Amber Archive Mar 2009: by date

Sunday, 1 March 2009
- Re: [AMBER] binding free energy Barbault Florent
- Re: [AMBER] Question about NAB module David A. Case
- RE: [AMBER] Question about NAB module Wei Huang
- Re: [AMBER] binding free energy Don.Bashford.stjude.org
- RE: [AMBER] binding free energy Ross Walker
Monday, 2 March 2009
- RE: [AMBER] Question about NAB module Andreas Svrcek-Seiler
- [AMBER] Pseudoatoms waleed zalloum
- Re: [AMBER] binding free energy Robert Duke
- [AMBER] calculate shear viscosity oguz gurbulak
- Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? David A. Case
- [AMBER] Re: using Gromacs for analysis oguz gurbulak
- [AMBER] assigning velocities to each atom without heating the system Parimal Kar
- Re: [AMBER] assigning velocities to each atom without heating the system Gustavo Seabra
- Re: [AMBER] assigning velocities to each atom without heating the system Parimal Kar
- RE: [AMBER] binding free energy Ross Walker
- RE: [AMBER] assigning velocities to each atom without heating the system Ross Walker
- Re: [AMBER] Pseudoatoms David A. Case
- [AMBER] How to restart the umbrella sampling jobs? Catein Catherine
- [AMBER] specification of antechamber AC file format? Nicholas Musolino
Tuesday, 3 March 2009
- [AMBER] inpcrd and prmtop m m
- Re: [AMBER] inpcrd and prmtop Hannes Loeffler
- RE: [AMBER] inpcrd and prmtop m m
- Re: [AMBER] inpcrd and prmtop FyD
- [AMBER] Fail to allocate ff Madhurima Jana
- Re: [AMBER] Fail to allocate ff Nicholas Musolino
- Re: Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? David A. Case
- Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? FyD
- Re: [AMBER] Fail to allocate ff Madhurima Jana
- RE: [AMBER] How to restart the umbrella sampling jobs? Ross Walker
- Re: [AMBER] inpcrd and prmtop Gustavo Seabra
- Re: [AMBER] Fail to allocate ff Gustavo Seabra
- Re: [AMBER] How to restart the umbrella sampling jobs? Gustavo Seabra
- [AMBER] A good way to use an Amber force field with NAMD? Sasha Buzko
- [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory Jeff Schwinefus
- Re: [AMBER] A good way to use an Amber force field with NAMD? Gustavo Seabra
- Re: [AMBER] A good way to use an Amber force field with NAMD? Adrian Roitberg
- Re: [AMBER] A good way to use an Amber force field with NAMD? Sasha Buzko
- RE: [AMBER] A good way to use an Amber force field with NAMD? Ross Walker
- Re: [AMBER] A good way to use an Amber force field with NAMD? Sasha Buzko
- Re: [AMBER] A good way to use an Amber force field with NAMD? Robert Duke
Wednesday, 4 March 2009
- [AMBER] angle between ligand ring plane and axis Jia Xu
- [AMBER] hydrogen bond . ..
- Re: [AMBER] hydrogen bond Carlos Simmerling
- [AMBER] Regarding leap aneesh cna
- Re: [AMBER] Regarding leap Carlos Simmerling
- [AMBER] unning MMPBSA in CHCl3 environment SAFAK OZHAN
- [AMBER] Thermodynamic Intergration problem Xiaohui Jiang [Contractor]
- [AMBER] Compilation and qmmm_div Benjamin Roberts
- RE: [AMBER] Compilation and qmmm_div Ross Walker
- RE: [AMBER] hydrogen bond Ross Walker
- RE: [AMBER] Thermodynamic Intergration problem Ross Walker
- RE: [AMBER] Thermodynamic Intergration problem Xiaohui Jiang [Contractor]
- Re: [AMBER] unning MMPBSA in CHCl3 environment Ray Luo
- Re: [AMBER] A good way to use an Amber force field with NAMD? Sasha Buzko
- [AMBER] radial distribution function mask iccy liu
- Re: [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory Thomas Cheatham III
- Re: [AMBER] H-Bonds Thomas Cheatham III
- [AMBER] What is the default position of the partial charges? Chih-Ying Lin
- [AMBER] solvent and counter ions Taufik Al-Sarraj
- Re: [AMBER] What is the default position of the partial charges? Thomas Cheatham III
- Re: [AMBER] solvent and counter ions Thomas Cheatham III
- Re: [AMBER] Regarding leap Gustavo Seabra
- Re: [AMBER] specification of antechamber AC file format? David A. Case
- Re: [AMBER] Compilation and qmmm_div Benjamin Roberts
- [AMBER] Segmentation faults Benjamin Roberts
- Re: [AMBER] solvent and counter ions Bill Ross
- [AMBER] AMBER installation : compilation error Catein Catherine
- [AMBER] DNA simulation: Problem with RMSD BERGY
- Re: [AMBER] DNA simulation: Problem with RMSD Thomas Cheatham
- Re: [AMBER] Regarding leap aneesh cna
- [AMBER] Fwd: please help me out bharat lakhani
- Re: [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory Jeff Schwinefus
- [AMBER] Re: Fw:How to creat .frcmod file FyD
Thursday, 5 March 2009
- [AMBER] please help me out bharat lakhani
- Re: [AMBER] please help me out FyD
- [AMBER] chemical shift penalty Jacopo Sgrignani
- Re: [AMBER] please help me out bharat lakhani
- [AMBER] divcon error during antechamber run, convergence problem drugdesign
- [AMBER] secstruct Beale, John
- Re: [AMBER] divcon error during antechamber run, convergence problem Martin Peters
- Re: [AMBER] secstruct Carlos Simmerling
- Re: [AMBER] Regarding leap Gustavo Seabra
- [AMBER] MM-PBSA decomp by residue and snapshot? Bradshaw, Richard
- [AMBER] Warning: name change in pdb file residue Donald Keidel
- RE: [AMBER] Warning: name change in pdb file residue Duggan, Brendan M.
- Re: [AMBER] solvent and counter ions Taufik Al-Sarraj
- Re: [AMBER] solvent and counter ions Bill Ross
- [AMBER] GBSA: dielectric symmetry Giacomo Bastianelli
- Re: [AMBER] chemical shift penalty David A. Case
- Re: [AMBER] GBSA: dielectric symmetry David A. Case
- Re: [AMBER] DNA simulation: Problem with RMSD BERGY
- [AMBER] High RMSD for DNA: A to B transition study BERGY
Friday, 6 March 2009
- [AMBER] Quality/size of HDD for Amber Francesco Pietra
- [AMBER] Solvate Box od amoeba water Hemant Gangwar
- [AMBER] catenan simulation problems Cristina Sisu
- Re: [AMBER] Solvate Box od amoeba water Wei Zhang
- Re: [AMBER] High RMSD for DNA: A to B transition study David A. Case
- Re: [AMBER] catenan simulation problems David A. Case
- Re: [AMBER] catenan simulation problems Cristina Sisu
- Re: [AMBER] catenan simulation problems Cristina S.D. Sisu
- Re: [AMBER] Quality/size of HDD for Amber M. L. Dodson
- Re: [AMBER] divcon error during antechamber run, convergence problem Andrew Voronkov
- Re: [AMBER] divcon error during antechamber run, convergence problem David A. Case
- [AMBER] Help with torsions in parm99.dat file Gregersen, Brent
- RE: [AMBER] Help with torsions in parm99.dat file Ross Walker
- RE: [AMBER] Help with torsions in parm99.dat file Gregersen, Brent
- [AMBER] Problem with particle-mesh Ewald method Yunjie Zhao
- Re: [AMBER] Problem with particle-mesh Ewald method steinbrt.rci.rutgers.edu
- RE: [AMBER] Problem with particle-mesh Ewald method Ross Walker
- RE: [AMBER] Help with torsions in parm99.dat file Ross Walker
Saturday, 7 March 2009
- Re: [AMBER] divcon error during antechamber run, convergence problem Andrew Voronkov
- [AMBER] analysis on Amber oguz gurbulak
- Re: [AMBER] analysis on Amber Thomas Cheatham
- Re: [AMBER] catenan simulation problems David A. Case
Sunday, 8 March 2009
- [AMBER] Fw:how to select force field Nancy
- [AMBER] nmoldyn2 with Amber Adrien Delmont
- Re: [AMBER] nmoldyn2 with Amber David Watson
- Re: [AMBER] nmoldyn2 with Amber David Watson
- RE: [AMBER] Fw:how to select force field Ross Walker
- Re: [AMBER] nmoldyn2 with Amber M. L. Dodson
- Re: [AMBER] nmoldyn2 with Amber M. L. Dodson
- Re: [AMBER] nmoldyn2 with Amber David Watson
- Re: [AMBER] nmoldyn2 with Amber Thomas Cheatham
- [AMBER] PMEMD error message neville forlemu
- Re: [AMBER] PMEMD error message Robert Duke
- RE: [AMBER] PMEMD error message Ross Walker
- Re: [AMBER] please help me out bharat lakhani
Monday, 9 March 2009
- Re: [AMBER] please help me out FyD
- [AMBER] addles segmentation fault gmail
- Re: [AMBER] please help me out bharat lakhani
- [AMBER] Particle-mesh Ewald method Yunjie Zhao
- Re: [AMBER] please help me out FyD
- [AMBER] 8Mureabox anna berteotti
- Re: [AMBER] addles segmentation fault Carlos Simmerling
- Re: [AMBER] addles segmentation fault xiaonan zhang
- Re: [AMBER] Help with torsions in parm99.dat file Astrid Maaß
- [AMBER] Restraint Mask length restriction !! Sampath Koppole
- Re: [AMBER] Restraint Mask length restriction !! David A. Case
- [AMBER] generalized distance restraint Rausch, Felix
- [AMBER] Free Energy Decomposition Problem ozlem ulucan
- Re: [AMBER] Restraint Mask length restriction !! Sampath Koppole
- Re: [AMBER] Restraint Mask length restriction !! David A. Case
- Re: [AMBER] Help with torsions in parm99.dat file Wei Zhang
- Re: [AMBER] Restraint Mask length restriction !! Sampath Koppole
- Re: [AMBER] generalized distance restraint Carlos Simmerling
- RE: [AMBER] generalized distance restraint Rausch, Felix
- Re: [AMBER] generalized distance restraint Carlos Simmerling
- Re: [AMBER] generalized distance restraint M. L. Dodson
- Re: [AMBER] Quality/size of HDD for Amber Gustavo Seabra
- RE: [AMBER] Restraint Mask length restriction !! Ross Walker
- RE: [AMBER] Particle-mesh Ewald method Ross Walker
- [AMBER] Changing Force Fields in "Midstream" Hopkins, Robert
- RE: [AMBER] Changing Force Fields in "Midstream" Ross Walker
- [AMBER] problem in rmsd Parimal Kar
- Re: [AMBER] problem in rmsd Thomas Cheatham
- Re: [AMBER] problem in rmsd Parimal Kar
- Re: [AMBER] problem in rmsd Thomas Cheatham
- [AMBER] PB Bomb from MM-PBSA of Amber 10 Zhu, Yong-Liang
Tuesday, 10 March 2009
- Re: [AMBER] problem in rmsd Hannes Loeffler
- Re: [AMBER] problem in rmsd Carlos Simmerling
- RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Wei Huang
- Re: [AMBER] 8Mureabox David A. Case
- [AMBER] PMEMD error message neville forlemu
- [AMBER] sulfotyrosine parameters Ryan Pavlovicz
- Re: [AMBER] PMEMD error message Robert Duke
- RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Zhu, Yong-Liang
- [AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero
- RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Wei Huang
- RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Ray Luo
- RE: [AMBER] Changing Force Fields in "Midstream" Hopkins, Robert
Wednesday, 11 March 2009
- RE: [AMBER] generalized distance restraint Rausch, Felix
- RE: [AMBER] 8Mureabox anna berteotti
- [AMBER] about MD simulation 廖青华
- Re: [AMBER] about MD simulation Carlos Simmerling
- Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? David A. Case
- [AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman
- RE: [AMBER] Seeking for suggestion related to plot the cluster out file Ross Walker
- Re: [AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman
- RE: [AMBER] Seeking for suggestion related to plot the cluster out file Ross Walker
- Re: [AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman
- 回复： [AMBER] about MD simulation 廖青华
- Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero
- Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? steinbrt.rci.rutgers.edu
- Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero
- Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? steinbrt.rci.rutgers.edu
- [AMBER] installing AmberTools on Windows machines David A. Case
- RE: [AMBER] Changing Force Fields in "Midstream" Hopkins, Robert
- Re: [AMBER] Changing Force Fields in "Midstream" Wei Zhang
- Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero
- RE: [AMBER] Changing Force Fields in "Midstream" Kristina Furse
- [AMBER] polarizable force field and solvent zeinab bagheri
- Re: [AMBER] Changing Force Fields in "Midstream" David A. Case
- [AMBER] Understanding the all.out file in the MM-PBSA output gmail
- [AMBER] polarizable force field and solvent zeinab bagheri
- Re: [AMBER] please help me out bharat lakhani
Thursday, 12 March 2009
- [AMBER] Problem with REMD parul sharma
- [AMBER] Problems with MM-PBSA Calculation after MD German Erlenkamp
- Re: [AMBER] Understanding the all.out file in the MM-PBSA output Hannes Kopitz
- Re: [AMBER] Problem with REMD Carlos Simmerling
- Re: [AMBER] Problems with MM-PBSA Calculation after MD Hannes Kopitz
- RE: [AMBER] Understanding the all.out file in the MM-PBSA output Ray Luo
- Re: [AMBER] please help me out rpaduri.chem.wayne.edu
- [AMBER] SMD in Amber10 Dmitri Nilov
- Re: [AMBER] SMD in Amber10 Adrian Roitberg
- RE: [AMBER] Changing Force Fields in "Midstream" Hopkins, Robert
- Re: [AMBER] NAB md function prints strange output Scott Brozell
- [AMBER] Thermodynamic Integration at higher values of clambda using AMBER 9 PRADEEP VENKATARAMAN
- Re: [AMBER] Thermodynamic Integration at higher values of clambda using AMBER 9 steinbrt.rci.rutgers.edu
- Re: [AMBER] High RMSD for DNA: A to B transition study SENTHIL KUMAR
Friday, 13 March 2009
- Re: [AMBER] SMD in Amber10 Dmitri Nilov
- [AMBER] Problem running test.pmemd.AMOEBA mloureiro.cesga.es
- Re: [AMBER] High RMSD for DNA: A to B transition study David A. Case
- [AMBER] to understand multiplicity in antechamber Alan
- [AMBER] Problem build pmemd Yiannis Georgiadis
- Re: [AMBER] Problem build pmemd Robert Duke
- Re: [AMBER] SMD in Amber10 Adrian Roitberg
- Re: [AMBER] Problem running test.pmemd.AMOEBA Robert Duke
- [AMBER] to understand multiplicity in antechamber Alan
- Re: [AMBER] SMD in Amber10 Dmitri Nilov
- Re: [AMBER] SMD in Amber10 Adrian Roitberg
- Re: [AMBER] SMD in Amber10 Dmitri Nilov
- [AMBER] doubt-reg_ Targeted molecular dynamics balaji nagarajan
- Re: [AMBER] to understand multiplicity in antechamber Scott Brozell
- [AMBER] problems compiling ambertool Per Jr. Greisen
- Re: [AMBER] problems compiling ambertool David A. Case
- Re: [AMBER] problems compiling ambertool Per Jr. Greisen
- Re: [AMBER] to understand multiplicity in antechamber Alan
Saturday, 14 March 2009
- Re: [AMBER] please help me out bharat lakhani
- Re: [AMBER] please help me out David A. Case
- [AMBER] suggestions for PB simulation Bala subramanian
- RE: [AMBER] please help me out Ross Walker
- Re: [AMBER] problems compiling ambertool Atro Tossavainen
- Re: [AMBER] Problem build pmemd Atro Tossavainen
Sunday, 15 March 2009
- [AMBER] sander.MPI and pmemd.MPI in Fedora 8 John Bennett
Monday, 16 March 2009
- Re: [AMBER] problems compiling ambertool Atro Tossavainen
- Re: [AMBER] problems compiling ambertool David A. Case
- [AMBER] Unit 5 Error on OPEN: nan.in Nancy
- Re: [AMBER] problems compiling ambertool Per Jr. Greisen
- Re: [AMBER] Unit 5 Error on OPEN: nan.in mathew k varghese
- Re: [AMBER] problems compiling ambertool David A. Case
- Re: [AMBER] problems compiling ambertool Per Jr. Greisen
- Re:Re: [AMBER] Unit 5 Error on OPEN: nan.in Nancy
- Re: [AMBER] problems compiling ambertool David A. Case
- Re: Re: [AMBER] Unit 5 Error on OPEN: nan.in Carlos Simmerling
- Re: [AMBER] problems compiling ambertool Per Jr. Greisen
- [AMBER] about mm-pbsa 廖青华
- [AMBER] about mm-pbsa 廖青华
- Re: [AMBER] problems compiling ambertool David A. Case
- RE: [AMBER] about mm-pbsa Wei Huang
- [AMBER] minimisation with igb=10 Bala subramanian
- Re: [AMBER] minimisation with igb=10 Carlos Simmerling
- Re: [AMBER] minimisation with igb=10 Bala subramanian
- Re: [AMBER] minimisation with igb=10 Carlos Simmerling
- RE: [AMBER] minimisation with igb=10 Ray Luo
- [AMBER] Actual force constant in SMD Dmitri Nilov
- [AMBER] Re: join two units in amber9 or amber10 Taufik Al-Sarraj
- [AMBER] mol2 - pdb conversion Taufik Al-Sarraj
- Re: [AMBER] problems compiling ambertool Per Jr. Greisen
- Re: [AMBER] problems compiling ambertool Bill Ross
- Re: [AMBER] Re: join two units in amber9 or amber10 Bill Ross
- [AMBER] Unit 5 Error on OPEN: nan.in Nancy
- [AMBER] Input file of the second stage RESP fitting Cen Gao
- [AMBER] regarding tutorial on united atom force field jani sahil
Tuesday, 17 March 2009
- Re: [AMBER] problems compiling ambertool Per Jr. Greisen
- [AMBER] Unit 5 Error on OPEN: nan.in Nancy
- Re: [AMBER] Unit 5 Error on OPEN: nan.in mathew k varghese
- Re: [AMBER] Unit 5 Error on OPEN: nan.in Jenny Iskrenova
- Re: [AMBER] problems compiling ambertool David A. Case
- Re: [AMBER] Input file of the second stage RESP fitting FyD
- Re:Re: [AMBER] Unit 5 Error on OPEN: nan.in Nancy
- [AMBER] removing center of mass Bala subramanian
- Re: [AMBER] mol2 - pdb conversion David A. Case
- [AMBER] convert .mol2 file to .pdb with atomtype definitions Pansy Patel
- Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions David A. Case
- Re: [AMBER] problems compiling ambertool Per Jr. Greisen
- Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions Pansy Patel
- Re: [AMBER] problems compiling ambertool David A. Case
- Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions Wei Zhang
- RE: [AMBER] convert .mol2 file to .pdb with atomtype definitions Pankaj R. Daga
- Re: [AMBER] temperature rises with igb=1 Carlos Simmerling
- [AMBER] temperature rises with igb=1 Bala subramanian
- Re: [AMBER] regarding tutorial on united atom force field Ray Luo
- RE: [AMBER] temperature rises with igb=1 Ross Walker
- Re: [AMBER] temperature rises with igb=1 Carlos Simmerling
- Re: [AMBER] problems compiling ambertool Bill Ross
- Re: [AMBER] Unit 5 Error on OPEN: nan.in Bill Ross
- Re: [AMBER] problems compiling ambertool Bill Ross
- [AMBER] CCL4 simulation sudipta
- [AMBER] error in constructing DNA from nucgen Pansy Patel
- Re: [AMBER] error in constructing DNA from nucgen Carlos Simmerling
- Re: [AMBER] error in constructing DNA from nucgen Pansy Patel
- RE: [AMBER] error in constructing DNA from nucgen Ross Walker
- Re: [AMBER] Input file of the second stage RESP fitting Cen Gao
- Re: [AMBER] error in constructing DNA from nucgen Bill Ross
- Re: [AMBER] CCL4 simulation David A. Case
Wednesday, 18 March 2009
- Re: [AMBER] CCL4 simulation sudipta
- [AMBER] About error of "vertex atom mismatch" 廖青华
- [AMBER] errors about install amber9 on MAC OS zgong.hust
- [AMBER] protein protrudes from unit cell Jeffrey
- Re: [AMBER] protein protrudes from unit cell Hannes Loeffler
- Re: [AMBER] TMD Carlos Simmerling
- Re: [AMBER] CCL4 simulation David A. Case
- Re: [AMBER] errors about install amber9 on MAC OS David A. Case
- [AMBER] sleap and check Alan
- Re: [AMBER] catenan simulation problems David A. Case
- Re: [AMBER] problems compiling ambertool Per Jr. Greisen
- Re: [AMBER] problems compiling ambertool David A. Case
- Re: [AMBER] problems compiling ambertool Per Jr. Greisen
- [AMBER] lipid bliayers Urszula Uciechowska
- Re: [AMBER] lipid bliayers Hannes Loeffler
- Re: [AMBER] Problem build pmemd Giorgos Lamprinidis
- Re: [AMBER] Problem build pmemd Robert Duke
- Re: [AMBER] sleap and check Wei Zhang
- Re: [AMBER] problem in running sander Carlos Simmerling
- RE: [AMBER] protein protrudes from unit cell Ross Walker
- Re: [AMBER] protein protrudes from unit cell Carlos Simmerling
- Re: [AMBER] problem in running sander Carlos Simmerling
- Re: [AMBER] mol2 - pdb conversion Taufik Al-Sarraj
- Re: [AMBER] sleap and check Alan
- Re: [AMBER] mol2 - pdb conversion David A. Case
- Re: [AMBER] IG not change at each restart of NPT simulation Hopkins, Robert
- RE: [AMBER] IG not change at each restart of NPT simulation Ross Walker
- RE: [AMBER] IG not change at each restart of NPT simulation Hopkins, Robert
- [AMBER] Mass of LP PRADEEP VENKATARAMAN
- [AMBER] simulation in water-oil (or water/hydrophobic-solvent) box ranga nath
- [AMBER] Metal in MD simulation priya priya
- [AMBER] About mm-pbsa 廖青华
Thursday, 19 March 2009
- Re: [AMBER] problem in running sander Kshatresh Dutta Dubey
- [AMBER] [about advanced tutorial 1] How could I get conformations for gaussian that have minimum energy? Youn Kyeung Lee
- [AMBER] error for nmode Dechang Li
- Re: [AMBER] temperature rises with igb=1 Bala subramanian
- Re: [AMBER] Mass of LP David A. Case
- Re: [AMBER] error for nmode David A. Case
- Re: [AMBER] temperature rises with igb=1 David A. Case
- Re: [AMBER] problem in running sander David A. Case
- RE: [AMBER] IG not change at each restart of NPT simulation Rajesh Raju
- Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke
- Re: [AMBER] IG not change at each restart of NPT simulation Adrian Roitberg
- Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke
- Re: [AMBER] Metal in MD simulation Jagadeesh, M.N., Ph.D.
- [AMBER] pmemd compile error.... Giorgos Lamprinidis
- RE: [AMBER] Metal in MD simulation Ross Walker
- Re: [AMBER] pmemd compile error.... Robert Duke
- Re: [AMBER] pmemd compile error.... Robert Duke
- Re: [AMBER] simulation in water-oil (or water/hydrophobic-solvent) box David A. Case
- [AMBER] protein PDB Chih-Ying Lin
- Re: [AMBER] Metal in MD simulation Bill Ross
- [AMBER] Parametrisation of Silicon based molecules for Amber simulations ? Marek Malý
- Re: [AMBER] Metal in MD simulation priya priya
- [AMBER] Help needed in amber parallel installation sushobhan.iiar.res.in
Friday, 20 March 2009
- Re: [AMBER] analysing DNA trajectory Bala subramanian
- [AMBER] QM/MM charges Jacopo Sgrignani
- [AMBER] Announcement of Model(l)ing'09 - The annual 2009 MGMS Meeting in Erlangen, Germany Harald Lanig
- Re: [AMBER] Help needed in amber parallel installation Carlos Simmerling
- Re: [AMBER] IG not change at each restart of NPT simulation Rajesh Raju
- Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke
- RE: [AMBER] QM/MM charges Ross Walker
- RE: [AMBER] Help needed in amber parallel installation Ross Walker
- [AMBER] MMGBSA IG Value Rajesh Raju
- Re: [AMBER] MMGBSA IG Value Carlos Simmerling
- Re: [AMBER] MMGBSA IG Value Rajesh Raju
- Re: [AMBER] MMGBSA IG Value Carlos Simmerling
- [AMBER] xmgrace Nancy
- Re: [AMBER] xmgrace mathew k varghese
- Re:Re: [AMBER] xmgrace Nancy
Saturday, 21 March 2009
- Re: [AMBER] simulation in water-oil (or water/hydrophobic-solvent) box ranga nath
- [AMBER] adding chain id to ptraj pdb output Paul Brandt
Sunday, 22 March 2009
- Re: [AMBER] Solvate Box od amoeba water Hemant Kumar
- Re: [AMBER] [about advanced tutorial 1] How could I get conformations for gaussian that have minimum energy? FyD
Monday, 23 March 2009
- Re: [AMBER] please help me out bharat lakhani
- [AMBER] about mm-pbsa 廖青华
- [AMBER] leap and chirality Karl Kirschner
- [AMBER] problem in installing AMBER10 Dr. Debaprasad Giri
- [AMBER] Regarding use of PME along with Implict solvation jani sahil
- Re: [AMBER] Regarding use of PME along with Implict solvation parul sharma
- Re: [AMBER] problem in installing AMBER10 David A. Case
- Re: [AMBER] adding chain id to ptraj pdb output Bala subramanian
- Re: [AMBER] Regarding use of PME along with Implict solvation jani sahil
- Re: [AMBER] leap and chirality David A. Case
- Re: [AMBER] leap and chirality Karl Kirschner
- Re: [AMBER] helical parameters Bala subramanian
- Re: [AMBER] leap and chirality Wei Zhang
- [AMBER] pmemd compile error Giorgos Lamprinidis
- Re: [AMBER] pmemd compile error Robert Duke
- Re: [AMBER] adding chain id to ptraj pdb output Joe Krahn
- [AMBER] errors on reading time series file in WHAM calculation gmail
- [AMBER] validation of parameters and request of suggestions Jeffrey
- [AMBER] continuam water Mannan
Tuesday, 24 March 2009
- Re: [AMBER] leap and chirality Karl Kirschner
- [AMBER] change in protein ligand order Hannes Wallnoefer
- Re: [AMBER] change in protein ligand order Hannes Loeffler
- [AMBER] validation of parameters and request suggestions Jeffrey
- Re: [AMBER] pmemd compile error.... case
- Re: [AMBER] pmemd compile error.... Robert Duke
- Re: [AMBER] change in protein ligand order Hannes Wallnoefer
- Re: [AMBER] leap and chirality Wei Zhang
- Re: [AMBER] continuam water Carlos Simmerling
- Re: [AMBER] please help me out bharat lakhani
- Re: [AMBER] errors on reading time series file in WHAM calculation Jenny Iskrenova
- Re: [AMBER] problem with amber installation nicholus bhattacharjee
- Re: [AMBER] change in protein ligand order Bill Ross
- [AMBER] POLARIZABLE WATER MODEL CHAMI F.
- Re: [AMBER] change in protein ligand order Hannes Wallnoefer
- [AMBER] create new crd files from transformed coordinates Donald Keidel
Wednesday, 25 March 2009
- [AMBER] question about pair wise per-residue energy decomposition; idecomp=3 wfli.biophy.nju.edu.cn
- Re: [AMBER] create new crd files from transformed coordinates case
- [AMBER] About Free energy decomposition Rajesh Raju
- [AMBER] Rosetta Academic Training Webinar Nir London
- Re: [AMBER] question about pair wise per-residue energy decomposition; idecomp=3 case
- [AMBER] How to reproduce a parallel PMEMD run? Siang Yip
- Re: [AMBER] How to reproduce a parallel PMEMD run? Robert Duke
Thursday, 26 March 2009
- [AMBER] Amber 10 and core i7 Supat Jiranusornkul
- [AMBER] To find radial distribution curve nicholus bhattacharjee
- [AMBER] installing resp on linux 64bit aditya chhikara
- Re: [AMBER] installing resp on linux 64bit FyD
- Re: [AMBER] installing resp on linux 64bit aditya chhikara
- [AMBER] Problem with "Atom does not have a type" Richard Tseng
- [AMBER] Fwd: AMBER: MM-PBSA in AMBER 10 Daniel Oehme
- Re: [AMBER] Fwd: AMBER: MM-PBSA in AMBER 10 Ray Luo
- [AMBER] Problem reading PDB file into XLEAP Hopkins, Robert
- [AMBER] Antechamber problem 欧阳德方
Friday, 27 March 2009
- Re: [AMBER] problem in installing AMBER10 Dr. Debaprasad Giri
- [AMBER] problem using amoeba Hemant Gangwar
- Re: [AMBER] Problem with "Atom does not have a type" David A. Case
- Re: [AMBER] problem in installing AMBER10 David A. Case
- Re: [AMBER] problem using amoeba Robert Duke
- Re: [AMBER] Antechamber problem David A. Case
- Re: [AMBER] Problem reading PDB file into XLEAP David A. Case
- [AMBER] Question Kshatresh Dutta Dubey
- RE: [AMBER] Question Rausch, Felix
- [AMBER] PMEMD 9 on MVAPICH / Infiniband problem Nick Holway
- Re: [AMBER] Antechamber problem Junmei Wang
- Re: [AMBER] Problem with "Atom does not have a type" Richard Tseng
- Re: [AMBER] Problem with "Atom does not have a type" Richard Tseng
- RE: [AMBER] Problem reading PDB file into XLEAP Hopkins, Robert
- RE: [AMBER] Antechamber problem 欧阳德方
- RE: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem Ross Walker
- [AMBER] Load protein complex to Xleap (Combine) Rilei Yu
Saturday, 28 March 2009
- Re: [AMBER] Question Kshatresh Dutta Dubey
- Re: [AMBER] Problem with "Atom does not have a type" David A. Case
- Re: [AMBER] Problem reading PDB file into XLEAP David A. Case
- Re: [AMBER] Question David A. Case
- Re: [AMBER] Load protein complex to Xleap (Combine) David A. Case
- RE: [AMBER] Problem reading PDB file into XLEAP - SLEAP Hopkins, Robert
- Re: [AMBER] Problem reading PDB file into XLEAP - SLEAP Wei Zhang
- Re: [AMBER] Load protein complex to Xleap (Combine) Rilei Yu
- Re: [AMBER] Load protein complex to Xleap (Combine) David A. Case
- Re: [AMBER] Load protein complex to Xleap (Combine) Rilei Yu
- Re: [AMBER] Load protein complex to Xleap (Combine) Rilei Yu
Sunday, 29 March 2009
- RE: [AMBER] Problem reading PDB file into XLEAP - SLEAP Hopkins, Robert
- Re: [AMBER] Problem reading PDB file into XLEAP - SLEAP David A. Case
- Re: [AMBER] Load protein complex to Xleap (Combine) David A. Case
- Re: [AMBER] Problem with "Atom does not have a type" Richard Tseng
- [AMBER] .rst file generation problem. Aravind S
- [AMBER] "rfree: End of file on unit 5" Remya S R
- Re: [AMBER] .rst file generation problem. Aravind S
Monday, 30 March 2009
- Re: [AMBER] "rfree: End of file on unit 5" mathew k varghese
- [AMBER] mm_pbsa problem Giorgos Lamprinidis
- [AMBER] Creating conditions for biased MD Francesco Pietra
- Re: [AMBER] .rst file generation problem. Carlos Simmerling
- Re: [AMBER] Creating conditions for biased MD Carlos Simmerling
- Re: [AMBER] Problem with "Atom does not have a type" case
- Re: [AMBER] mm_pbsa problem case
- Re: [AMBER] mm_pbsa problem Giorgos Lamprinidis
- [AMBER] amber tools installation Jayalakshmi Sridhar
- Re: [AMBER] amber tools installation case
- [AMBER] Announcing NMR validation web interface iCing Alan
- RE: [AMBER] mm_pbsa problem Ray Luo
- [AMBER] BINDER/xaLeap Taufik Al-Sarraj
- RE: [AMBER] BINDER/xaLeap Ross Walker
- RE: [AMBER] BINDER/xaLeap taufik.alsarraj.utoronto.ca
- [AMBER] problem with the results in the .out file! Aravind S
Tuesday, 31 March 2009
- Re: [AMBER] .rst file generation problem. Aravind S
- [AMBER] how to convert secstruct output file into plot or pictorial representation Siddharth Rastogi
- Re: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem fohm fohm
- Re: [AMBER] .rst file generation problem. Carlos Simmerling
- Re: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem Robert Duke
- Re: [AMBER] problem with the results in the .out file! Gustavo Seabra
- [AMBER] modifying LYN Marius Retegan
- [AMBER] combine many coord files into trajectory file Peter Gannett
- Re: [AMBER] combine many coord files into trajectory file Carlos Simmerling
- Re: [AMBER] combine many coord files into trajectory file Peter Gannett
- Re: [AMBER] modifying LYN FyD
- Re: [AMBER] modifying LYN Marius Retegan
- [AMBER] ambmol2? Taufik Al-Sarraj

Last message date: Wed Apr 01 2009 - 01:18:02 PDT
Archived on: Fri Nov 22 2024 - 05:53:45 PST

Amber Archive Mar 2009 by date