Amber Archive Feb 2009: by date

Saturday, 31 January 2009
- [AMBER] Citing AMBER Tools... Aydin, Cihan
- Re: [AMBER] Test run on Solaris 10 X 86 Atro Tossavainen
- [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? liu junjun
Sunday, 1 February 2009
- [AMBER] the output files oguz gurbulak
- Re: [AMBER] Question on heating for homology based model. Carlos Simmerling
- Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? Carlos Simmerling
- Re: [AMBER] REMD fixed atoms Carlos Simmerling
- Re: [AMBER] the output files Carlos Simmerling
- Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? David A. Case
- Re: [AMBER] RE: Tutorial 5 George Tzotzos
Monday, 2 February 2009
- [AMBER] strip frames from crd file aneesh cna
- [AMBER] strip frames from crd file aneesh cna
- Re: [AMBER] strip frames from crd file Carlos Simmerling
- [AMBER] md simulation on parallel PMEMD oguz gurbulak
- Re: [AMBER] md simulation on parallel PMEMD David A. Case
- Re: [AMBER] md simulation on parallel PMEMD Carlos Simmerling
- Re: [AMBER] md simulation on parallel PMEMD Robert Duke
- Re: [AMBER] Dr. Ramesh here kureeckal ramesh
- [AMBER] precision in the trajectory files Jenny Iskrenova
- Re: [AMBER] precision in the trajectory files Adrian Roitberg
- Re: [AMBER] precision in the trajectory files David A. Case
- Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? liu junjun
- [AMBER] Radius of Gyration Beale, John
- [AMBER] Langevin dynamics Antonios Samiotakis
- Re: [AMBER] Test run on Solaris 10 X 86 Manikandan Chandrasekaran
- Re: [AMBER] Langevin dynamics David A. Case
- [AMBER] DFT SK parameter for P atom Qizhi Cui
- Re: [AMBER] DFT SK parameter for P atom Adrian Roitberg
- Re: [AMBER] DFT SK parameter for P atom Qizhi Cui
- Re: [AMBER] Test run on Solaris 10 X 86 Atro Tossavainen
Tuesday, 3 February 2009
- [AMBER] Micelles set-up?? Alexander Schierholt
- [AMBER] creating a restart file from md.out oguz gurbulak
- Re: [AMBER] creating a restart file from md.out Carlos Simmerling
- Re: [AMBER] creating a restart file from md.out oguz gurbulak
- [AMBER] nab compile error with -scalapack chaitanya koppisetty
- Re: [AMBER] creating a restart file from md.out Carlos Simmerling
- Re: [AMBER] nab compile error with -scalapack David A. Case
- Re: [AMBER] creating a restart file from md.out oguz gurbulak
- [AMBER] -MMTSB instalation flag ? Marek Malý
- Re: [AMBER] creating a restart file from md.out Carlos Simmerling
- Re: [AMBER] -MMTSB instalation flag ? Scott Brozell
- [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun drugdesign
- Re: [AMBER] precision in the trajectory files Jenny Iskrenova
- Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Ye MEI
- Re: [AMBER] -MMTSB instalation flag ? Marek Malý
- Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Carlos Simmerling
- RE: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Ross Walker
- Re: [AMBER] -MMTSB instalation flag ? Scott Brozell
- Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Carlos Simmerling
- Re: [AMBER] nab compile error with -scalapack chaitanya koppisetty
- [AMBER] out error . ..
- Re: [AMBER] adding MG2 problem Scott Brozell
- Re: [AMBER] out error Carlos Simmerling
- Re: [AMBER] Test run on Solaris 10 X 86 Manikandan Chandrasekaran
- [AMBER] MKL error ? Marek Malý
- RE: [AMBER] MKL error ? Ross Walker
- Re: [AMBER] Radius of Gyration priya priya
- Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun drugdesign
Wednesday, 4 February 2009
- Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Carlos Simmerling
- Re: [AMBER] Test run on Solaris 10 X 86 Atro Tossavainen
- RE: [AMBER] adding MG2 problem Rausch, Felix
- [AMBER] a question about umbrella sampling (US) xiaoqin huang
- Re: [AMBER] a question about umbrella sampling (US) Carlos Simmerling
- Re: [AMBER] Test run on Solaris 10 X 86 Manikandan Chandrasekaran
- [AMBER] PDB of a specific frame Jason A. Ford-Green
- Re: [AMBER] PDB of a specific frame Carlos Simmerling
- RE: [AMBER] a question about umbrella sampling (US) xiaoqin huang
- [AMBER] compiling errors Gard Nelson
- [AMBER] Restarting an MD Simulation Hopkins, Robert
- Re: [AMBER] compiling errors Carlos Simmerling
- RE: [AMBER] compiling errors Ross Walker
- RE: [AMBER] Restarting an MD Simulation Ross Walker
- [AMBER] pmemd installation in intelmpi Vijay Manickam Achari
- [AMBER] Compiling Carnal Amber7 in Amber9 Vijay Manickam Achari
- RE: [AMBER] Restarting an MD Simulation Ross Walker
- [AMBER] production run terminates due to (*) symbols in xxx.rst Vijay Manickam Achari
- Re: [AMBER] pmemd installation in intelmpi Robert Duke
- [AMBER] how can i deal with large number atoms Wang,Ying
- [AMBER] How to build reference coordinate file for targeted MD gmail
- Re: [AMBER] Test run on Solaris 10 X 86 Atro Tossavainen
Thursday, 5 February 2009
- [AMBER] error in executing sander.MPI in amber9 Vijay Manickam Achari
- Re: [AMBER] pmemd installation in intelmpi Vijay Manickam Achari
- Re: [AMBER] production run terminates due to (*) symbols in xxx.rst vallespardojl.chem.leidenuniv.nl
- Re: [AMBER] production run terminates due to (*) symbols in xxx.rst Vijay Manickam Achari
- Re: [AMBER] error in executing sander.MPI in amber9 Atro Tossavainen
- Re: [AMBER] How to build reference coordinate file for targeted MD Carlos Simmerling
- Re: [AMBER] How to build reference coordinate file for targeted MD xiaonan zhang
- Re: [AMBER] MKL error ? Marek Malý
- [AMBER] Solvation potential and free energies guardiani.fi.infn.it
- Re: [AMBER] Solvation potential and free energies Carlos Simmerling
- Re: [AMBER] Solvation potential and free energies Lorenzo Gontrani
- [AMBER] parameter files for D-amino acid Vsatheesh Patil
- [AMBER] pmemd on BlueGene/P? Hannes Loeffler
- Re: [AMBER] pmemd on BlueGene/P? Robert Duke
- Re: [AMBER] parameter files for D-amino acid Carlos Simmerling
- Re: [AMBER] parameter files for D-amino acid vijayaraj.clri.res.in
- Re: [AMBER] parameter files for D-amino acid FyD
- Re: [AMBER] parameter files for D-amino acid Carlos Simmerling
- Re: [AMBER] parameter files for D-amino acid Andrew Purkiss-Trew
- Re: [AMBER] parameter files for D-amino acid Carlos Simmerling
- Re: [AMBER] Citing AMBER Tools... David A. Case
- Re: [AMBER] REM_hybrid test fails on AIX Shan-ho Tsai
- Re: [AMBER] Compiling Carnal Amber7 in Amber9 Bill Ross
- Re: [AMBER] production run terminates due to (*) symbols in xxx.rst Bill Ross
- RE: [AMBER] MKL error ? Ross Walker
- RE: [AMBER] production run terminates due to (*) symbols in xxx.rst Ross Walker
- Re: [AMBER] MKL error ? Marek Malý
- Re: [AMBER] pmemd on BlueGene/P? Carlos P Sosa
- Re: [AMBER] production run terminates due to (*) symbols in xxx.rst Vijay Manickam Achari
- Re: [AMBER] How to build reference coordinate file for targeted MD gmail
- [AMBER] amber9 installation problem in SMP IA64 Vijay Manickam Achari
- [AMBER] mpirun problem in HPC Vijay Manickam Achari
Friday, 6 February 2009
- RE: [AMBER] mpirun problem in HPC Ross Walker
- RE: [AMBER] How to build reference coordinate file for targeted MD Ross Walker
- Re: [AMBER] pmemd on BlueGene/P? Hannes Loeffler
- [AMBER] second derivative matrix calculation Marie Brut
- [AMBER] extract frames from a .mdcrd vallespardojl.chem.leidenuniv.nl
- [AMBER] MSD and stress tensors oguz gurbulak
- Re: [AMBER] extract frames from a .mdcrd Carlos Simmerling
- Re: [AMBER] second derivative matrix calculation David A. Case
- Re: [AMBER] amber9 installation problem in SMP IA64 David A. Case
- Re: [AMBER] Solvation potential and free energies David A. Case
- [AMBER] script to convert GLYCAM ff in CHARMM format ABEL Stephane 175950
- Re: [AMBER] script to convert GLYCAM ff in CHARMM format Lachele Foley (Lists)
- RE : [AMBER] script to convert GLYCAM ff in CHARMM format ABEL Stephane 175950
- [AMBER] Resp charge . ..
- Re: [AMBER] Test run on Solaris 10 X 86 Manikandan Chandrasekaran
- [AMBER] ptraj fails to recognize binary REMD output Kevin Wiehe
- [AMBER] distance calculation by reading in the restraint file xiaoqin huang
- RE: [AMBER] distance calculation by reading in the restraint file xiaoqin huang
- Re: [AMBER] extract frames from a .mdcrd Bill Ross
- Re: [AMBER] Resp charge Jason A. Ford-Green
- Re: [AMBER] distance calculation by reading in the restraint file David A. Case
- Re: [AMBER] distance calculation by reading in the restraint file David A. Case
- RE: [AMBER] distance calculation by reading in the restraint file xiaoqin huang
Saturday, 7 February 2009
- [AMBER] MD analysis oguz gurbulak
Sunday, 8 February 2009
- [AMBER] Stability of a long NPT md trajectory? Bill K
Monday, 9 February 2009
- [AMBER] second derivative matrix Marie Brut
- [AMBER] NAB md function prints strange output Jochen Heil
- Re: [AMBER] Stability of a long NPT md trajectory? Carlos Simmerling
- Re: [AMBER] NAB md function prints strange output David A. Case
- Re: [AMBER] the output files oguz gurbulak
- Re: [AMBER] the output files Carlos Simmerling
- Re: [AMBER] Stability of a long NPT md trajectory? Robert Duke
- Re: [AMBER] second derivative matrix Adrian Roitberg
- [AMBER] APS & ff03 Mahmoud A. A. Ibrahim
- Re: [AMBER] second derivative matrix David A. Case
- [AMBER] parmchk s. Bill
- RE: [AMBER] parmchk Ross Walker
- [AMBER] hbond analysis aneesh cna
- Re: [AMBER] hbond analysis Bala subramanian
- Re: [AMBER] hbond analysis Carlos Simmerling
- [AMBER] Solvating inside of a channel Daniel Smith
- Re: [AMBER] Stability of a long NPT md trajectory? Bill K
- Re: [AMBER] Stability of a long NPT md trajectory? Carlos Simmerling
- Re: [AMBER] Stability of a long NPT md trajectory? Adrian Roitberg
- Re: [AMBER] Stability of a long NPT md trajectory? Robert Duke
- Re: [AMBER] Stability of a long NPT md trajectory? Carlos Simmerling
- Re: [AMBER] Stability of a long NPT md trajectory? Robert Duke
- [AMBER] Confusion regarding box size parul sharma
- Re: [AMBER] Stability of a long NPT md trajectory? Bill K
Tuesday, 10 February 2009
- Re: [AMBER] amber9 installation problem in SMP IA64 Vijay Manickam Achari
- Re: [AMBER] Confusion regarding box size vallespardojl.chem.leidenuniv.nl
- Re: [AMBER] extract frames from a .mdcrd vallespardojl.chem.leidenuniv.nl
- [AMBER] Irregularity in box during md parul sharma
- Re: [AMBER] Irregularity in box during md Carlos Simmerling
- Re: [AMBER] extract frames from a .mdcrd Carlos Simmerling
- Re: [AMBER] the output files oguz gurbulak
- Re: [AMBER] the output files Carlos Simmerling
- Re: [AMBER] NAB md function prints strange output Jochen Heil
- Re: [AMBER] amber9 installation problem in SMP IA64 David A. Case
- Re: [AMBER] NAB md function prints strange output David A. Case
- Re: [AMBER] Confusion regarding box size Wei Zhang
- Re: [AMBER] Confusion regarding box size parul sharma
- Re: [AMBER] Stability of a long NPT md trajectory? Robert Duke
- Re: [AMBER] the output files oguz gurbulak
- [AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND] Patrick Schopf
- Re: [AMBER] the output files Carlos Simmerling
- [AMBER] Scaling of dipole interactions Diddo Diddens
- RE : [AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND] ABEL Stephane 175950
- [AMBER] formate parameters Dmitri Nilov
- Re: [AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND] FyD
- [AMBER] array out of bound in Amber10 tests Shan-ho Tsai
- Re: [AMBER] array out of bound in Amber10 tests David A. Case
- Re: [AMBER] Irregularity in box during md Bill Ross
- [AMBER] reg . run TMD balaji nagarajan
- RE: [AMBER] the output files Ross Walker
- Re: [AMBER] reg . run TMD Carlos Simmerling
- RE: [AMBER] amber9 installation problem in SMP IA64 Ross Walker
- Re: [AMBER] Stability of a long NPT md trajectory? Bill K
- Re: [AMBER] Stability of a long NPT md trajectory? Robert Duke
- [AMBER] Solvating the interior of a channel Daniel Smith
- Re: [AMBER] array out of bound in Amber10 tests Shan-ho Tsai
- Re: [AMBER] array out of bound in Amber10 tests David A. Case
- [AMBER] AMBER: chiral restraint on protein amit jain
- [AMBER] how to get amber 10 Prem Prakash Pathak
- RE: [AMBER] how to get amber 10 Ross Walker
- Re: [AMBER] Compiling Carnal Amber7 in Amber9 Vijay Manickam Achari
Wednesday, 11 February 2009
- [AMBER] nmr refinement of dimer Sally Pias
- RE: [AMBER] amber9 installation problem in SMP IA64 Vijay Manickam Achari
- Re: [AMBER] nmr refinement of dimer Therese Malliavin
- Re: [AMBER] AMBER: chiral restraint on protein David A. Case
- Re: [AMBER] nmr refinement of dimer David A. Case
- Re: [AMBER] amber9 installation problem in SMP IA64 David A. Case
- Re: [AMBER] Solvating the interior of a channel Shozeb Haider
- [AMBER] Chlorine containing molecule CHAMI F.
- Re: [AMBER] Chlorine containing molecule Carlos Simmerling
- Re: [AMBER] array out of bound in Amber10 tests Shan-ho Tsai
- Re: [AMBER] Solvating the interior of a channel Jason A. Ford-Green
- Re: [AMBER] array out of bound in Amber10 tests Carlos Simmerling
- RE: [AMBER] Compiling Carnal Amber7 in Amber9 Ross Walker
- RE: [AMBER] Compiling Carnal Amber7 in Amber9 Bill Ross
- Re: [AMBER] array out of bound in Amber10 tests Shan-ho Tsai
Thursday, 12 February 2009
- RE: [AMBER] Compiling Carnal Amber7 in Amber9 Vijay Manickam Achari
- Re: [AMBER] amber9 installation problem in SMP IA64 Vijay Manickam Achari
- Re: [AMBER] nmr refinement of dimer Sally Pias
- RE: [AMBER] amber9 installation problem in SMP IA64 Vijay Manickam Achari
- [AMBER] Optimization problem Daniel Emery
- [AMBER] error in xleap: ligand binding using MMand QMMM tech kureeckal ramesh
- Re: [AMBER] Compiling Carnal Amber7 in Amber9 David A. Case
- Re: [AMBER] Optimization problem David A. Case
- Re: [AMBER] nmr refinement of dimer David A. Case
- Re: [AMBER] Optimization problem Daniel Emery
- Re: [AMBER] Optimization problem Carlos Simmerling
- Re: [AMBER] error in xleap: ligand binding using MMand QMMM tech Gustavo Seabra
- Re: [AMBER] Optimization problem David A. Case
- Re: [AMBER] Optimization problem Gustavo Seabra
- RE: [AMBER] amber9 installation problem in SMP IA64 Ross Walker
- RE: [AMBER] Compiling Carnal Amber7 in Amber9 Ross Walker
- [AMBER] H-bond information Beale, John
- [AMBER] projections of trajectories onto the first 2 principal eigenvectors Carra, Claudio (JSC-SK)[USRA]
- RE: [AMBER] Compiling Carnal Amber7 in Amber9 Bill Ross
- [AMBER] atoms fly out of the box in NVT calculations iccy liu
- Re: [AMBER] atoms fly out of the box in NVT calculations Carlos Simmerling
- [AMBER] non bonded parameteters index Swarup Gupta
- Re: [AMBER] non bonded parameteters index Alessandro Nascimento
- Re: [AMBER] non bonded parameteters index Adrian Roitberg
- Re: [AMBER] atoms fly out of the box in NVT calculations Ross Walker
- [AMBER] How to jude whether the trajectory is stable or not Jeffrey
Friday, 13 February 2009
- Re: [AMBER] projections of trajectories onto the first 2 principal eigenvectors Hannes Loeffler
- Re: [AMBER] projections of trajectories onto the first 2 principal eigenvectors Hannes Loeffler
- Re: [AMBER] array out of bound in Amber10 tests Carlos Simmerling
- Re: [AMBER] Solvating the interior of a channel Daniel Smith
- [AMBER] Beginner question Heath Watts
- Re: [AMBER] Beginner question Carlos Simmerling
- Re: [AMBER] Beginner question Barbault Florent
- [AMBER] Question about improper torsions... Antonios Samiotakis
- [AMBER] New atom type with 7 bonds Akansha Saxena
- Re: [AMBER] Beginner question Heath Watts
- Re: [AMBER] Beginner question Heath Watts
Saturday, 14 February 2009
- [AMBER] install Amber 10 to Macbook Adrien Delmont
- Re: [AMBER] Question about improper torsions... David A. Case
- Re: [AMBER] install Amber 10 to Macbook David A. Case
Sunday, 15 February 2009
- [AMBER] Any link to a major QM code? Francesco Pietra
- Re: [AMBER] install Amber 10 to Macbook Tyler Luchko
- Re: [AMBER] install Amber 10 to Macbook David Watson
- Re: [AMBER] Solvating the interior of a channel Daniel Smith
- RE: [AMBER] atoms fly out of the box in NVT calculations iccy liu
- Re: [AMBER] Any link to a major QM code? Gustavo Seabra
- Re: [AMBER] Any link to a major QM code? Adrian Roitberg
Monday, 16 February 2009
- [AMBER] Error running sander.MPI Vijay Manickam Achari
- Re: [AMBER] Error running sander.MPI Carlos Simmerling
- [AMBER] Error installing Amber David Patiño
- [AMBER] Iron 2+ parameters Hrvoje Brkić
- [AMBER] density and volume in NVT ensamble oguz gurbulak
- Re: [AMBER] density and volume in NVT ensamble Carlos Simmerling
- Re: [AMBER] density and volume in NVT ensamble Andrew Purkiss-Trew
- Re: [AMBER] Error installing Amber David A. Case
- Re: [AMBER] density and volume in NVT ensamble oguz gurbulak
- Re: [AMBER] density and volume in NVT ensamble oguz gurbulak
- Re: [AMBER] New atom type with 7 bonds David A. Case
- Re: [AMBER] density and volume in NVT ensamble Carlos Simmerling
Friday, 6 February 2009
- Re: [AMBER] density and volume in NVT ensamble Adrian Roitberg
Monday, 16 February 2009
- Re: [AMBER] density and volume in NVT ensamble oguz gurbulak
- Re: [AMBER] density and volume in NVT ensamble Andrew Purkiss-Trew
- Re: [AMBER] Any link to a major QM code? Francesco Pietra
- Re: [AMBER] Iron 2+ parameters Syed Tarique Moin
- Re: [AMBER] Any link to a major QM code? Gustavo Seabra
- Re: [AMBER] array out of bound in Amber10 tests Shan-ho Tsai
- [AMBER] contant force pulling simulation with amber 10 li hui
- Re: [AMBER] contant force pulling simulation with amber 10 Gustavo Seabra
- Re: [AMBER] Iron 2+ parameters FyD
- [AMBER] can ptraj output the trajectory of the residue CM? Jose Borreguero
- [AMBER] using ptraj Molecular Dynamics
- Re: [AMBER] using ptraj Carlos Simmerling
- [AMBER] Normal errors on job kill? ben rodriguez
- [AMBER] Amber 9 Install - AMBERBUILDFLAGS error ben rodriguez
- Re: [AMBER] Normal errors on job kill? David A. Case
- Re: [AMBER] Amber 9 Install - AMBERBUILDFLAGS error David A. Case
Tuesday, 17 February 2009
- RE: [AMBER] Error running sander.MPI Rausch, Felix
- [AMBER] parallel run error balaji nagarajan
- Re: [AMBER] Error running sander.MPI Anselm Horn
- Re: [AMBER] using ptraj Molecular Dynamics
- Re: [AMBER] using ptraj Carlos Simmerling
- Re: [AMBER] parallel run error Carlos Simmerling
- [AMBER] constph tutorial help Prem Prakash Pathak
- [AMBER] (no subject) Beale, John
- Re: [AMBER] (no subject) Carlos Simmerling
- Re: [AMBER] using ptraj Molecular Dynamics
- Re: [AMBER] using ptraj Carlos Simmerling
- Re: [AMBER] using ptraj Molecular Dynamics
- Re: [AMBER] using ptraj Carlos Simmerling
- [AMBER] MD simulation with a partially flexible system Jeffrey
- Re: [AMBER] MD simulation with a partially flexible system Carlos Simmerling
- Re: [AMBER] Error installing Amber David Patiño
- [AMBER] DM complexation . ..
- Re: [AMBER] DM complexation Carlos Simmerling
- RE: [AMBER] DM complexation . ..
- Re: [AMBER] DM complexation Carlos Simmerling
- [AMBER] How to get the energy of a molecule in a whole system Wang,Ying
- [AMBER] restraint angle m m
- Re: [AMBER] restraint angle David A. Case
- [AMBER] PMF calculation Arnaud
- [AMBER] Need suggestion on payment for Ph.D student majored in molecular simulation Xu Dong
- Re: [AMBER] Need suggestion on payment for Ph.D student majored in molecular simulation Adrian Roitberg
- [AMBER] glycam and solvateoct command Heath Watts
- Re: [AMBER] glycam and solvateoct command Barbault Florent
- [AMBER] problem compiling nmode.c Shan-ho Tsai
- Re: [AMBER] glycam and solvateoct command Heath Watts
- Re: Re: [AMBER] MD simulation with a partially flexible system Jeffrey
- Re: [AMBER] PMF calculation David A. Case
- Re: [AMBER] problem compiling nmode.c David A. Case
- [AMBER] NVT vs NPT Chih-Ying Lin
- [AMBER] reg.Targeted molecular dynamics balaji nagarajan
- [AMBER] Scientific Linux 5.2 Catein Catherine
Wednesday, 18 February 2009
- [AMBER] protein monomerizartion times and simulation with implicit solvent drugdesign
- Re: [AMBER] reg.Targeted molecular dynamics Simon Becker
- Re: [AMBER] protein monomerizartion times and simulation with implicit solvent Carlos Simmerling
- Re: [AMBER] NVT vs NPT Carlos Simmerling
- [AMBER] Re: AMBER: GBSA EGB = NaN Markus Kaukonen
- Re: Re: [AMBER] MD simulation with a partially flexible system Carlos Simmerling
- [AMBER] IG not change at each restart of NPT simulation Jeffrey
- Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke
- Re: [AMBER] IG not change at each restart of NPT simulation Carlos Simmerling
- RE: [AMBER] reg.Targeted molecular dynamics balaji nagarajan
- [AMBER] How to constrain the hydrogen bonding distances... Majeed Shaik
- Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke
- Re: [AMBER] How to constrain the hydrogen bonding distances... Carlos Simmerling
- Re: [AMBER] How to constrain the hydrogen bonding distances... David A. Case
- Re: [AMBER] IG not change at each restart of NPT simulation Adrian Roitberg
- Re: [AMBER] glycam and solvateoct command Lachele Foley (Lists)
- [AMBER] g(r) extrapolation Lorenzo Gontrani
- [AMBER] ./configure_amber: line 1211: cd: netcdf/src: No such file or directory Andrew Olson
- Re: [AMBER] g(r) extrapolation Thomas Cheatham III
- Re: [AMBER] ./configure_amber: line 1211: cd: netcdf/src: No such file or directory David A. Case
- [AMBER] question about ptraj hydrogen bond analysis monica bhattacharee
- [AMBER] (NTB /= 0 && NTP /= 0) but IFBOX == 0 error Majeed Shaik
- Re: [AMBER] question about ptraj hydrogen bond analysis Thomas Cheatham III
- Re: [AMBER] (NTB /= 0 && NTP /= 0) but IFBOX == 0 error David A. Case
- [AMBER] Re: AMBER: How do you evaluate forces on a fixed atom? Bill Kowallis
- [AMBER] test charge Dan Kaps
- Re: [AMBER] test charge David A. Case
- [AMBER] distance matrix plot and secondary structure analysis Siddharth Rastogi
Thursday, 19 February 2009
- Re: [AMBER] g(r) extrapolation Lorenzo Gontrani
- [AMBER] Protein motions comparison Dmitry Osolodkin
- Re: [AMBER] Protein motions comparison Hannes Loeffler
- Re: [AMBER] distance matrix plot and secondary structure analysis Carlos Simmerling
- Re: [AMBER] secstruct Carlos Simmerling
- [AMBER] Re: AMBER: GBSA EGB = NaN Markus Kaukonen
- [AMBER] secstruct Beale, John
- [AMBER] dipole correlation function Jeffrey
- Re: [AMBER] dipole correlation function Carlos Simmerling
- RE: [AMBER] secstruct Maxime Louet
- Re: [AMBER] secstruct Carlos Simmerling
- Re: [AMBER] problem compiling nmode.c Shan-ho Tsai
- [AMBER] paper of interest for FF development/solvent models David Mobley
- Re: Re: [AMBER] dipole correlation function Jeffrey
- Re: Re: [AMBER] dipole correlation function Carlos Simmerling
- [AMBER] linux install problem Andrew Olson
- [AMBER] (no subject) Andrew Olson
- Re: [AMBER] linux install problem Gustavo Seabra
- Re: Re: Re: [AMBER] dipole correlation function Jeffrey
- [AMBER] Antechamber kureeckal ramesh
- Re: [AMBER] test charge Dan Kaps
- Re: [AMBER] test charge David A. Case
Friday, 20 February 2009
- [AMBER] Problem with NVT and NPT parul sharma
- Re: [AMBER] Problem with NVT and NPT Adrian Roitberg
- [AMBER] Parmchk wrongly calculates missing parameters (fwd) Gijs Schaftenaar
- Re: [AMBER] Problem with NVT and NPT parul sharma
- Re: [AMBER] Problem with NVT and NPT Carlos Simmerling
- [AMBER] ACS computational chemistry awards - March 9th deadline Carlos Simmerling
- Re: [AMBER] test charge Dan Kaps
- Re: [AMBER] test charge Jenny Iskrenova
- [AMBER] order of "upper" and "lower" bounds in the makeDIS_RST inputs Piotr Cieplak
- [AMBER] reg.targeted molecular dynamics balaji nagarajan
Saturday, 21 February 2009
- Re: [AMBER] reg.targeted molecular dynamics Carlos Simmerling
- [AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation Xu Dong
- Re: [AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation Carlos Simmerling
- Re: [AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation Xu Dong
- Re: [AMBER] order of "upper" and "lower" bounds in the makeDIS_RST inputs David A. Case
Sunday, 22 February 2009
- RE: [AMBER] reg.targeted molecular dynamics balaji nagarajan
- Re: [AMBER] reg.targeted molecular dynamics Carlos Simmerling
- RE: [AMBER] reg.targeted molecular dynamics balaji nagarajan
Monday, 23 February 2009
- [AMBER] PME doesn't work parul sharma
- Re: [AMBER] reg.targeted molecular dynamics Carlos Simmerling
- Re: [AMBER] PME doesn't work Carlos Simmerling
- Re: [AMBER] PME doesn't work parul sharma
- Re: [AMBER] PME doesn't work Carlos Simmerling
- Re: [AMBER] PME doesn't work Robert Duke
- [AMBER] PMEMD vs GROMACS? Sasha Buzko
- [AMBER] problem with amber installation nicholus bhattacharjee
- [AMBER] follow-up to previous discussion: nmr refinement of dimer Sally Pias
- [AMBER] About the croase grainded FF James W
Tuesday, 24 February 2009
- Re: [AMBER] PMEMD vs GROMACS? Vlad Cojocaru
- Re: [AMBER] PMEMD vs GROMACS? Hannes Loeffler
- Re: [AMBER] About the croase grainded FF Vlad Cojocaru
- Re: [AMBER] PMEMD vs GROMACS? Vlad Cojocaru
- Re: [AMBER] problem with amber installation Carlos Simmerling
- [AMBER] (no subject) Beale, John
- Re: [AMBER] follow-up to previous discussion: nmr refinement of dimer David A. Case
- [AMBER] amber tools reading netcdf files Jeremy Harris
- [AMBER] perform an analysis using ptraj oguz gurbulak
- Re: [AMBER] PMEMD vs GROMACS? Sasha Buzko
- Re: [AMBER] amber tools reading netcdf files Chris Moth
- RE: [AMBER] amber tools reading netcdf files Cojocaru,Vlad
- [AMBER] Equilibration Scaling to System Size Hopkins, Robert
- Re: [AMBER] Equilibration Scaling to System Size Carlos Simmerling
- Re: [AMBER] problem with amber installation nicholus bhattacharjee
Wednesday, 25 February 2009
- RE: [AMBER] reg.targeted molecular dynamics balaji nagarajan
- RE: [AMBER] reg.targeted molecular dynamics balaji nagarajan
- Re: [AMBER] reg.targeted molecular dynamics Carlos Simmerling
- Re: [AMBER] problem with amber installation Carlos Simmerling
- Re: [AMBER] problem with amber installation David A. Case
- [AMBER] problem about trajectory analysis Adrien Delmont
- RE: [AMBER] problem with amber installation Ross Walker
- RE: [AMBER] reg.targeted molecular dynamics Ross Walker
- [AMBER] (no subject) waleed zalloum
- [AMBER] ptraj analyze Beale, John
- [AMBER] Simulated annealing Ibrahim Moustafa
- Re: [AMBER] ptraj analyze Thomas Cheatham III
- Re: [AMBER] (no subject) Thomas Cheatham III
- Re: [AMBER] problem about trajectory analysis Thomas Cheatham III
- Re: [AMBER] Simulated annealing Carlos Simmerling
- [AMBER] Error in using Amber sri noraima othman
- RE: [AMBER] Error in using Amber Ross Walker
- Re: [AMBER] Error in using Amber sri noraima othman
Thursday, 26 February 2009
- [AMBER] tleap errors !! Sampath Koppole
- [AMBER] MD simulation at constant pH Francesco Pietra
- [AMBER] Current Amber10 bugfix.all doesn't apply cleanly Mark Dixon
- [AMBER] PLUMED release 1.0.0 available Massimiliano Bonomi
- Re: [AMBER] tleap errors !! David A. Case
- [AMBER] extra torsion terms in tleap.top-file Astrid Maaß
- [AMBER] H-Bonds Beale, John
- Re: [AMBER] Simulated annealing Ibrahim Moustafa
- Re: [AMBER] Simulated annealing David A. Case
- Re: [AMBER] Simulated annealing Carlos Simmerling
- [AMBER] (no subject) Lake, Thomas
- RE: [AMBER] Simulated annealing Hu, Shaowen (JSC-SK)[Universities Space Research Association (USRA)]
- Re: [AMBER] (no subject) Carlos Simmerling
- Re: [AMBER] Simulated annealing Carlos Simmerling
- RE: [AMBER] Simulated annealing Hu, Shaowen (JSC-SK)[Universities Space Research Association (USRA)]
- Re: [AMBER] Simulated annealing Ibrahim Moustafa
- [AMBER] MD simulations on a protein with FAD and NADH Mannan
- RE: [AMBER] MD simulations on a protein with FAD and NADH Ross Walker
Friday, 27 February 2009
- Re: [AMBER] MD simulations on a protein with FAD and NADH FyD
- RE: [AMBER] reg.targeted molecular dynamics balaji nagarajan
- [AMBER] A problem with xleap and pdb file nancy4619
- [AMBER] Re: Antechamber kureeckal ramesh
- Re: [AMBER] Re: Antechamber FyD
- Re: [AMBER] A problem with xleap and pdb file David A. Case
- [AMBER] I need a professional help about xleap and pdb file nancy4619
- Re: [AMBER] I need a professional help about xleap and pdb file Peter Gannett
- Re:Re: [AMBER] A problem with xleap and pdb file nancy4619
- Re:Re: [AMBER] A problem with xleap and pdb file Peter Gannett
- RE: [AMBER] reg.targeted molecular dynamics Ross Walker
- RE: Re: [AMBER] A problem with xleap and pdb file Ross Walker
- Re: [AMBER] Current Amber10 bugfix.all doesn't apply cleanly Mark Dixon
- [AMBER] using Gromacs for analysis oguz gurbulak
- Re: [AMBER] using Gromacs for analysis Bala subramanian
- [AMBER] Partial entropy calculations ? Marek Malý
- Re: [AMBER] Partial entropy calculations ? Piotr Cieplak
Saturday, 28 February 2009
- [AMBER] PCL waleed zalloum
- RE: [AMBER] PCL Ross Walker
- [AMBER] a query Molecular Dynamics
- [AMBER] IMPORTANT INFO: Regarding Anonymous postings to the AMBER mailing list. Ross Walker
- [AMBER] Question about NAB module Wei Huang

Last message date: Sun Mar 01 2009 - 01:09:59 PST
Archived on: Wed Apr 17 2024 - 05:53:39 PDT

Amber Archive Feb 2009 by date