Amber Archive May 2007: by date

Tuesday, 1 May 2007
- AMBER: mm-pbsa error with nm = 1 Hayden Eastwood
- Re: AMBER: mm-pbsa error with nm = 1 Urszula Uciechowska
- Re: AMBER: mm-pbsa error with nm = 1 Cenk Andac
- AMBER: Problem with SCC-DFTB parameter files 한재범
- AMBER: Steered MD & Jarzynski's equality James W
Wednesday, 2 May 2007
- Re: AMBER: Steered MD & Jarzynski's equality Adrian Roitberg
- Re: AMBER: Steered MD & Jarzynski's equality James W
- AMBER: Group declaration question cristian obiol
- RE: AMBER: mm-pbsa error with nm = 1 Hayden Eastwood
- RE: AMBER: mm-pbsa error with nm = 1 Cenk Andac
- RE: AMBER: mm-pbsa error with nm = 1 Hayden Eastwood
- Re: AMBER: Steered MD & Jarzynski's equality Gustavo Seabra
- Re: AMBER: Problem with SCC-DFTB parameter files Gustavo Seabra
- RE: AMBER: mm-pbsa error with nm = 1 Cenk Andac
- Re: AMBER: Steered MD & Jarzynski's equality David Mobley
- RE: AMBER: Problem with SCC-DFTB parameter files Ross Walker
- Re: AMBER: Problem with SCC-DFTB parameter files M. L. Dodson
- Re: AMBER: Problem with SCC-DFTB parameter files Gustavo Seabra
- Re: AMBER: Group declaration question Bill Ross
- AMBER: command line alternatives for teLeap Neelanjana Sengupta
Thursday, 3 May 2007
- Re: AMBER: Steered MD & Jarzynski's equality wang
- AMBER: md output file deepti nayar
- AMBER: Potential of mean force, how to calculate rate of dissociation? Catein Catherine
- Re: AMBER: md output file Gustavo Seabra
- distance constraint [Was: Re: AMBER: Steered MD & Jarzynski's equality] Gustavo Seabra
- Re: AMBER: Potential of mean force, how to calculate rate of dissociation? Jerome.GOLEBIOWSKI.unice.fr
- Re: AMBER: command line alternatives for teLeap David A. Case
- Re: AMBER: Problem with calcpka.pl and constant pH David A. Case
- AMBER: DivCon calculation in Amber9 Wang, Xuelin
- Re: AMBER: Potential of mean force, how to calculate rate of dissociation? David Mobley
- AMBER: Chemical shift: simulation vs. experiment Mingfeng Yang
- Re: AMBER: Potential of mean force, how to calculate rate of dissociation? Catein Catherine
- Re: AMBER: Chemical shift: simulation vs. experiment Mingfeng Yang
- Re: AMBER: Chemical shift: simulation vs. experiment Adrian Roitberg
Friday, 4 May 2007
- Re: AMBER: Chemical shift: simulation vs. experiment Mingfeng Yang
- Re: AMBER: Chemical shift: simulation vs. experiment Mingfeng Yang
- Re: AMBER: Potential of mean force, how to calculate rate of dissociation? Jerome.GOLEBIOWSKI.unice.fr
- AMBER: Tutorial 3: MM-PBSA.....implicit solvent for MD calculations? Catein Catherine
- AMBER: Rate of Dissociation Catein Catherine
- AMBER: B or E Dihedral Labels in RDPARM output Mark Williamson
- AMBER: Average PDB - Unusual Bonds Seth Lilavivat
- RE: AMBER: Average PDB - Unusual Bonds Hayden Eastwood
- Re: AMBER: B or E Dihedral Labels in RDPARM output Thomas Cheatham III
- RE: AMBER: Average PDB - Unusual Bonds Ross Walker
- Re: AMBER: Potential of mean force, how to calculate rate of dissociation? Thomas Steinbrecher
- Re: AMBER: Potential of mean force, how to calculate rate of dissociation? David Mobley
- Re: AMBER: Rate of Dissociation David Mobley
- Re: AMBER: Potential of mean force, how to calculate rate of dissociation? Thomas Steinbrecher
- Re: AMBER: Rate of Dissociation Sean Rathlef
- AMBER: Simulated Annealing - Best way to create randomness Seth Lilavivat
- Re: AMBER: Potential of mean force, how to calculate rate of dissociation? David Mobley
- Re: AMBER: Potential of mean force, how to calculate rate of dissociation? Catein Catherine
- Re: AMBER: Rate of Dissociation Catein Catherine
- AMBER: RE: RE: AMBER: Problem with SCC-DFTB parameter files 한재범
- AMBER: polarizable water models. Karen Callahan
Sunday, 6 May 2007
- Re: AMBER: polarizable water models. David A. Case
- AMBER: FW: Query regarding using tleap for preparing carbohydrate molecule Ross Walker
- Re: AMBER: Rate of Dissociation wang
- Re: AMBER: Potential of mean force, how to calculate rate of dissociation? wang
- AMBER: REF file problem deepti nayar
Monday, 7 May 2007
- Re: AMBER: REF file problem Gustavo Seabra
- Re: AMBER: Potential of mean force, how to calculate rate of dissociation? Gustavo Seabra
- Re: AMBER: FW: Query regarding using tleap for preparing carbohydrate molecule Gustavo Seabra
- AMBER: Atoms closer to 2 angstroms to each other Christopher Gaughan
- Re: AMBER: Atoms closer to 2 angstroms to each other David A. Case
- RE: AMBER: FW: Query regarding using tleap for preparing carbohydrate molecule Ross Walker
- RE: AMBER: REF file problem Ross Walker
- RE: AMBER: Atoms closer to 2 angstroms to each other Ross Walker
- AMBER: GB Energy Spreads for MD Structures adelene.Stanford.EDU
- Re: AMBER: GB Energy Spreads for MD Structures David A. Case
- AMBER: Keq computations Sean Rathlef
- AMBER: NAB MD Output adelene.Stanford.EDU
- AMBER: PME memory requirement Russell Brown
- Re: AMBER: Keq computations Carlos Simmerling
- Re: AMBER: NAB MD Output Russell Brown
- Re: AMBER: PME memory requirement Robert Duke
- AMBER: PMF define dehedral angel and distance restrainst for center of mass of domains. Catein Catherine
Tuesday, 8 May 2007
- Re: AMBER: NAB MD Output Andreas Svrcek-Seiler
- Re: AMBER: PMF define dehedral angel and distance restrainst for center of mass of domains. Carlos Simmerling
- AMBER: query regarding parameter files for manganese and mercuric ions neetu.imtech.res.in
- AMBER: Complexes Beale, John
- Re: AMBER: Complexes M. L. Dodson
- Re: AMBER: Complexes M. L. Dodson
- AMBER: simulations stops in half way Vijay Manickam Achari
Wednesday, 9 May 2007
- AMBER: hybrid remd Geoff Wood
- AMBER: Compiling parallel Amber9 on Linux cluster Jesus Angulo
- AMBER: hybrid remd Geoff Wood
- AMBER: pmemd source issues Thomas Zeiser
- AMBER: leap problem Achuth Prabhu
- AMBER: leap problem Achuth Prabhu
- AMBER: leap problem Achuth Prabhu
- Re: AMBER: simulations stops in half way Robert Duke
- Re: AMBER: pmemd source issues Robert Duke
- AMBER: Covert NOEs form Xplor to Amber saccenti.cerm.unifi.it
- Re: AMBER: pmemd source issues Thomas Zeiser
- RE: AMBER: Compiling parallel Amber9 on Linux cluster Ross Walker
- Re: AMBER: pmemd source issues Robert Duke
- Re: AMBER: hybrid remd Asim Okur
- Re: AMBER: hybrid remd Geoff Wood
- Re: AMBER: hybrid remd Carlos Simmerling
- Re: AMBER: hybrid remd Geoff Wood
- Re: AMBER: hybrid remd Carlos Simmerling
- AMBER: Amber 9 compile on OS X Knut Langsetmo
- AMBER: (no subject) Dingguo Xu
- Re: AMBER: hybrid remd Geoff Wood
- Fwd: AMBER: MM-PBSA: Can't finish the binding energy process jitrayut jitonnom
Thursday, 10 May 2007
- AMBER: Missing BELE for MM in 1 (residue 47) AYTUG TUNCEL
- AMBER: umbrella sampling: distance restraint Catein Catherine
- AMBER: restraint_wt and fixing chi deepti nayar
- AMBER: use of pucker function in ptraj Ben Tan
- Re: AMBER: hybrid remd Carlos Simmerling
- Re: AMBER: hybrid remd Geoff Wood
- Re: AMBER: pmemd source issues Thomas Zeiser
- Re: AMBER: umbrella sampling: distance restraint Jerome.GOLEBIOWSKI.unice.fr
- AMBER: query regarding parameter files for manganese neetu.imtech.res.in
- Re: AMBER: hybrid remd Carlos Simmerling
- Re: AMBER: use of pucker function in ptraj Thomas Cheatham III
- Re: AMBER: restraint_wt and fixing chi Thomas Cheatham III
- AMBER: Electrostatic Energy in MD Simulation (GB) adelene.Stanford.EDU
- Re: AMBER: Electrostatic Energy in MD Simulation (GB) David A. Case
- AMBER: need help to calculate IR spectra from amber trajectory S.Sundar Raman
- AMBER: bug in reprocessing with PB? David Mobley
- Re: AMBER: bug in reprocessing with PB? Carlos Simmerling
- RE: AMBER: bug in reprocessing with PB? Ray Luo
- AMBER: Sander (Amber 9) crash on cortex Evan Kelly
- Re: AMBER: bug in reprocessing with PB? David A. Case
- Re: AMBER: need help to calculate IR spectra from amber trajectory Adrian Roitberg
- Re: AMBER: bug in reprocessing with PB? David Mobley
- Re: AMBER: bug in reprocessing with PB? David Mobley
- Re: AMBER: hybrid remd Geoff Wood
- Re: AMBER: Sander (Amber 9) crash on cortex David A. Case
- AMBER: single phospholipid molecule in vacuo Kliman, Michal
- RE: AMBER: Sander (Amber 9) crash on cortex Ross Walker
- Re: AMBER: (no subject) David A. Case
- Re: AMBER: leap problem David A. Case
- RE: AMBER: bug in reprocessing with PB? Ray Luo
- Re: AMBER: Amber 9 compile on OS X David A. Case
- Re: AMBER: single phospholipid molecule in vacuo David A. Case
- AMBER: Rotations about center of mass of an isolated system Jennie Thomas
- Re: AMBER: Sander (Amber 9) crash on cortex Evan Kelly
- Re: AMBER: Sander (Amber 9) crash on cortex Thomas Cheatham
- Re: AMBER: Sander (Amber 9) crash on cortex Robert Duke
Friday, 11 May 2007
- AMBER: how to solvate the protein with different solvents Rachel
- AMBER: antechamber Santanu Roy
- AMBER: correlation between PBTOT and GBTOT values in a MD trajectory Giulio Rastelli
- RE: AMBER: correlation between PBTOT and GBTOT values in a MD trajectory Ray Luo
- AMBER: binding energy_decomposition per residue Srinivas Odde
- Re: AMBER: antechamber Scott Brozell
- AMBER: missing impropers for nitros? David Mobley
- AMBER: Re: missing impropers for nitros? David Mobley
- AMBER: distance.restraint for two groups of atoms (center of mass) Catein Catherine
- AMBER: PMF for DG calculation. Catein Catherine
- AMBER: PMF along 1D axis or every axis Catein Catherine
- AMBER: PMF: WHAM result Catein Catherine
- AMBER: antechamber Santanu Roy
Saturday, 12 May 2007
- Re: AMBER: antechamber David A. Case
- Re: AMBER: distance.restraint for two groups of atoms (center of mass) David A. Case
- Re: AMBER: missing impropers for nitros? David A. Case
- AMBER: PMEMD and restart files Austin B. Yongye
- AMBER: Small scale compute environments M. L. Dodson
- Re: AMBER: PMEMD and restart files Robert Duke
- AMBER: problem about the coordinates out the box Shaoqing.Zhang.mail.uh.edu
Sunday, 13 May 2007
- AMBER: restraining atoms deepti nayar
Monday, 14 May 2007
- AMBER: polymer Achuth Prabhu
- Re: AMBER: missing impropers for nitros? David Mobley
- Re: AMBER: PMF for DG calculation. David Mobley
- Re: AMBER: PMF for DG calculation. David A. Case
- Re: AMBER: Rotations about center of mass of an isolated system David A. Case
- Re: AMBER: restraining atoms Thomas Cheatham III
- Re: AMBER: Small scale compute environments Robert Duke
- Re: AMBER: Small scale compute environments M. L. Dodson
- Re: AMBER: Rotations about center of mass of an isolated system Jennie Thomas
- AMBER: Energy Spread using GB & Langevin Dynamics (NAB) adelene.Stanford.EDU
- Re: AMBER: Rotations about center of mass of an isolated system David A. Case
- Re: AMBER: Energy Spread using GB & Langevin Dynamics (NAB) David A. Case
- Re: AMBER: Rotations about center of mass of an isolated system Jennie Thomas
- Re: AMBER: Rotations about center of mass of an isolated system David A. Case
Tuesday, 15 May 2007
- AMBER: assigning of head atom as null. SHARAD gupta
- Re: AMBER: Energy Spread using GB & Langevin Dynamics (NAB) Andreas Svrcek-Seiler
- AMBER: Finding x-displacement Ben Tan
- AMBER: Heat of Vaporization Rita Cassia
- Re: AMBER: Energy Spread using GB & Langevin Dynamics (NAB) David A. Case
- Re: AMBER: Heat of Vaporization David A. Case
- Re: AMBER: Heat of Vaporization Thomas Cheatham III
- Re: AMBER: Heat of Vaporization David A. Case
- AMBER: constant pH with 25 titrable sites tri nam Vo
- AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj j j
- Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj Carlos Simmerling
- Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj j j
- Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj Gustavo Seabra
- RE: AMBER: Heat of Vaporization Falck da Silva Eirik
- Re: AMBER: Heat of Vaporization David A. Case
- Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj Carlos Simmerling
- AMBER: total energies during MM-PBSA Hu, Shaowen (JSC-SK)[USRA]
- AMBER: AMBER8 compiler with intel 9.1 compiler Peter Z. Qin
Wednesday, 16 May 2007
- Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj j j
- Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj j j
- Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj Carlos Simmerling
- Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj Carlos Simmerling
- Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj j j
- Re: AMBER: Heat of Vaporization Rita Cassia
- AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set" S. Jamal Rahi
- Re: AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set" Carlos Simmerling
- AMBER: MM-PBSA calculation with GB dynamic Andrea - Tisacali
- AMBER: total energies during MM-PBSA Hu, Shaowen (JSC-SK)[USRA]
- Re: AMBER: MM-PBSA calculation with GB dynamic Carlos Simmerling
- Re: AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set" Thomas Steinbrecher
- AMBER: protonate Christopher Gaughan
- Re: AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set" David A. Case
- Re: AMBER: protonate saccenti.cerm.unifi.it
- AMBER: Ignore my reply to Amber protonate! saccenti.cerm.unifi.it
- AMBER: Minimization with heme group saccenti.cerm.unifi.it
- Re: AMBER: protonate David A. Case
- Re: AMBER: protonate David A. Case
- AMBER: Re: Minimization with heme group saccenti.cerm.unifi.it
- AMBER: work with constant pH on amber8 tri nam Vo
- AMBER: work with constant pH on amber8 tri nam Vo
- Re: AMBER: work with constant pH on amber8 David A. Case
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Scott Brozell
- AMBER: NOC 3.0 is released mchen2.mailer.fsu.edu
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Peter Z. Qin
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler David A. Case
- AMBER: hbond ptraj Catein Catherine
- Re: AMBER: hbond ptraj Thomas Cheatham
- Re: AMBER: hbond ptraj Catein Catherine
- AMBER: Is the simulation reasonable ? (SMD : dissocation antibody-antigen) wang
Thursday, 17 May 2007
- AMBER: high energy with mm_gbsa igb=5 AYTUG TUNCEL
- Re: AMBER: hbond ptraj Chris Moth
- AMBER: deeper problem with the energetics Pankaj R. Daga
- Re: AMBER: deeper problem with the energetics Carlos Simmerling
- Re: AMBER: hbond ptraj Thomas Cheatham
- AMBER: Average structure Steve Seibold
- Re: AMBER: Average structure Thomas Cheatham
- Re: AMBER: Is the simulation reasonable ? (SMD : dissocation antibody-antigen) Adrian Roitberg
- AMBER: multiple excecution of sander Achuth Prabhu
- Re: AMBER: multiple excecution of sander Carlos Simmerling
- AMBER: NAB Average Structure adelene.Stanford.EDU
- Re: AMBER: NAB Average Structure David A. Case
- Re: AMBER: deeper problem with the energetics Pankaj R. Daga
- Re: AMBER: NAB Average Structure adelene.Stanford.EDU
- Re: AMBER: NAB Average Structure Andreas Svrcek-Seiler
- Re: AMBER: NAB Average Structure David A. Case
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Peter Z. Qin
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Peter Z. Qin
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler David A. Case
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler David A. Case
- Re :Re: AMBER: multiple excecution of sander Achuth Prabhu
- AMBER: high energy with mm_gbsa igb=5 AYTUG TUNCEL
Friday, 18 May 2007
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Mark Williamson
- AMBER: Some questions on mm_pbsa Hu, Shaowen (JSC-SK)[USRA]
- AMBER: Temperature Drift in MD (NAB) adelene.Stanford.EDU
- Re: AMBER: Temperature Drift in MD (NAB) David A. Case
- Re: AMBER: Temperature Drift in MD (NAB) adelene.Stanford.EDU
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Peter Z. Qin
Saturday, 19 May 2007
- AMBER: Statictical significance of differences in energy mean values between different simulations Mostafa Sadighi
- Re: AMBER: Temperature Drift in MD (NAB) David A. Case
Sunday, 20 May 2007
- AMBER: antechamber question Francesco Pietra
- Re: AMBER: antechamber question David A. Case
- Re: AMBER: antechamber question Francesco Pietra
- AMBER: Langevin dynamics in NAB David A. Case
- AMBER: [AMBER] QM/MM-DFTB 박민희
- AMBER: QM/MM-DRFTB 박민희
Monday, 21 May 2007
- AMBER: Docking with AMber Urszula Uciechowska
- AMBER: ambpdb gives empty cpin Achuth Prabhu
- AMBER: Pi-pi interactions Roberto Veiga
- Re: AMBER: Pi-pi interactions Jiri Sponer
- Re: AMBER: Pi-pi interactions David Cerutti
- Re: AMBER: Pi-pi interactions Jiri Sponer
- Re: AMBER: Pi-pi interactions Adrian Roitberg
- Re: AMBER: deeper problem with the energetics Carlos Simmerling
- Re: Re :Re: AMBER: multiple excecution of sander Carlos Simmerling
- Re: AMBER: Pi-pi interactions Roberto Veiga
- AMBER: REMD error Jason K
- Re: AMBER: Pi-pi interactions Jiri Sponer
- Re: AMBER: REMD error Carlos Simmerling
- Re: AMBER: QM/MM-DRFTB Gustavo Seabra
- Fwd: AMBER: missing impropers for nitros? David Mobley
- RE: AMBER: missing impropers for nitros? Junmei Wang
- Re: AMBER: QM/MM-DRFTB Gustavo Seabra
- AMBER: dielectric constant in GB/SA Shuting Wei
- Re: AMBER: Docking with AMber David A. Case
Tuesday, 22 May 2007
- Re: AMBER: Pi-pi interactions Roberto Veiga
- Re: AMBER: Pi-pi interactions Jiri Sponer
- Re: AMBER: ambpdb gives empty cpin tri nam Vo
- AMBER: antechamber question Yao Xin
- AMBER: Ionic strength in pbsa Hu, Shaowen (JSC-SK)[USRA]
- RE: AMBER: antechamber question Junmei Wang
- Re: AMBER: REMD error Jason K
- AMBER: Simulated Annealing - Start with Poor Structure Seth Lilavivat
- Re: AMBER: Ionic strength in pbsa Qizhi Cui
- RE: AMBER: Ionic strength in pbsa Hu, Shaowen (JSC-SK)[USRA]
- Re: AMBER: Simulated Annealing - Start with Poor Structure Carlos Simmerling
- Re: AMBER: REMD error Carlos Simmerling
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Scott Brozell
- AMBER: hbond ptraj pls help. Catein Catherine
- AMBER: (no subject) Catein Catherine
- AMBER: MM/GBSA error message Catein Catherine
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Peter Z. Qin
Wednesday, 23 May 2007
- Re: AMBER: hbond ptraj pls help. Kateryna Miroshnychenko
- Re: AMBER: hbond ptraj pls help. Catein Catherine
- Re: AMBER: hbond ptraj pls help. Kateryna Miroshnychenko
- AMBER: Minimization increases energy Hayden Eastwood
- AMBER: Minimization increases energy Hayden Eastwood
- Re: AMBER: Minimization increases energy saccenti.cerm.unifi.it
- AMBER: inconsistency between PBSA and GBSA AYTUG TUNCEL
- AMBER: inconsistency between PBSA and GBSA AYTUG TUNCEL
Thursday, 24 May 2007
- Re: AMBER: adding polar hydrogens j j
- Re: AMBER: adding polar hydrogens j j
- Re: AMBER: REMD error Jason K
- Re: AMBER: REMD error Carlos Simmerling
- AMBER: thermodynamic integration Servaas Michielssens
- Re: AMBER: REMD error Carlos Simmerling
- AMBER: NAB normal mode output nadiav.soton.ac.uk
- AMBER: rfree: Error input file Steve Seibold
- Re: AMBER: rfree: Error input file Carlos Simmerling
- AMBER: Steve Seibold
- RE: AMBER: rfree: Error input file Steve Seibold
- AMBER: parameter file for Fe-S cluster devrani mitra
- Re: AMBER: NAB normal mode output David A. Case
- Re: AMBER: thermodynamic integration David A. Case
Friday, 25 May 2007
- Re: AMBER: thermodynamic integration Servaas Michielssens
- Re: AMBER: NAB normal mode output Andreas Svrcek-Seiler
- AMBER: grid output: bulk water density mathew k varghese
- AMBER: pi-pi interactions Sara Alexandra Moura
- AMBER: Less error Urszula Uciechowska
- Re: AMBER: Less error Carlos Simmerling
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Peter Z. Qin
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Scott Brozell
Saturday, 26 May 2007
- AMBER: software to extract data from the output file?? Avinash Kumar
- Re: AMBER: software to extract data from the output file?? Steven Winfield
- AMBER: inconsistency between PBSA and GBSA - help AYTUG TUNCEL
- Re: AMBER: software to extract data from the output file?? Gustavo Seabra
Sunday, 27 May 2007
- AMBER: Question about determination of hydration points in binding sites Cenk Andac
- AMBER: Calculating RMS for each residue? tri nam Vo
- AMBER: Antechamber Catein Catherine
- AMBER: water count mathew k varghese
- Re: AMBER: Antechamber Cenk Andac
Monday, 28 May 2007
- AMBER: Amber 9 install on Debian Linux amd64 Francesco Pietra
- Re: AMBER: Antechamber Francesco Pietra
- Re: AMBER: water count Carlos Simmerling
- AMBER: divcon missing in Antechamber 1.27 Neelanjana Sengupta
- AMBER: Re: divcon missing in Antechamber 1.27 Neelanjana Sengupta
- Re: AMBER: divcon missing in Antechamber 1.27 David A. Case
- Re: AMBER: divcon missing in Antechamber 1.27 Neelanjana Sengupta
Tuesday, 29 May 2007
- AMBER: 64-bit pgf90 revisited Ingvar Lagerstedt
- AMBER: Les analyse Urszula Uciechowska
- Re: AMBER: Les analyse Carlos Simmerling
- Re: AMBER: Les analyse Wei Zhang
- Re: AMBER: divcon missing in Antechamber 1.27 David A. Case
- AMBER: error in running sander devrani mitra
- Re: AMBER: error in running sander Carlos Simmerling
- Re: AMBER: error in running sander devrani mitra
- AMBER: Hydration points Cenk Andac
- Re: AMBER: error in running sander Carlos Simmerling
- Re: AMBER: Hydration points Carlos Simmerling
- Re: AMBER: error in running sander devrani mitra
- Re: AMBER: error in running sander Carlos Simmerling
- RE: AMBER: error in running sander Ross Walker
- Re: AMBER: error in running sander devrani mitra
- Re: AMBER: error in running sander devrani mitra
- Re: AMBER: error in running sander Thomas Cheatham
Wednesday, 30 May 2007
- AMBER: Umbrella Sampling for the twist angle of a DNA base pairs Catein Catherine
- AMBER: electric field calculation lishan yao
- AMBER: Atomic positional Fluctuations Sandeep Kaushik
- AMBER: Umbrella Sampling for the twist angle of a DNA base pairs Catein Catherine
- AMBER: (no subject) Catein Catherine
- AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8 Andrew Borgert
- Re: AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8 Carlos Simmerling
Tuesday, 29 May 2007
- RE: AMBER: error in running sander Ross Walker
Wednesday, 30 May 2007
- Re: AMBER: (no subject) M. L. Dodson
- Re: AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8 kkirschn.hamilton.edu
- AMBER: cutoff & speed-up of GBSA Wei Chen
- AMBER: junk in `Noshake mask` output section Ben Sattelle
- Re: AMBER: Hydration points Cenk Andac
- Re: AMBER: junk in `Noshake mask` output section David A. Case
- Re: AMBER: cutoff & speed-up of GBSA Carlos Simmerling
- Re: AMBER: junk in `Noshake mask` output section Ben Sattelle
- Re: AMBER: electric field calculation David A. Case
- Re: AMBER: error in running sander devrani mitra
- Re: AMBER: error in running sander devrani mitra
Thursday, 31 May 2007
- AMBER: LES Urszula Uciechowska
- Re: AMBER: LES Carlos Simmerling
- Re: AMBER: electric field calculation lishan yao
- Re: AMBER: LES Urszula Uciechowska
- Re: AMBER: LES Carlos Simmerling
- AMBER: RESTRAINTMASK Roberto Veiga
- AMBER: Solvent models Francesco Pietra
- Re: AMBER: RESTRAINTMASK David A. Case
- Re: AMBER: electric field calculation David A. Case
- AMBER: Reg restraint value obtained during umbrella sampling D.Usharani
- Re: AMBER: Reg restraint value obtained during umbrella sampling Jerome.GOLEBIOWSKI.unice.fr
- Re: AMBER: Reg restraint value obtained during umbrella sampling D.Usharani
- Re: AMBER: Reg restraint value obtained during umbrella sampling David A. Case
- Re: AMBER: cutoff & speed-up of GBSA Wei Chen
- Re: AMBER: cutoff & speed-up of GBSA Carlos Simmerling
- Re: AMBER: cutoff & speed-up of GBSA David A. Case
- Re: AMBER: Solvent models FyD
- Re: AMBER: Reg restraint value obtained during umbrella sampling David A. Case
- Re: AMBER: cutoff & speed-up of GBSA Wei Chen
- Re: AMBER: cutoff & speed-up of GBSA Julien Michel
- AMBER: les/nudged elastic band Tamara Rogers
- RE: AMBER: les/nudged elastic band Ross Walker
Thursday, 3 May 2007
- [AMBER] defining the mixed 1-4 scaling in amber 11 and sleap Toshifumi Yui
- Re: [AMBER] defining the mixed 1-4 scaling in amber 11 and sleap Toshifumi Yui

Last message date: Tue May 03 2011 - 19:00:02 PDT
Archived on: Sun Nov 24 2024 - 05:53:47 PST

Amber Archive May 2007 by date