Amber Archive Apr 2009: by date

Tuesday, 31 March 2009
- Re: [AMBER] ambmol2? Junmei Wang
- [AMBER] Maxwell-Boltzmann distribution and ig=-1 Naser Alijabbari
- [AMBER] a layer of water Nancy
- Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Carlos Simmerling
- Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Naser Alijabbari
- Re: [AMBER] ambmol2? Taufik Al-Sarraj
- Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Carlos Simmerling
- Re: [AMBER] ambmol2? Junmei Wang
- Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Naser Alijabbari
- RE: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Ross Walker
Wednesday, 1 April 2009
- Re: [AMBER] a layer of water oguz gurbulak
- Re: [AMBER] mm_pbsa problem Giorgos Lamprinidis
- [AMBER] constant-pH: appearance of not titrated residues during the Monte Carlo simulation Therese Malliavin
- Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Carlos Simmerling
- [AMBER] run protein with structural Ca+ sarah genare
- [AMBER] Failure to compile amber9 serial ifort gcc Francesco Pietra
- Re: [AMBER] Failure to compile amber9 serial ifort gcc Alessandro Nascimento
- [AMBER] fillratio error in mmpbsa m m
- [AMBER] calculation of Pi-Pi interaction energy aneesh cna
- [AMBER] calculation of Pi-Pi interaction energy Jacopo Sgrignani
- Re: [AMBER] calculation of Pi-Pi interaction energy Jiri Sponer
- Re: [AMBER] ambmol2? David A. Case
- [AMBER] yacc parser Francesco Pietra
- Re: [AMBER] fillratio error in mmpbsa Han Ming
- [AMBER] make test.serial.QMMM michael bane
- [AMBER] ptraj and namd charmm dcd Sandro L. Fornili
- Re: [AMBER] ptraj and namd charmm dcd Thomas Cheatham III
- Re: [AMBER] yacc parser Mark Williamson
- Re: [AMBER] make test.serial.QMMM Seth Hayik
- [AMBER] FF Parameters Transformations ...? Marek Malý
- RE: [AMBER] fillratio error in mmpbsa Ray Luo
- Re: [AMBER] AmberTools compilation error Marius Retegan
- [AMBER] Fwd: yacc parser Francesco Pietra
- RE: [AMBER] Problem reading PDB file into XLEAP - SLEAP Hopkins, Robert
- Re: [AMBER] problem with the results in the .out file! Aravind S
Thursday, 2 April 2009
- [AMBER] Help: An error happened when I calculate mm/pbsa thirsty
- [AMBER] please help me out bharat lakhani
- [AMBER] Counter-ions waleed zalloum
- RE: [AMBER] problem in input Rausch, Felix
- Re: [AMBER] Failure to compile amber9 serial ifort gcc Francesco Pietra
- Re: [AMBER] Help: An error happened when I calculate mm/pbsa Carlos Simmerling
- [AMBER] number of waters in first and second solvation shell Siddharth Rastogi
- Re: [AMBER] yacc parser David A. Case
- [AMBER] explicit ion with igb=1 Bala subramanian
- Re: [AMBER] explicit ion with igb=1 Carlos Simmerling
- [AMBER] Averaging simulations Naser Alijabbari
- Re: [AMBER] Averaging simulations Carlos Simmerling
- Re: [AMBER] yacc parser Francesco Pietra
- RE: [AMBER] Failure to compile amber9 serial ifort gcc Ross Walker
- Re: [AMBER] Failure to compile amber9 serial ifort gcc Francesco Pietra
- Re: [AMBER] please help me out David A. Case
- [AMBER] Error in trajin and rms Pansy Patel
- [AMBER] parallel installation of amber on sun Per Jr. Greisen
- [AMBER] long polymer chain and image command in ptraj iccy liu
- RE: [AMBER] Error in trajin and rms iccy liu
- Re: [AMBER] Error in trajin and rms Carlos Simmerling
- RE: [AMBER] Error in trajin and rms Pansy Patel
- [AMBER] Contour plot Beale, John
- Re: [AMBER] Contour plot Gustavo Seabra
- Re: [AMBER] parallel installation of amber on sun Atro Tossavainen
- RE: [AMBER] problem in input balaji nagarajan
- Re: [AMBER] parallel installation of amber on sun Per Jr. Greisen
- [AMBER] How to delete the frames at specific intervals Mannan
- [AMBER] How to find out residence time of water molecules Mannan
- Re: [AMBER] How to find out residence time of water molecules Bala subramanian
Friday, 3 April 2009
- Re: [AMBER] Help: An error happened when I calculate mm/pbsa thirsty
- Re: [AMBER] How to find out residence time of water molecules Hannes Loeffler
- RE: [AMBER] problem in input Rausch, Felix
- Re: [AMBER] parallel installation of amber on sun Atro Tossavainen
- Re: [AMBER] How to delete the frames at specific intervals Bala subramanian
- [AMBER] (no subject) chenquan
- Re: [AMBER] parallel installation of amber on sun Per Jr. Greisen
- [AMBER] How to create parameter file for unknown residue nicholus bhattacharjee
- [AMBER] Could not find angle parameter chenquan
- Re: [AMBER] How to create parameter file for unknown residue Marius Retegan
- Re: [AMBER] Could not find angle parameter Marius Retegan
- [AMBER] antechamber & multiple low-energy conformations Alessandro Nascimento
- Re: [AMBER] (no subject) David A. Case
- [AMBER] amber9 serial compilation issues Francesco Pietra
- [AMBER] NALA-ALA-CALA peptide with antechamber Alan
- Re: [AMBER] amber9 serial compilation issues David A. Case
- [AMBER] ptraj problem Ed Pate
- Re: [AMBER] ptraj problem Thomas Cheatham III
- Re: [AMBER] parallel installation of amber on sun Atro Tossavainen
- Re: [AMBER] amber9 serial compilation issues Francesco Pietra
- Re: [AMBER] parallel installation of amber on sun Atro Tossavainen
- [AMBER] Generate AM1-CM2 charges using antechamber Sishi Tang
Saturday, 4 April 2009
- [AMBER] parameter for amoeba Hemant Kumar
- Re: [AMBER] problem in installing AMBER10 Dr. Debaprasad Giri
- Re: [AMBER] NALA-ALA-CALA peptide with antechamber David A. Case
- [AMBER] LYN again Marius Retegan
- Re: [AMBER] Umbrella test David A. Case
- Re: [AMBER] constant-pH: appearance of not titrated residues during the Monte Carlo simulation David A. Case
- [AMBER] deffision Nancy
- [AMBER] error in MM PBSA Vikas Sharma
- Re: [AMBER] error in MM PBSA Hemant Gangwar
- Re: [AMBER] error in MM PBSA David A. Case
- [AMBER] error in MM PBSA Vikas Sharma
Sunday, 5 April 2009
- Re: [AMBER] LYN again FyD
- [AMBER] error in MM PBSA Vikas Sharma
Monday, 6 April 2009
- Re: [AMBER] FF Parameters Transformations ...? Karl Kirschner
- [AMBER] pmemd compilation/make failed - mkl_vml_service_threader_z_1i_c_1o Vijay Manickam Achari
- [AMBER] sander.MPI parallel run problem Dechang Li
- Re: [AMBER] long polymer chain and image command in ptraj Karl Kirschner
- [AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule. Soni Mufaddal Saifee
- [AMBER] MM-PBSA error while running heat.in Vikas Sharma
- [AMBER] ssh and make test.parallel Francesco Pietra
- Re: [AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule. Carlos Simmerling
- Re: [AMBER] sander.MPI parallel run problem Carlos Simmerling
- Re: [AMBER] ssh and make test.parallel Atro Tossavainen
- Re: Re: [AMBER] sander.MPI parallel run problem Dechang Li
- Re: Re: Re: [AMBER] sander.MPI parallel run problem Dechang Li
- Re: Re: [AMBER] sander.MPI parallel run problem Carlos Simmerling
- [AMBER] problem with secstruct action command in ptraj nicholus bhattacharjee
- [AMBER] testing RRR with antechamber Alan
- [AMBER] zwitterionic form of ARG and antechamber Alan
- [AMBER] Amber with AMOEBA force-field Tomasio, Susana
- Re: [AMBER] Amber with AMOEBA force-field David A. Case
- Re: [AMBER] Amber with AMOEBA force-field Wei Zhang
- RE: [AMBER] Amber with AMOEBA force-field Tomasio, Susana
- RE: [AMBER] Amber with AMOEBA force-field Tomasio, Susana
- Re: [AMBER] Amber with AMOEBA force-field Wei Zhang
- Re: [AMBER] Amber with AMOEBA force-field Wei Zhang
- Re: [AMBER] Amber with AMOEBA force-field David A. Case
- RE: [AMBER] Amber with AMOEBA force-field Tomasio, Susana
- [AMBER] Sander waleed_zalloum.yahoo.com
- RE: [AMBER] Amber with AMOEBA force-field Tomasio, Susana
- Re: [AMBER] LYN again Marius Retegan
- Re: [AMBER] pmemd compilation/make failed -mkl_vml_service_threader_z_1i_c_1o Robert Duke
- Re: [AMBER] LYN again FyD
- Re: [AMBER] ssh and make test.parallel Francesco Pietra
- [AMBER] MM-PBSA: decompose energy error Lucilla Angeli
- [AMBER] Sander Stalling Steve Seibold
- [AMBER] Do I need to modify the cap residues nicholus bhattacharjee
- RE: [AMBER] Sander Stalling Ross Walker
- RE: [AMBER] Do I need to modify the cap residues Ross Walker
- [AMBER] sequence function taufik.alsarraj.utoronto.ca
- Re: [AMBER] sequence function taufik.alsarraj.utoronto.ca
- Re: [AMBER] Sander Stalling Robert Duke
- Re: [AMBER] Do I need to modify the cap residues nicholus bhattacharjee
- [AMBER] Negative "number of measurements" in PTRAJ Jenny Iskrenova
- Re: [AMBER] Do I need to modify the cap residues David A. Case
- Re: [AMBER] FF Parameters Transformations ...? Marek Malý
- Re: [AMBER] ssh and make test.parallel Atro Tossavainen
- [AMBER] number_rec_numbers in mm_pbsa Zhu, Yong-Liang
- 回复： [AMBER] number_rec_numbers in mm_pbsa 廖青华
- [AMBER] Amber on GPU Sasha Buzko
- RE: [AMBER] Amber on GPU Ross Walker
- [AMBER] deffision coefficient Nancy
- [AMBER] A question about SMD force constant Jackie. J. Shen
- Re: [AMBER] deffision coefficient David A. Case
- Re: [AMBER] pmemd compilation/make failed -mkl_vml_service_threader_z_1i_c_1o Vijay Manickam Achari
- [AMBER] ambmask question Ed Pate
- Re: [AMBER] Do I need to modify the cap residues nicholus bhattacharjee
- RE: [AMBER] Do I need to modify the cap residues Ross Walker
- Re: [AMBER] Amber on GPU Sasha Buzko
Tuesday, 7 April 2009
- [AMBER] Problems with running two separate jobs in the same time Antonija Tomić
- [AMBER] how to add charge in metal ion bharat lakhani
- [AMBER] missing violations of the covalent geometry Helena P M Tossavainen
- [AMBER] errors while testing Per Jr. Greisen
- Re: [AMBER] errors while testing Atro Tossavainen
- [AMBER] Problem with CAP residues Tomasio, Susana
- Re: [AMBER] A question about SMD force constant Carlos Simmerling
- Re: [AMBER] Problem with CAP residues FyD
- Re: [AMBER] missing violations of the covalent geometry David A. Case
- [AMBER] TI production runs stop after a certain Step number Hannes Wallnoefer
- Re: [AMBER] missing violations of the covalent geometry Helena P M Tossavainen
- Re: [AMBER] pmemd compilation/make failed-mkl_vml_service_threader_z_1i_c_1o Robert Duke
- Re: [AMBER] pmemd compilation/makefailed-mkl_vml_service_threader_z_1i_c_1o Robert Duke
- Re: [AMBER] TI production runs stop after a certain Step number steinbrt.rci.rutgers.edu
- RE: [AMBER] Problems with running two separate jobs in the same time Ross Walker
- RE: [AMBER] how to add charge in metal ion Ross Walker
- [AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana
- RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana
- Re: [AMBER] test/amoeba - forrtl: severe (64): input conversion error David A. Case
- Re: [AMBER] Negative "number of measurements" in PTRAJ Thomas Cheatham
- Re: [AMBER] test/amoeba - forrtl: severe (64): input conversion error Wei Zhang
- [AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra
- Re: [AMBER] TI production runs stop after a certain Step number Ilyas Yildirim
- [AMBER] PBSA Radii option quantum_mania.yahoo.com
- RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana
- Re: [AMBER] specification of antechamber AC file format? Nicholas Musolino
- [AMBER] Source of new CYX residue parameters in ff03ua Chris Moth
- [AMBER] prmtop residue format taufik.alsarraj.utoronto.ca
- RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana
- Re: [AMBER] prmtop residue format David A. Case
- Re: [AMBER] test/amoeba - forrtl: severe (64): input conversion error David A. Case
- Re: [AMBER] top2mol2 taufik.alsarraj.utoronto.ca
- RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana
- [AMBER] ptraj randomizeions taufik.alsarraj.utoronto.ca
- [AMBER] MMPB(GB)SA on trimer quantum_mania.yahoo.com
- Re: [AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule. Soni Mufaddal Saifee
- [AMBER] compare MMPBSA result m m
- Re: [AMBER] pmemd compilation/makefailed-mkl_vml_service_threader_z_1i_c_1o Vijay Manickam Achari
- [AMBER] problem with antechamber aneesh cna
Wednesday, 8 April 2009
- Re: [AMBER] ssh and make test.parallel Francesco Pietra
- [AMBER] please help me out bharat lakhani
- Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Atro Tossavainen
- Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra
- Re: [AMBER] errors while testing Per Jr. Greisen
- Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Atro Tossavainen
- Re: [AMBER] TI production runs stop after a certain Step number Hannes Wallnoefer
- Re: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threader_z_1i_c_1o Robert Duke
- Re: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threader_z_1i_c_1o Robert Duke
- Re: [AMBER] TI production runs stop after a certain Step number steinbrt.rci.rutgers.edu
- RE: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threade_z_1i_c_1o Ross Walker
- Re: [AMBER] TI production runs stop after a certain Step number Hannes Wallnoefer
- Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra
- Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra
- Re: [AMBER] test/amoeba - forrtl: severe (64): input conversion error Wei Zhang
- [AMBER] Failures of tests Per Jr. Greisen
- RE: [AMBER] please help me out Ross Walker
- Re: [AMBER] please help me out Hugh Heldenbrand
- RE: [AMBER] Failures of tests Seetin, Matthew
- RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana
- Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so M. L. Dodson
- Re: [AMBER] Failures of tests Per Jr. Greisen
- RE: [AMBER] compare MMPBSA result Ray Luo
- Re: [AMBER] please help me out David A. Case
- [AMBER] Thermodynamic Integration and belly Ignacio J. General
- [AMBER] ntwr taufik.alsarraj.utoronto.ca
- Re: [AMBER] ntwr Carlos Simmerling
- Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Atro Tossavainen
- Re: Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so Atro Tossavainen
- Re: [AMBER] ntwr taufik.alsarraj.utoronto.ca
- Re: [AMBER] Failures of tests Atro Tossavainen
- Re: [AMBER] ntwr Carlos Simmerling
- Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra
- Re: Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra
- Re: Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so Atro Tossavainen
- Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Atro Tossavainen
- [AMBER] force fields Mark M Huntress
- RE: [AMBER] force fields Ross Walker
- [AMBER] please help me out bharat lakhani
Thursday, 9 April 2009
- [AMBER] how to plot this kind of map? lnin_1431.sina.com
- Re: [AMBER] how to plot this kind of map? Dechang Li
- RE: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threade_z_1i_c_1o Vijay Manickam Achari
- RE: [AMBER] Problems with running two separate jobs in the same time Antonija Tomić
- Re: [AMBER] please help me out David A. Case
- Re: [AMBER] hpux sander.serial failure info David A. Case
- Re: [AMBER] Failures of tests Per Jr. Greisen
- [AMBER] RST file waleed zalloum
- [AMBER] Release of R.E.D. Server FyD
- [AMBER] antechamber problems Jia Xu
- Re: [AMBER] antechamber problems David A. Case
- Re: [AMBER] antechamber problems Nicholas Musolino
- [AMBER] Sander and multiple residues Dan Kaps
- Re: [AMBER] Sander and multiple residues Carlos Simmerling
- Re: [AMBER] Sander and multiple residues Dan Kaps
- Re: [AMBER] Sander and multiple residues Carlos Simmerling
- Re: [AMBER] Sander and multiple residues Bill Ross
- [AMBER] igb=0 vs. igb=6 give different answers Hugh Heldenbrand
- Re: [AMBER] Amber on GPU Sasha Buzko
- Re: [AMBER] igb=0 vs. igb=6 give different answers David A. Case
- [AMBER] basepair balaji nagarajan
Friday, 10 April 2009
- Re: [AMBER] RST file David A. Case
- Re: [AMBER] Sander and multiple residues Dan Kaps
- Re: [AMBER] Sander and multiple residues Dan Kaps
- Re: [AMBER] Sander and multiple residues David A. Case
- Re: [AMBER] antechamber problems Jia Xu
- Re: [AMBER] Sander and multiple residues Dan Kaps
- Re: [AMBER] Sander and multiple residues Bill Ross
- Re: [AMBER] Sander and multiple residues Dan Kaps
- Re: [AMBER] Sander and multiple residues Bill Ross
- [AMBER] ptraj (vector and corrplane) taufik.alsarraj.utoronto.ca
Saturday, 11 April 2009
- [AMBER] Amber 1.2 tools test suite failure? Jim Parker
- RE: [AMBER] Amber 1.2 tools test suite failure? Ross Walker
- Re: [AMBER] Solved-Amber 1.2 tools test suite failure Jim Parker
- RE: [AMBER] Solved-Amber 1.2 tools test suite failure Ross Walker
- [AMBER] install and test Amber 10 parallel on Ubuntu 8.10 Jim Parker
- [AMBER] MD on GPU: an existing commercial implementation Sasha Buzko
- [AMBER] Re: install and test Amber 10 parallel on Ubuntu 8.10 Jim Parker
Sunday, 12 April 2009
- [AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm Alan
- Re: [AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm Wei Zhang
- Re: [AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm Alan
Monday, 13 April 2009
- [AMBER] problem with explicit solvent in TMD balaji nagarajan
- Re: [AMBER] problem with explicit solvent in TMD Carlos Simmerling
- [AMBER] Energy minimisation and NaN vivek.viv.sharma.gmail.com
- [AMBER] atom types in pdb files Dan Kaps
- [AMBER] Thermodynamic Integration and belly Ignacio J. General
- RE: [AMBER] problem with explicit solvent in TMD Ross Walker
- RE: [AMBER] atom types in pdb files Kristina Furse
- Re: [AMBER] Thermodynamic Integration and belly steinbrt.rci.rutgers.edu
- Re: [AMBER] Thermodynamic Integration and belly Ignacio J. General
- Re: [AMBER] Energy minimisation and NaN David A. Case
- Re: [AMBER] atom types in pdb files Dan Kaps
- [AMBER] error saving prmtop and inpcrd files of complex in MM-PBSA Vikas Sharma
- Re: [AMBER] atom types in pdb files David A. Case
- [AMBER] restrained minimization quantum_mania.yahoo.com
- Re: [AMBER] restrained minimization David A. Case
- [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Marek Malý
- RE: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Ross Walker
- [AMBER] chosing complex in amber Vikas Sharma
Tuesday, 14 April 2009
- Re: [AMBER] basepair Bala subramanian
- Re: [AMBER] how to add charge in metal ion bharat lakhani
- [AMBER] Questions on targeted MD with explicit solvent Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA].
- [AMBER] [qm/mm] qmcharge for acidic a.a. in proteins sychen
- [AMBER] antechamber and wrong net charge with gasteiger method Alan
- Re: [AMBER] antechamber and wrong net charge with gasteiger method David A. Case
- RE: [AMBER] [qm/mm] qmcharge for acidic a.a. in proteins Ross Walker
- [AMBER] my FF m m
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Marek Malý
- RE: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Ross Walker
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Marek Malý
- [AMBER] Source of new CYX residue parameters in ff03ua Chris Moth
- [AMBER] water bonding with protein Mark M Huntress
- RE: [AMBER] Source of new CYX residue parameters in ff03ua Ross Walker
Wednesday, 15 April 2009
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Karl Kirschner
Tuesday, 14 April 2009
- [AMBER] hbond_ptraj_eror balaji nagarajan
Wednesday, 15 April 2009
- Re: [AMBER] water bonding with protein David A. Case
- Re: [AMBER] hpux sander.serial failure info David A. Case
- [AMBER] mean of character in frcmod.ff03 chenquan
- Re: [AMBER] my FF David A. Case
- Re: [AMBER] force fields Gustavo Seabra
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Carlos Simmerling
- RE: [AMBER] mean of character in frcmod.ff03 Ross Walker
- [AMBER] help- regarding - TMD balaji nagarajan
- RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA].
- Re: [AMBER] specification of antechamber AC file format? Nicholas Musolino
- RE: [AMBER] mean of character in frcmod.ff03 chenquan
- RE: [AMBER] help- regarding - TMD balaji nagarajan
- [AMBER] please help me out bharat lakhani
Thursday, 16 April 2009
- [AMBER] missing amber force field parameters Neha Gandhi
- Re: [AMBER] missing amber force field parameters FyD
- [AMBER] pmemd in amber10 - compile failed in HPC Vijay Manickam Achari
- [AMBER] 1-4 vdW, GB MM difference Jimmy Heimdal
- Re: [AMBER] pmemd in amber10 - compile failed in HPC Robert Duke
- Re: [AMBER] specification of antechamber AC file format? David A. Case
- [AMBER] ambertools failed - SMP IA64 Vijay Manickam Achari
- Re: [AMBER] specification of antechamber AC file format? Nicholas Musolino
- RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA].
- Re: [AMBER] ambertools failed - SMP IA64 David A. Case
- [AMBER] Van der Waals atom types Antonio Morreale
- Re: [AMBER] 1-4 vdW, GB MM difference David A. Case
- [AMBER] Amber and CHARMM summer school David A. Case
- [AMBER] Bad value during integer read by sander Collins Nganou
- [AMBER] sulfonamide parameters valeria.lapietra.unina.it
- RE: [AMBER] help- regarding - TMD balaji nagarajan
- [AMBER] polarizable force field for 18-crown-6 Gert von Helden
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Marek Malý
- [AMBER] help regarding force fields Vikas Sharma
- [AMBER] Right force fields Vikas Sharma
Friday, 17 April 2009
- Re: [AMBER] polarizable force field for 18-crown-6 Piotr Cieplak
- [AMBER] radius of gyration Beale, John
- Re: [AMBER] Right force fields Patrick Schopf
- Re: [AMBER] Right force fields Vikas Sharma
- Re: [AMBER] Right force fields Patrick Schopf
- [AMBER] Density in MD simulation Ibrahim Moustafa
- Re: [AMBER] Density in MD simulation Carlos Simmerling
- [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? quantum_mania.yahoo.com
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Lachele Foley (Lists)
- Re: [AMBER] Density in MD simulation Ibrahim Moustafa
- [AMBER] Backbone restraint Rilei Yu
- Re: [AMBER] Backbone restraint Carlos Simmerling
- Re: [AMBER] Backbone restraint Rilei Yu
- [AMBER] help_me to know the reason balaji nagarajan
Saturday, 18 April 2009
- [AMBER] please read this mail bharat lakhani
- Re: [AMBER] help_me to know the reason Carlos Simmerling
- Re: [AMBER] Backbone restraint Carlos Simmerling
- Re: [AMBER] please read this mail David A. Case
- [AMBER] about saltcon zgong.hust
Sunday, 19 April 2009
- [AMBER] Atom type error Vikas Sharma
- Re: [AMBER] about saltcon Carlos Simmerling
- Re: [AMBER] Atom type error nicholus bhattacharjee
- Re: [AMBER] Atom type error Carlos Simmerling
- Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra
- Re: [AMBER] Atom type error Vikas Sharma
- Re: [AMBER] Atom type error Vikas Sharma
- Re: [AMBER] Atom type error David A. Case
- Re: [AMBER] Atom type error Vikas Sharma
- RE: [AMBER] Atom type error Ross Walker
Monday, 20 April 2009
- Re: [AMBER] Atom type error Vikas Sharma
- [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Marek Malý
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Karl Kirschner
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail FyD
- RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA].
- Re: [AMBER] help- regarding - TMD Carlos Simmerling
- RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA].
- Re: [AMBER] help- regarding - TMD Carlos Simmerling
- RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA].
- Re: [AMBER] Creating conditions for biased MD Francesco Pietra
- Re: [AMBER] Creating conditions for biased MD Carlos Simmerling
- [AMBER] Partial interactions Ignacio J. General
- Re: [AMBER] Partial interactions steinbrt.rci.rutgers.edu
- Re: Re: [AMBER] Backbone restraint Jackie. J. Shen
- Re: Re: [AMBER] Backbone restraint Rilei Yu
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Marek Malý
- [AMBER] My step size Vikas Sharma
- Re: [AMBER] Atom type error Vikas Sharma
Tuesday, 21 April 2009
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Karl Kirschner
- [AMBER] atom numbers Vikas Sharma
- RE: [AMBER] My step size Ross Walker
- Re: [AMBER] atom numbers David A. Case
- Re: [AMBER] Partial interactions Ignacio J. General
- Re: [AMBER] My step size Vikas Sharma
- Re: [AMBER] Partial interactions steinbrt.rci.rutgers.edu
- [AMBER] Number of LES copies in ptraj Thomas Exner
- Re: [AMBER] atom numbers Vikas Sharma
- Re: [AMBER] atom numbers David A. Case
- Re: [AMBER] atom numbers Vikas Sharma
- Re: [AMBER] atom numbers Vikas Sharma
- Re: [AMBER] atom numbers David A. Case
- Re: [AMBER] atom numbers Vikas Sharma
- Re: [AMBER] Creating conditions for biased MD Francesco Pietra
- Re: [AMBER] Creating conditions for biased MD Carlos Simmerling
- Re: [AMBER] help- regarding - TMD Carlos Simmerling
- RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA].
- Re: [AMBER] help- regarding - TMD Carlos Simmerling
- Re: [AMBER] Creating conditions for biased MD Francesco Pietra
- Re: [AMBER] Creating conditions for biased MD Carlos Simmerling
- Re: [AMBER] Creating conditions for biased MD Francesco Pietra
- [AMBER] Set start timestep for mdcrd traj output quantum_mania.yahoo.com
- [AMBER] Set start timestep for mdcrd traj output quantum_mania.yahoo.com
- RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA].
- [AMBER] Flexible ring simulation Dong Xu
- Re: [AMBER] Set start timestep for mdcrd traj output Carlos Simmerling
- Re: [AMBER] help- regarding - TMD Carlos Simmerling
- [AMBER] per atom energies in sander/pmemd Tamara Rogers
- Re: [AMBER] Set start timestep for mdcrd traj output Dong Xu
- [AMBER] Disulfide bond Dong Xu
- Re: [AMBER] Disulfide bond Wei Zhang
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Marek Malý
- Re: [AMBER] Disulfide bond Dong Xu
- Re: [AMBER] Disulfide bond Wei Zhang
- Re: [AMBER] My step size Vikas Sharma
- Re: [AMBER] Disulfide bond quantum_mania.yahoo.com
- [AMBER] bintraj and amber 10 Naser Alijabbari
Wednesday, 22 April 2009
- [AMBER] help regarding step size Vikas Sharma
- Re: [AMBER] help regarding step size Carlos Simmerling
- Re: [AMBER] Creating conditions for biased MD Francesco Pietra
- Re: [AMBER] help regarding step size Vikas Sharma
- RE: [AMBER] bintraj and amber 10 Ross Walker
- Re: [AMBER] help regarding step size Carlos Simmerling
- Re: [AMBER] Disulfide bond Wei Zhang
- Re: [AMBER] Creating conditions for biased MD Bill Ross
- Re: [AMBER] Creating conditions for biased MD Francesco Pietra
- [AMBER] uncharged c and n terminal amino acids Christopher Materese
- Re: [AMBER] uncharged c and n terminal amino acids David A. Case
- Re: [AMBER] Partial interactions Ignacio J. General
- [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko
- RE: [AMBER] Problem with RNA hairpin unwinding in explicit water Seetin, Matthew
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Carlos Simmerling
- [AMBER] Amber Sulfate Ion Parameters Gary Clark
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Carlos Simmerling
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Thomas Cheatham III
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko
- RE: [AMBER] Problem with RNA hairpin unwinding in explicit water matthew_seetin.urmc.rochester.edu
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko
- Re: [AMBER] bintraj and amber 10 Naser Alijabbari
- Re: [AMBER] Partial interactions steinbrt.rci.rutgers.edu
- Re: [AMBER] help regarding step size Vikas Sharma
- Re: [AMBER] Amber Sulfate Ion Parameters FyD
- Re: [AMBER] Amber Sulfate Ion Parameters FyD
Thursday, 23 April 2009
- [AMBER] error in output file Vikas Sharma
- Re: [AMBER] error in output file Carlos Simmerling
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Karl Kirschner
- Re: [AMBER] error in output file Vikas Sharma
- Re: [AMBER] error in output file Hemant Kumar
- [AMBER] nmod no run proprely in mmbsa mohamed mohamed
- Re: [AMBER] nmod no run proprely in mmbsa David A. Case
- [AMBER] Regarding syntax for freezing different atoms Jorgen Simonsen
- [AMBER] Amber Installation problem 주태성
- RE: [AMBER] Amber Installation problem Ross Walker
- RE: [AMBER] Regarding syntax for freezing different atoms Ross Walker
- RE: [AMBER] error in output file Ross Walker
- RE: [AMBER] bintraj and amber 10 Ross Walker
- Re: [AMBER] error in output file Vikas Sharma
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Marek Malý
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Karl Kirschner
- Re: [AMBER] error in output file Vikas Sharma
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Marek Malý
- [AMBER] NAB bug with parmbsc0 David A. Case
- Re: [AMBER] bintraj and amber 10 Chris Moth
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Bill Ross
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko
- [AMBER] Unit name with loadMol2 command Nicholas Musolino
- Re: [AMBER] Amber Sulfate Ion Parameters Gary Clark
- [AMBER] CY3 dye parameters jcmoore.student.umass.edu
- Re: [AMBER] Unit name with loadMol2 command David A. Case
- Re: [AMBER] bintraj and amber 10 Naser Alijabbari
- [AMBER] Amber Installation problem 주태성
Friday, 24 April 2009
- [AMBER] Equilibrium bond lengths and angle values Dmitri Nilov
- [AMBER] Simulated annealing waleed zalloum
- Re: [AMBER] Partial interactions Ignacio J. General
- Re: [AMBER] Simulated annealing Carlos Simmerling
- Re: [AMBER] Simulated annealing waleed zalloum
- Re: [AMBER] Simulated annealing Carlos Simmerling
- Re: [AMBER] Partial interactions steinbrt.rci.rutgers.edu
- Re: [AMBER] Partial interactions Ignacio J. General
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko
- Re: [AMBER] Partial interactions steinbrt.rci.rutgers.edu
- Re: [AMBER] Equilibrium bond lengths and angle values FyD
- Re: [AMBER] CY3 dye parameters FyD
Saturday, 25 April 2009
- Re: [AMBER] bintraj and amber 10 Naser Alijabbari
- Re: [AMBER] CY3 dye parameters Brent Krueger
- [AMBER] restraint constant Dong Xu
- [AMBER] Papers on Amber package usage Andrew Voronkov
- [AMBER] amber question Vikas Sharma
Sunday, 26 April 2009
- Re: [AMBER] amber question Barbault Florent
- Re: [AMBER] amber question Vikas Sharma
- Re: [AMBER] amber question Vikas Sharma
- Re: [AMBER] Papers on Amber package usage David A. Case
- [AMBER] Water-molecules sikander azam
- [AMBER] Install 주태성
- [AMBER] Using smd with fixed atom nandy.physics.iisc.ernet.in
- Re: [AMBER] Water-molecules case
- RE: [AMBER] AmberTools compiling error Ross Walker
Monday, 27 April 2009
- [AMBER] Error with calculation of the potential energy Per Jr. Greisen
- Re: [AMBER] Error with calculation of the potential energy Carlos Simmerling
- [AMBER] Mixing of forcefields in case of covaletly bonded systems Marek Malý
- [AMBER] MM-GBSA Free enegy decomposition Rajesh Raju
- [AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing Tommaso Cupido
- Re: [AMBER] Error with calculation of the potential energy Per Jr. Greisen
- Re: [AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing David A. Case
- Re: [AMBER] Error with calculation of the potential energy Robert Duke
- Re: [AMBER] Error with calculation of the potential energy Robert Duke
- Re: [AMBER] Error with calculation of the potential energy Per Jr. Greisen
- Re: [AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing Piotr Cieplak
- Re: [AMBER] Error with calculation of the potential energy Robert Duke
- [AMBER] pmemd compilation error john smith
- Re: [AMBER] pmemd compilation error Robert Duke
- [AMBER] Best rms fit for correlation and covariance analysis Cihan Aydin
- [AMBER] dipole autocorrelation functions aneesh cna
Tuesday, 28 April 2009
- Re: [AMBER] Equilibrium bond lengths and angle values Dmitri Nilov
- Fwd: [AMBER] MM-GBSA Free enegy decomposition Rajesh Raju
- [AMBER] transport properties oguz gurbulak
- [AMBER] ERROR In Restraint file. Catein Catherine
- [AMBER] ERROR In Restraint file. Catein Catherine
- Re: [AMBER] ERROR In Restraint file. David A. Case
- Re: [AMBER] Best rms fit for correlation and covariance analysis Bill Ross
- [AMBER] Restraining counterions? Francesco Pietra
- Re: [AMBER] reg-TMD Carlos Simmerling
- Re: [AMBER] Restraining counterions? Bill Ross
- [AMBER] ANAL problems E.M.
- Re: [AMBER] ANAL problems Bill Ross
- [AMBER] Using AMBER force fields in NAMD Michael Zimmermann
- [AMBER] parallel problem of QM/MM calculation for AMBER 9 liu junjun
- [AMBER] The PDB file was not recognized by Amber, what can i do? Houyang Chen
- Re: [AMBER] The PDB file was not recognized by Amber, what can i do? Carlos Simmerling
- RE: [AMBER] Using AMBER force fields in NAMD Ross Walker
- RE: [AMBER] Using AMBER force fields in NAMD Piotr Cieplak
- RE: [AMBER] parallel problem of QM/MM calculation for AMBER 9 Ross Walker
- RE: [AMBER] Using AMBER force fields in NAMD Thomas Cheatham III
- Re: [AMBER] The PDB file was not recognized by Amber, what can i do? Barbault Florent
- Re: [AMBER] ANAL problems Edward M
- RE: [AMBER] ERROR In Restraint file. Catein Catherine
- Re: [AMBER] ERROR In Restraint file. David A. Case
- [AMBER] Nonterminal, was not found in name map Sunita Patel
- Re: [AMBER] parallel problem of QM/MM calculation for AMBER 9 liu junjun
- RE: [AMBER] Nonterminal, was not found in name map Ross Walker
- RE: [AMBER] The PDB file was not recognized by Amber, what can i do? Houyang Chen
- RE: [AMBER] The PDB file was not recognized by Amber, what can i do? Ross Walker
- [AMBER] REd program! R. A.
- RE: [AMBER] Nonterminal, was not found in name map Bill Ross
- Re: [AMBER] The PDB file was not recognized by Amber, what can i do? Barbault Florent
Wednesday, 29 April 2009
- Re: [AMBER] The PDB file was not recognized by Amber, what can i do? Markus Kaukonen
- Re: [AMBER] reg-TMD Carlos Simmerling
- Re: [AMBER] reg-TMD Carlos Simmerling
- [AMBER] (no subject) waleed zalloum
- Re: [AMBER] REd program! FyD
- [AMBER] input error in TI calculation Hannes Wallnoefer
- [AMBER] test/amoeba: forrtl: error (78): process killed (SIGTERM) Tomasio, Susana
- Re: [AMBER] (no subject) David A. Case
- Re: [AMBER] test/amoeba: forrtl: error (78): process killed (SIGTERM) Wei Zhang
- Re: [AMBER] (no subject) waleed zalloum
- Re: [AMBER] input error in TI calculation David A. Case
- Re: [AMBER] AmberTools compiling error Farly Walsh
- RE: [AMBER] test/amoeba: forrtl: error (78): process killed (SIGTERM) Tomasio, Susana
- RE: [AMBER] reg-TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA].
- [AMBER] chain restrain x TI Josmar R. da Rocha
- RE: [AMBER] The PDB file was not recognized by Amber, what can i do? Houyang Chen
- [AMBER] Amber FF and Glycam Dong Xu
- RE: [AMBER] reg-TMD balaji nagarajan
- [AMBER] MM-PBSA energy decomposition Dong Xu
- [AMBER] hbond-error in amber9 balaji nagarajan
- [AMBER] Influence about HIS-HIE-HIS-HIP Rilei Yu
- [AMBER] how to add charge on metal ions bharat lakhani
Thursday, 30 April 2009
- Re: [AMBER] MM-PBSA energy decomposition Hannes Kopitz
- Re: [AMBER] hbond-error in amber9 Alessandro S. Nascimento
- Re: [AMBER] Influence about HIS-HIE-HIS-HIP David A. Case
- Re: [AMBER] Amber FF and Glycam Lachele Foley (Lists)
- [AMBER] Request an error Collins Nganou
- Re: [AMBER] chain restrain x TI David A. Case
- Re: [AMBER] Amber FF and Glycam Carlos Simmerling
- [AMBER] (no subject) Collins Nganou
- [AMBER] Make parallel test faillure Collins Nganou
- RE: [AMBER] Make parallel test faillure Ross Walker
- Re: [AMBER] (no subject) David A. Case

Last message date: Wed May 20 2009 - 13:55:33 PDT
Archived on: Mon Apr 22 2024 - 05:53:43 PDT

Amber Archive Apr 2009 by date