaneously by leap rpaduri.chem.wayne.edu
- Re: [AMBER] four prepin/frcmod files be read simultaneously by leap Yi Mao
- [AMBER] RE: RE: amber force filed for RNA Ross Walker
- [AMBER] RE: same result Ross Walker
- [AMBER] Amber Parameters for Iron Heme covalently boud to carbon monoxide Osmar Norberto de Souza
- RE: [AMBER] PBSA: PB bomb in pb_setgrd() Ray Luo
- Re: [AMBER] four prepin/frcmod files be read simultaneously by leap David A. Case
- [AMBER] PHOSPHOTHREONINE Khaled Barakat
- Re: [AMBER] PHOSPHOTHREONINE David A. Case
- RE: [AMBER] MD Ross Walker
- [AMBER] Using GAFF with a covalently bound ligand or label Sale, Kenneth L
- Re: [AMBER] Re: AMBER: ligand parameter Bo Baker
- Re: [AMBER] Using GAFF with a covalently bound ligand or label David A. Case
- [AMBER] Non-planarity of amide atoms after optimization Sanghwa Han
- RE: [AMBER] Re: AMBER: ligand parameter Ross Walker
Thursday, 8 January 2009
- Re: [AMBER] RE: same result zgong.hust
- [AMBER] how many processors for parallel test michael
- Re: [AMBER] how many processors for parallel test David A. Case
- Re: [AMBER] how many processors for parallel test michael bane
- Re: [AMBER] how many processors for parallel test David A. Case
- Re: [AMBER] how many processors for parallel test michael bane
- [AMBER] Can we use Amber? Casey,Richard
- [AMBER] Can we use AMBER? Casey,Richard
- [AMBER] mairun wl2290.columbia.edu
- [AMBER] lone pairs on CYX and MET Beale, John
- RE: [AMBER] lone pairs on CYX and MET Ross Walker
- RE: [AMBER] mairun Ross Walker
- [AMBER] Need help with point to plane distance calculation in nab M. L. Dodson
- RE: [AMBER] Can we use AMBER? Ross Walker
- Re: [AMBER] Need help with point to plane distance calculation in nab IN SUK JOUNG
- Re: [AMBER] Need help with point to plane distance calculation in nab M. L. Dodson
- Re: [AMBER] Need help with point to plane distance calculation in nab IN SUK JOUNG
- Re: [AMBER] Need help with point to plane distance calculation in nab M. L. Dodson
- RE: [AMBER] mairun wl2290.columbia.edu
- RE: [AMBER] mairun Ross Walker
- RE: [AMBER] mairun wl2290.columbia.edu
- RE: [AMBER] mpirun Ross Walker
- [AMBER] force-field for cyclic oligosaccharide using leap Madhurima Jana
Friday, 9 January 2009
- [AMBER] NAB entropy calcualtion chaitanya koppisetty
- Re: [AMBER] NAB entropy calcualtion Andreas Svrcek-Seiler
- [AMBER] ambpdb is changing atom names, a feature or bug? Markus Kaukonen
- Re: [AMBER] ambpdb is changing atom names, a feature or bug? David A. Case
- Re: [AMBER] NAB entropy calcualtion David A. Case
- [AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai
- Re: [AMBER] problem building AmberTools/sleap on AIX Wei Zhang
- Re: [AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai
- [AMBER] "bad atom type" Akansha Saxena
- Re: [AMBER] problem building AmberTools/sleap on AIX Bill Ross
- Re: [AMBER] ambpdb is changing atom names, a feature or bug? Bill Ross
- Re: [AMBER] ambpdb is changing atom names, a feature or bug? David A. Case
- [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba
- Re: [AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai
- Re: [AMBER] problem building AmberTools/sleap on AIX Wei Zhang
- [AMBER] implicit and explicit simulation: salt effect Catein Catherine
- [AMBER] mm-GBSA from implicit Catein Catherine
- Re: [AMBER] implicit and explicit simulation: salt effect David Watson
- Re: [AMBER] implicit and explicit simulation: salt effect David LeBard
Saturday, 10 January 2009
- Re: Re: [AMBER] ambpdb is changing atom names, a feature or bug? Ye Mei
- Re: [AMBER] number-of-EPS-exceeds-MAXESP FyD
- [AMBER] Off topic. Hardware problem Francesco Pietra
- Re: [AMBER] mm-GBSA from implicit Carlos Simmerling
- Re: [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba
- Re: Re: [AMBER] ambpdb is changing atom names, a feature or bug? David A. Case
- Re: [AMBER] implicit and explicit simulation: salt effect David A. Case
- Re: [AMBER] implicit and explicit simulation: salt effect David A. Case
- Re: [AMBER] number-of-EPS-exceeds-MAXESP FyD
Sunday, 11 January 2009
- Re: [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba
- Re: [AMBER] Re: AMBER: ligand parameter Bo Baker
- Re: [AMBER] Re: AMBER: ligand parameter David Watson
- Re: [AMBER] Re: AMBER: ligand parameter Bo Baker
- Re: [AMBER] Re: AMBER: ligand parameter Yu Chen
- [AMBER] force-field for cyclic oligosaccharide using leap Madhurima Jana
- [AMBER] Can't reproduce RESP charges Sanghwa Han
- [AMBER] Amber 9 installation problem on Ubuntu drugdesign
- Re: [AMBER] number-of-EPS-exceeds-MAXESP FyD
- Re: [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba
Monday, 12 January 2009
- Re: [AMBER] Amber 9 installation problem on Ubuntu David A. Case
- [AMBER] Release of the R.E.D.-III.1 tools FyD
- Re: [AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai
- [AMBER] Parallelepiped periodic box Ian Streeter
- [AMBER] Writing out trajectory in NAB xxxzzzyyy xxxzzzyyy
- Re: [AMBER] Writing out trajectory in NAB David A. Case
- [AMBER] crystal waters Carmen Domene
- Re: [AMBER] crystal waters steinbrt.rci.rutgers.edu
- Re: [AMBER] crystal waters Carmen Domene
- Re: [AMBER] crystal waters steinbrt.rci.rutgers.edu
- [AMBER] multisander error Justine Condo
- Re: [AMBER] multisander error David Watson
- RE: [AMBER] multisander error Ross Walker
- Re: [AMBER] multisander error Justine Condo
- Re: [AMBER] multisander error Justine Condo
- RE: [AMBER] multisander error Ross Walker
- Re: [AMBER] multisander error Justine Condo
Tuesday, 13 January 2009
- [AMBER] error in sander (Amber10) archana sonawani
- [AMBER] errorin sander---Amber10 archana sonawani
- Re: [AMBER] Can't reproduce RESP charges FyD
- RE: [AMBER] Re: AMBER: questions about equilibram wei zhang
- Re: [AMBER] errorin sander---Amber10 David A. Case
- [AMBER] amber9 in fedora10 Bala subramanian
- Re: [AMBER] amber9 in fedora10 Mark Williamson
- RE: [AMBER] amber9 in fedora10 Ross Walker
- Re: [AMBER] amber9 in fedora10 Bala subramanian
- Re: [AMBER] amber9 in fedora10 Eric
- [AMBER] principal component vector onto C-alpha Carra, Claudio (JSC-SK)[USRA]
- [AMBER] Re: AMBER: Re: nmode error: bad nonbon (amber 10) Jeremy Harris
- Re: [AMBER] principal component vector onto C-alpha S.Sundar Raman
- [AMBER] Divcon or Mopac Cen Gao
- [AMBER] PTRAJ: solvent accessible surface area Catein Catherine
Wednesday, 14 January 2009
- Re: [AMBER] Divcon or Mopac Martin Peters
- [AMBER] ptraj, CHARMM PSF and CMAP Hannes Loeffler
- [AMBER] charges in topology file vallespardojl.chem.leidenuniv.nl
- Re: [AMBER] charges in topology file Carlos Simmerling
- [AMBER] reaction coordinates Rausch, Felix
- Re: [AMBER] reaction coordinates David A. Case
- Re: [AMBER] Re: AMBER: Re: nmode error: bad nonbon (amber 10) David A. Case
- [AMBER] antechamber cation failure Rausch, Felix
- [AMBER] NPT md with PME method for a water box Jeffrey
- [AMBER] molecular mechanic minimisation with amber momo momo
- Re: [AMBER] PTRAJ: solvent accessible surface area steinbrt.rci.rutgers.edu
- Re: [AMBER] PTRAJ: solvent accessible surface area Carlos Simmerling
- [AMBER] Dipole command in ptraj musa özboyacı
- RE: [AMBER] ptraj, CHARMM PSF and CMAP Ross Walker
- [AMBER] pmemd | Compilation problem with ifort and mvapich environment fohm fohm
- RE: [AMBER] antechamber cation failure Ross Walker
- RE: [AMBER] pmemd | Compilation problem with ifort and mvapich environment Ross Walker
- RE: [AMBER] molecular mechanic minimisation with amber Ross Walker
- RE: [AMBER] NPT md with PME method for a water box Ross Walker
- [AMBER] bad energy??!! momo momo
- RE: [AMBER] bad energy??!! Ross Walker
- [AMBER] Postdoc Position Available at SDSC/UCSD Ross Walker
- [AMBER] Dipole command in ptraj musa özboyacı
- [AMBER] xmgrace and plotting time evolution of a defined variable Naser Alijabbari
- Re: [AMBER] xmgrace and plotting time evolution of a defined variable Mark Williamson
- RE: [AMBER] reaction coordinates Catein Catherine
- [AMBER] Error in xleap archana sonawani
Thursday, 15 January 2009
- RE: [AMBER] Error in xleap Ross Walker
- [AMBER] Using a restart file Simone Swift
- Re: [AMBER] Using a restart file Carlos Simmerling
- RE: [AMBER] Using a restart file Ross Walker
- [AMBER] Ligand Diffusion Studies? Jason A. Ford-Green
- [AMBER] restraint of REMD z g
- [AMBER] sander not working archana sonawani
- Re: [AMBER] Using GAFF with a covalently bound ligand or label Markus Kaukonen
Friday, 16 January 2009
- Re: [AMBER] Using GAFF with a covalently bound ligand or label FyD
- Re: [AMBER] restraint of REMD Carlos Simmerling
- Re: [AMBER] sander not working David A. Case
- Re: [AMBER] sander not working Carlos Simmerling
- [AMBER] nab conjgrad min problem Jeremy Harris
- Re: [AMBER] nab conjgrad min problem David A. Case
- [AMBER] RE: Tutorial 5 Ross Walker
- [AMBER] (no subject) Lake, Thomas
- Re: [AMBER] (no subject) Carlos Simmerling
- Re: [AMBER] (no subject) Jenny Iskrenova
- Re: [AMBER] (no subject) Carlos Simmerling
- Re: [AMBER] (no subject) David A. Case
- Re: [AMBER] Parallelepiped periodic box David A. Case
- Re: [AMBER] RE: Tutorial 5 George Tzotzos
- Re: [AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai
- [AMBER] Heat and Equilibrate Hybrid GB solvent? Jason A. Ford-Green
- Re: [AMBER] problem building AmberTools/sleap on AIX Wei Zhang
- Re: [AMBER] Heat and Equilibrate Hybrid GB solvent? Carlos Simmerling
- Re: [AMBER] (no subject) Jenny Iskrenova
- [AMBER] Use of Amber in distributed calculations drugdesign
Saturday, 17 January 2009
- Re: [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba
- Re: [AMBER] Use of Amber in distributed calculations M. L. Dodson
- Re: [AMBER] Use of Amber in distributed calculations M. L. Dodson
- [AMBER] To stop the AMBER's list Furia Gargano
- [AMBER] to remove AMBER list Furia Gargano
- RE: [AMBER] to remove AMBER list Ross Walker
- Re: [AMBER] (no subject) David A. Case
Sunday, 18 January 2009
- Re: [AMBER] (no subject) Carlos Simmerling
- RE: [AMBER] (no subject) Ross Walker
- [AMBER] AMBER efficiency: Intel vs. AMD Swarup Gupta
- Re: [AMBER] AMBER efficiency: Intel vs. AMD Ye MEI
Monday, 19 January 2009
- [AMBER] how to set up "Two molecules tied with an Elastic band of 20A in implicit solvent" Jagadeesh, M.N., Ph.D.
- RE: [AMBER] Duplicate residues George Tzotzos
- Re: [AMBER] Duplicate residues David A. Case
- [AMBER] RESP charges for Fe in heme Carina Backtorp
- [AMBER] Atom types George Tzotzos
- Re: [AMBER] nab conjgrad min problem Jeremy Harris
- RE: [AMBER] AMBER efficiency: Intel vs. AMD Ross Walker
- RE: [AMBER] Atom types Ross Walker
- RE: [AMBER] Atom types George Tzotzos
- Re: [AMBER] (no subject) Jenny Iskrenova
- Re: [AMBER] Duplicate residues Bill Ross
- [AMBER] errors on REMD z g
Tuesday, 20 January 2009
- Re: [AMBER] errors on REMD Carlos Simmerling
- Re: [AMBER] errors on REMD z g
- Re: [AMBER] errors on REMD Carlos Simmerling
- Re: [AMBER] how to set up "Two molecules tied with an Elastic band of 20A in implicit solvent" Carlos Simmerling
- [AMBER] analysis Adrien Delmont
- [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. Marek Malý
- RE: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. Niel Henriksen
- Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. David A. Case
- [AMBER] MD vs scattering Chih-Ying Lin
- RE: [AMBER] MD vs scattering Ross Walker
- Re: RE: [AMBER] MD vs scattering Chih-Ying Lin
- [AMBER] solvent mixture iccy liu
- [AMBER] How to calculate cavity volume from MD structures? ben rodriguez
- Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. Marek Malý
Wednesday, 21 January 2009
- [AMBER] prot-DNA simulation deepti nayar
- Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. David A. Case
- Re: [AMBER] How to calculate cavity volume from MD structures? Jason A. Ford-Green
- [AMBER] AMBER External keyword Mahmoud A. A. Ibrahim
- [AMBER] how to use those water models off the list in amber? GZ Zhang
- Re: [AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai
- Re: [AMBER] prot-DNA simulation Thomas Cheatham III
- Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. Marek Malý
- Re: [AMBER] how to use those water models off the list in amber? Lauren Wickstrom
- [AMBER] reg . parallel run balaji nagarajan
Thursday, 22 January 2009
- Re: [AMBER] how to use those water models off the list in amber? David A. Case
- [AMBER] (no subject) Lake, Thomas
- [AMBER] restraining atoms neville forlemu
- Re: [AMBER] restraining atoms Carlos Simmerling
- RE: [AMBER] (no subject) Ross Walker
- RE: [AMBER] reg . parallel run Ross Walker
- [AMBER] MM - PBSA problem musa özboyacı
- RE: [AMBER] MM - PBSA problem Ray Luo
- [AMBER] non-natural amino acids Arturas Ziemys
- [AMBER] reg.parallel run error balaji nagarajan
- Re: [AMBER] MM - PBSA problem musa özboyacı
- RE: [AMBER] reg.parallel run error Ross Walker
- [AMBER] REM_hybrid test fails on AIX Shan-ho Tsai
- Re: [AMBER] how to use those water models off the list in amber? GZ Zhang
- Re: [AMBER] MM - PBSA problem Cenk \(Jenk\) Andac
- Re: [AMBER] non-natural amino acids FyD
- RE: [AMBER] MM - PBSA problem Niel Henriksen
- Re: [AMBER] errors on REMD z g
Friday, 23 January 2009
- [AMBER] reg.error in parallel run balaji nagarajan
- Re: [AMBER] MM - PBSA problem musa özboyacı
- [AMBER] charge derivation for ATP molecule using antechamber prachi munjal
- Re: [AMBER] MM - PBSA problem Cenk \(Jenk\) Andac
- RE: [AMBER] reg.error in parallel run Ross Walker
- [AMBER] RE: errors on remd Ross Walker
- Re: [AMBER] charge derivation for ATP molecule using antechamber David A. Case
- Re: [AMBER] "Could not find bond parameter" George Tzotzos
- RE: [AMBER] "Could not find bond parameter" Ross Walker
- [AMBER] reg.parallel.run error balaji nagarajan
- [AMBER] error on open distatance restraint gmail
- Re: [AMBER] error on open distatance restraint David A. Case
- RE: [AMBER] reg.parallel.run error Ross Walker
Saturday, 24 January 2009
- Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. David A. Case
- [AMBER] reg.parallel.run.error balaji nagarajan
- [AMBER] Very weird topology problem ranqi zhu
- [AMBER] AmberTools and ptraj clustering on Mac OS X David Watson
- Re: [AMBER] Very weird topology problem Peter Gannett
- Re: [AMBER] AMBER External keyword Gustavo Seabra
- Re: [AMBER] solvent mixture Gustavo Seabra
- Re: [AMBER] error on open distatance restraint xiaonan zhang
Sunday, 25 January 2009
- [AMBER] xleap problem oguz gurbulak
- Re: [AMBER] MM - PBSA problem musa özboyacı
- Re: [AMBER] xleap problem David A. Case
- Re: [AMBER] MM - PBSA problem David A. Case
- Re: [AMBER] MM - PBSA problem David A. Case
- Re: [AMBER] xleap problem oguz gurbulak
- [AMBER] RE:xleap problem oguz gurbulak
- [AMBER] xleap problem oguz gurbulak
- [AMBER] xleap problem oguz gurbulak
- [AMBER] xleap problem oguz gurbulak
- Re: [AMBER] MM - PBSA problem Cenk \(Jenk\) Andac
- [AMBER] deduce correlation from covariance matrix Yi Mao
- Re: [AMBER] xleap problem David A. Case
- [AMBER] using binary trajectories from NAMD in PTRAJ karthik s
Monday, 26 January 2009
- Re: [AMBER] MM - PBSA problem musa özboyacı
- Re: [AMBER] MM - PBSA problem Cenk \(Jenk\) Andac
- Re: [AMBER] MM - PBSA problem musa özboyacı
- RE: [AMBER] using binary trajectories from NAMD in PTRAJ Wei Huang
- [AMBER] thioglycoside Alexander Schierholt
- Re: [AMBER] thioglycoside FyD
- Re: [AMBER] thioglycoside Lachele Foley (Lists)
- Re: [AMBER] MM - PBSA problem Cenk \(Jenk\) Andac
- Re: [AMBER] MM - PBSA problem musa özboyacı
- Re: [AMBER] errors on REMD Carlos Simmerling
- Re: [AMBER] Antechamber Connectivity George Tzotzos
- [AMBER] antechamber : missed atoms Khaled Barakat
- Re: [AMBER] antechamber : missed atoms Khaled Barakat
- Re: [AMBER] antechamber : missed atoms Khaled Barakat
- Re: [AMBER] antechamber : missed atoms Sean Johnston
- [AMBER] RE:xleap problem oguz gurbulak
- Re: [AMBER] Antechamber Connectivity David Watson
- Re: [AMBER] antechamber : missed atoms Khaled Barakat
- Re: [AMBER] RE:xleap problem M. L. Dodson
- Re: [AMBER] RE:xleap problem oguz gurbulak
- Re: [AMBER] using binary trajectories from NAMD in PTRAJ karthik s
Tuesday, 27 January 2009
- [AMBER] atom types deepti nayar
- [AMBER] reg: targeted molecular dynamics balaji nagarajan
- Re: [AMBER] reg: targeted molecular dynamics Carlos Simmerling
- [AMBER] Rosetta Academic Training Workshop Nir London
- [AMBER] reg.Targeted molecular dynamics balaji nagarajan
- [AMBER] reg.Targeted molecular dynamics balaji nagarajan
- Re: [AMBER] Antechamber ligand prep George Tzotzos
- Re: [AMBER] Antechamber ligand prep David A. Case
- Re: [AMBER] atom types David A. Case
- Re: [AMBER] RE:xleap problem David A. Case
- Re: [AMBER] antechamber : missed atoms David A. Case
- Re: [AMBER] Antechamber ligand prep George Tzotzos
- Re: [AMBER] Antechamber ligand prep David A. Case
- Re: [AMBER] Antechamber ligand prep David Watson
- Re: [AMBER] Antechamber ligand prep George Tzotzos
- [AMBER] NOTICE: File size limits on AMBER reflector Ross Walker
- Re: [AMBER] Antechamber ligand prep George Tzotzos
- [AMBER] distance restraint and SHAKE Michael J Yonkunas
- Re: [AMBER] distance restraint and SHAKE Thomas Cheatham III
- Re: [AMBER] Building atom and angle parameters George Tzotzos
- [AMBER] topology file for GLY with amino and carboxyl group? Jose Borreguero
- Re: [AMBER] topology file for GLY with amino and carboxyl group? FyD
- [AMBER] large resp charges for non-natural amino acid Arturas Ziemys
Wednesday, 28 January 2009
- [AMBER] PhD position in Computational Structural Biology at Cambridge, UK Swanand Gore
- [AMBER] GAFF conjugated ring system dihedrals Floris Buelens
- [AMBER] Watercap... some querries Waqas Nasir
- Re: [AMBER] Watercap... some querries David A. Case
- Re: [AMBER] Watercap... some querries Waqas Nasir
- Re: [AMBER] reg.Targeted molecular dynamics Carlos Simmerling
- Re: [AMBER] Watercap... some querries Robert Duke
- [AMBER] generating top file using antechmaber sarvin moghaddam
- Re: [AMBER] generating top file using antechmaber Wei Zhang
- Re: [AMBER] generating top file using antechmaber Wei Zhang
- Re: [AMBER] generating top file using antechmaber sarvin moghaddam
- [AMBER] Compilation and usage of NAB in parallel ? Marek Malý
- Re: [AMBER] large resp charges for non-natural amino acid FyD
Thursday, 29 January 2009
- [AMBER] atomic charge m m
- Re: [AMBER] atomic charge Barbault Florent
- [AMBER] Problem in pb simulation, PB_Bomb Waqas Nasir
- [AMBER] Dr. Ramesh here kureeckal ramesh
- [AMBER] Atome Type Mahmoud A. A. Ibrahim
- [AMBER] Installation error - Amber10 Ananda Rama Krishnan Selvaraj
- Re: [AMBER] Installation error - Amber10 Andreas Svrcek-Seiler
- Re: [AMBER] generating top file using antechmaber David A. Case
- Re: [AMBER] Atome Type David A. Case
- Re: [AMBER] Compilation and usage of NAB in parallel ? David A. Case
- [AMBER] Problem in watercap simulation, PB_Bomb Waqas Nasir
- Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys
- Re: [AMBER] generating top file using antechmaber sarvin moghaddam
- Re: [AMBER] RE:xleap problem oguz gurbulak
- Re: [AMBER] RE:xleap problem M. L. Dodson
- Re: [AMBER] generating top file using antechmaber Wei Zhang
- Re: [AMBER] Dr. Ramesh here rpaduri.chem.wayne.edu
- RE: [AMBER] Problem in watercap simulation, PB_Bomb Ray Luo
- Re: [AMBER] Installation error - Amber10 David A. Case
- Re: [AMBER] GAFF conjugated ring system dihedrals David A. Case
- [AMBER] Alpha helix plot Beale, John
- Re: [AMBER] large resp charges for non-natural amino acid FyD
- Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys
- Re: [AMBER] large resp charges for non-natural amino acid FyD
- [AMBER] failure to run antechamber with amber 10 Francesco Pietra
- Re: [AMBER] failure to run antechamber with amber 10 David A. Case
- Re: [AMBER] failure to run antechamber with amber 10 George Tzotzos
- [AMBER] AmberTools 1.2 James W. Caldwell
- Re: [AMBER] Dr. Ramesh here kureeckal ramesh
- Re: [AMBER] Dr. Ramesh here kureeckal ramesh
Friday, 30 January 2009
- Re: [AMBER] failure to run antechamber with amber 10 Francesco Pietra
- [AMBER] adding MG2 problem balaji nagarajan
- [AMBER] Xleap - solvatebox - counterions Arnaud
- Re: [AMBER] AmberTools 1.2 David A. Case
- [AMBER] help momo momo
- RE: [AMBER] help Ross Walker
- [AMBER] Amber top file to Charmm top file sarvin moghaddam
- Re: [AMBER] Compilation and usage of NAB in parallel ? Marek Malý
- Re: [AMBER] Compilation and usage of NAB in parallel ? David A. Case
- Re: [AMBER] Compilation and usage of NAB in parallel ? Marek Malý
- Re: [AMBER] Xleap - solvatebox - counterions David A. Case
- Re: [AMBER] Dr. Ramesh here David A. Case
- [AMBER] REMD fixed atoms Maxime Louet
- Re: [AMBER] Xleap - solvatebox - counterions Bill Ross
- [AMBER] thermo, entropy by quasiharmonic method Carra, Claudio (JSC-SK)[USRA]
- Re: [AMBER] Alpha helix plot Carlos Simmerling
- Re: [AMBER] thermo, entropy by quasiharmonic method David A. Case
- [AMBER] RE: Tutorial 5 Ross Walker
Saturday, 31 January 2009
- Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys
- Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys
- RE: [AMBER] Xleap - solvatebox - counterions amirhossein taghavi
- [AMBER] Test run on Solaris 10 X 86 Manikandan Chandrasekaran
- [AMBER] Question on heating for homology based model. drugdesign
- Re: [AMBER] Test run on Solaris 10 X 86 David A. Case

Last message date: Sun Feb 01 2009 - 01:22:26 PST
Archived on: Fri Nov 22 2024 - 05:53:44 PST

Amber Archive Jan 2009 by date