Amber Archive Apr 2010: by date

Wednesday, 31 March 2010
- Re: [AMBER] reg-Generalized Born Approach maya maya
- [AMBER] antechamber monica.imtech.res.in
Thursday, 1 April 2010
- Re: [AMBER] antechamber Dmitri Nilov
- Re: [AMBER] Problem with solvationbox command monica.imtech.res.in
- [AMBER] QMMM Iron Dmitry Mukha
- Re: [AMBER] antechamber monica.imtech.res.in
- Re: [AMBER] antechamber Dmitry Nilov
- [AMBER] QMMM Iron Dmitry Mukha
- [AMBER] SASA Beale, John
- [AMBER] Problems during AMBER 10 compilation. Zuzanna K. Scigacz
- Re: [AMBER] reg-Generalized Born Approach case
- Re: [AMBER] reg-Generalized Born Approach Carlos Simmerling
- Re: [AMBER] antechamber case
- Re: [AMBER] SASA case
- Re: [AMBER] Problems during AMBER 10 compilation. case
- [AMBER] Water models ? xuemeiwang1103
- Re: [AMBER] Water models ? Carlos Simmerling
- [AMBER] SANDER BOMB in subroutine sc_check_and_adjust Atom coordinate disagreement imtiaz shafiq
- [AMBER] correct syntax for assinging scmask to two atoms of different molecules imtiaz shafiq
- Re: [AMBER] correct syntax for assinging scmask to two atoms of different molecules steinbrt.rci.rutgers.edu
- RE: [AMBER] QMMM Iron Ross Walker
- RE: [AMBER] QMMM Iron Ross Walker
- Re: [AMBER] QMMM Iron Gustavo Seabra
- [AMBER] Segmentation Fault Beale, John
- RE: [AMBER] Segmentation Fault Ross Walker
- [AMBER] How to perform backbone and residues restraint at the same time Rilei Yu
- [AMBER] Problem with an output file lee lior
- Re: [AMBER] Problem with an output file Jason Swails
Friday, 2 April 2010
- Re: [AMBER] How to perform backbone and residues restraint at the same time case
- [AMBER] how to achieve the 2D periodic boundary kecy_w.sina.com
- [AMBER] problem with frcmod parameter pxq
- Re: [AMBER] problem with frcmod parameter case
- Re: [AMBER] problem with frcmod parameter Bill Ross
- Re: Re: [AMBER] problem with frcmod parameter pxq
- [AMBER] Regarding RDF calculation in Ptraj aneesh cna
- [AMBER] thermodynamic integration Hyma vathi
- [AMBER] COOH group:extra undesired bond::NO reply :-( Jio M
Saturday, 3 April 2010
- [AMBER] problem when doing bond in tleap pxq
- Re: [AMBER] How to perform backbone and residues restraint at the same time Rilei Yu
- [AMBER] MMPBSA-on-cluster Rilei Yu
- [AMBER] 转发: MMPBSA-on-cluster Rilei Yu
- [AMBER] MMPBSA-ON-CLUSTER Rilei Yu
- [AMBER] Sorry for my multiple-email (making mistake!) Rilei Yu
- Re: [AMBER] MMPBSA-ON-CLUSTER Bill Miller III
- Re: [AMBER] MMPBSA-ON-CLUSTER Jason Swails
- Re: [AMBER] COOH group:extra undesired bond::NO reply :-( case
- Re: [AMBER] problem when doing bond in tleap case
- Re: [AMBER] thermodynamic integration steinbrt.rci.rutgers.edu
- [AMBER] makeANG_rst values Andrew Olson
- Re: [AMBER] makeANG_rst values case
- Re: [AMBER] MMPBSA-ON-CLUSTER Rilei Yu
- Re: [AMBER] MMPBSA-ON-CLUSTER Bill Miller III
- Re: [AMBER] MMPBSA-ON-CLUSTER Rilei Yu
- Re: [AMBER] MMPBSA-ON-CLUSTER Jason Swails
Sunday, 4 April 2010
- Re: [AMBER] COOH group:extra undesired bond::NO reply :-( Jio M
- Re: [AMBER] MMPBSA-ON-CLUSTER Rilei Yu
- Re: [AMBER] MMPBSA-ON-CLUSTER Bill Miller III
- Re: Re: [AMBER] problem when doing bond in tleap pxq
- [AMBER] SASA Chih-Ying Lin
- Re: [AMBER] antechamber monica.imtech.res.in
- [AMBER] rna simulation Asfa Ali
- Re: [AMBER] rna simulation shamoon siddiqui
- [AMBER] antechamber monica.imtech.res.in
- Re: [AMBER] rna simulation Asfa Ali
- Re: [AMBER] rna simulation shamoon siddiqui
- Re: [AMBER] rna simulation Asfa Ali
- Re: [AMBER] rna simulation shamoon siddiqui
Monday, 5 April 2010
- [AMBER] undo iwrap wrapping Paul Brandt
- Re: [AMBER] rna simulation Jason Swails
- Re: [AMBER] undo iwrap wrapping Carlos Simmerling
- Re: [AMBER] antechamber case
- Re: [AMBER] Regarding RDF calculation in Ptraj Daniel Roe
- [AMBER] error in reading namelist cntrl Hyma vathi
- Re: [AMBER] error in reading namelist cntrl Carlos Simmerling
- Re: [AMBER] error in reading namelist cntrl case
- [AMBER] not sure of the atomtype in .prep pxq
- Re: [AMBER] error in reading namelist cntrl Hyma vathi
- Re: [AMBER] error in reading namelist cntrl case
- Re: [AMBER] rna simulation Bill Ross
- Re: [AMBER] rna simulation Bill Ross
- [AMBER] amber10 installation on SGI IRIX 6.5 Eruysal, Ferdi
- Re: [AMBER] amber10 installation on SGI IRIX 6.5 Bill Ross
- [AMBER] ligand exchange John S
- [AMBER] Unit of atomic fluctuation unit nicholus bhattacharjee
- Re: [AMBER] amber10 installation on SGI IRIX 6.5 Atro Tossavainen
- Re: [AMBER] Unit of atomic fluctuation unit Kshatresh Dutta Dubey
Tuesday, 6 April 2010
- [AMBER] antechamber Asfa Ali
- [AMBER] USING PTRAJ TO PROCESS PMEMD TRAJECTORY COORDINTES DATA Juan Carlos
- [AMBER] Re: ligand exchange John S
- Re: [AMBER] Problems during AMBER 10 compilation. Zuzanna K. Ścigacz
- [AMBER] Unit of analyze modes with ptraj Samuel Genheden
- Re: [AMBER] Re: ligand exchange case
- Re: [AMBER] antechamber case
- Re: [AMBER] Problems during AMBER 10 compilation. case
- Re: [AMBER] Problems during AMBER 10 compilation. Zuzanna K. Ścigacz
- Re: [AMBER] Problems during AMBER 10 compilation. case
- Re: [AMBER] Problems during AMBER 10 compilation. Zuzanna K. Ścigacz
- Re: [AMBER] Problems during AMBER 10 compilation. case
- Re: [AMBER] Problems during AMBER 10 compilation. Zuzanna K. Ścigacz
- Re: [AMBER] USING PTRAJ TO PROCESS PMEMD TRAJECTORY COORDINTES DATA Robert Duke
- Re: [AMBER] Problems during AMBER 10 compilation. case
- Re: [AMBER] USING PTRAJ TO PROCESS PMEMD TRAJECTORY COORDINTES DATA Daniel Roe
- [AMBER] Files for Charged serine in proteins? Dean Cuebas
- Re: [AMBER] Problems during AMBER 10 compilation. Bill Ross
- Re: [AMBER] Problems during AMBER 10 compilation. Bill Ross
- Re: [AMBER] Problems during AMBER 10 compilation. Zuzanna K. Ścigacz
- [AMBER] radius of gyration Ganesh Kamath
- [AMBER] question about EVB Ganesh Kamath
- Re: [AMBER] makeANG_rst values Andrew Olson
- Re: [AMBER] makeANG_rst values case
- [AMBER] COOH group:extra undesired bond Jio M
Wednesday, 7 April 2010
- Re: [AMBER] AMBER10 installation: make test error 1 Anna Dejardin
- Re: [AMBER] Energy units in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] Energy units in mm-pbsa calculations Jason Swails
- [AMBER] Traceback: not available, complile with -ftrace = frame Yunfen Wang
- Re: [AMBER] Traceback: not available, complile with -ftrace = frame Jason Swails
- [AMBER] Amber99FFSB parameter files for Gaussian Senthil Natesan
- [AMBER] amber 5 manual William Flak
- [AMBER] dummy atom William Flak
- [AMBER] Chirality Restraint Ilyas Yildirim
- RE: [AMBER] Chirality Restraint Seetin, Matthew
- [AMBER] Umbrella Sampling with distances; setting of r1 and r4 in the restraint Matthias Wildauer
- [AMBER] non bonded interactions (vanderwaal and electrostatic) Ganesh Kamath
- RE: [AMBER] Umbrella Sampling with distances; setting of r1 and r4 in the restraint Seetin, Matthew
- Re: [AMBER] Umbrella Sampling with distances; setting of r1 and r4 in the restraint case
- Re: [AMBER] Umbrella Sampling with distances; setting of r1 and r4 in the restraint Matthias Wildauer
- Re: [AMBER] non bonded interactions (vanderwaal and electrostatic) Barbault Florent
- [AMBER] energy decomposition Ganesh Kamath
- Re: [AMBER] energy decomposition Bill Miller III
- [AMBER] contiguous trajectory without iwrap=1 Emmanuel Baribefe Naziga
- Re: [AMBER] contiguous trajectory without iwrap=1 Bill Ross
- Re: [AMBER] contiguous trajectory without iwrap=1 Emmanuel Baribefe Naziga
- Re: [AMBER] contiguous trajectory without iwrap=1 Bill Ross
- Re: [AMBER] contiguous trajectory without iwrap=1 Jacky Zhao
- Re: [AMBER] contiguous trajectory without iwrap=1 Carlos Simmerling
- Re:Re: [AMBER] Traceback: not available, complile with -ftrace = frame Yunfen Wang
- Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame Jason Swails
- [AMBER] Ptraj Problem Jagdeesh C
- Re: [AMBER] Ptraj Problem Jason Swails
- Re: [AMBER] Energy units in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in
- Re:Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame Yunfen Wang
Thursday, 8 April 2010
- [AMBER] question on section 2 of MM-PBSA tutorial Andrew Voronkov
- [AMBER] Fortran runtime error :bad value duiring floating point read Yunfen Wang
- Re: [AMBER] Fortran runtime error :bad value duiring floating point read Trevor Gokey
- Re: [AMBER] USING PTRAJ TO PROCESS PMEMD TRAJECTORY COORDINTES DATA Juan Carlos
- [AMBER] regGB maya maya
- [AMBER] mmpbsa-job-killed Rilei Yu
- [AMBER] angle force constants in GAFF João Sardinha
- Re: [AMBER] mmpbsa-job-killed mish
- Re:Re: [AMBER] Fortran runtime error :bad value duiring floating point read Yunfen Wang
- Re: [AMBER] angle force constants in GAFF case
- Re: [AMBER] Energy units in mm-pbsa calculations Jason Swails
- Re: Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame Jason Swails
- Re: [AMBER] angle force constants in GAFF João Sardinha
- Re: [AMBER] regGB case
- Re: Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame Bill Ross
- Re: [AMBER] amber 5 manual case
- [AMBER] I do need your help, please William Flak
- [AMBER] multiconformational RESP fitting with antechamber Yi Shang
- [AMBER] developing amber force field Necmettin Pirinccioglu
- Re: [AMBER] amber 5 manual William Flak
- Re: [AMBER] amber 5 manual case
- Re:Re: Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame Yunfen Wang
- Re: [AMBER] developing amber force field InSuk Joung
- Re: Re: Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame Jason Swails
- RE: [AMBER] mmpbsa-job-killed Ross Walker
- RE: [AMBER] I do need your help, please Ross Walker
- RE: [AMBER] multiconformational RESP fitting with antechamber Ross Walker
- Re: [AMBER] regGB maya maya
- [AMBER] vlimit exceeded for step Rilei Yu
Friday, 9 April 2010
- Re[2]: [AMBER] developing amber force field Necmettin Pirinccioglu
- Re: Re[2]: [AMBER] developing amber force field Karl N. Kirschner
- Re[4]: [AMBER] developing amber force field Necmettin Pirinccioglu
- Re: [AMBER] vlimit exceeded for step Jason Swails
- Re: [AMBER] vlimit exceeded for step Thomas Cheatham III
- [AMBER] Solvent Beale, John
- [AMBER] Fwd: .rst file corrupted manikanthan bhavaraju
- Re: [AMBER] Solvent Ganesh Kamath
- Re:Re: Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame Bill Ross
- [AMBER] mmpbsa-problem Dima A Sabbah
- Re: Re[4]: [AMBER] developing amber force field Diego Javier Alonso de Armiño
- RE: [AMBER] vlimit exceeded for step Ross Walker
- [AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test Ibrahim Moustafa
- Re: [AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test Jason Swails
- [AMBER] Install AMBER problem. Trojan 007
- Re: [AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test Ibrahim Moustafa
- Re: [AMBER] Install AMBER problem. Jason Swails
- Re: [AMBER] vlimit exceeded for step Rilei Yu
- RE: [AMBER] mmpbsa-job-killed Rilei Yu
- Re: [AMBER] vlimit exceeded for step Jason Swails
Saturday, 10 April 2010
- Re: [AMBER] vlimit exceeded for step Rilei Yu
- RE: [AMBER] Install AMBER problem. Trojan 007
Sunday, 11 April 2010
- [AMBER] slightly off topic: suggestions for DNA single strand simulations Amedeo Capobianco
Monday, 12 April 2010
- [AMBER] problem with XLEAP on X-client run on windows machine... Babu Kannappan
Sunday, 11 April 2010
- Re: [AMBER] problem with XLEAP on X-client run on windows machine... Lachele Foley (Lists)
- [AMBER] distrbuting an excess charge Homa Azizian
- [AMBER] RAMD gokul algates
- [AMBER] regarding antechamber Asfa Ali
Monday, 12 April 2010
- [AMBER] Installation on sles11 on ibm-power6-cpus German Erlenkamp
- Re: [AMBER] RAMD Vlad Cojocaru
- [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)... Silvia Carlotto
- [AMBER] vacuum bubbles generated after heating Nicee
- Re: [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)... Jason Swails
- Re: [AMBER] vacuum bubbles generated after heating Jason Swails
- Re: [AMBER] distrbuting an excess charge Jason Swails
- [AMBER] PROBLEM WITH PMEMD PERFORMANCE Juan Carlos
- [AMBER] Does the frequency of output affect MD simulation in AMBER10? Nancy
- Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Carlos Simmerling
- Re: [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)... Silvia Carlotto
- Re: [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)... Carlos Simmerling
- Re: [AMBER] regarding antechamber case
- Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing
- Re: [AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test Daniel Roe
- Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Carlos Simmerling
- Re: [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)... Daniel Roe
- Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing
- Re: [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)... Lachele Foley (Lists)
- Re: [AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test Ibrahim Moustafa
- [AMBER] Second Request Dima A Sabbah
- Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Carlos Simmerling
- [AMBER] trying to use antechamber with -nc 0 for a molecule Alan
- [AMBER] how to pick certain water molecular from a .mdcrd pxq
- Re: [AMBER] trying to use antechamber with -nc 0 for a molecule case
- Re: [AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test Daniel Roe
- Re: [AMBER] PROBLEM WITH PMEMD PERFORMANCE Tom Joseph
- Re: [AMBER] trying to use antechamber with -nc 0 for a molecule Alan
- Re: [AMBER] trying to use antechamber with -nc 0 for a molecule zoran matovic
- [AMBER] Vlimit error in ABMD Emmanuel Baribefe Naziga
- [AMBER] Amber11, pure QM PBC aapeters.ncsu.edu
- Re: [AMBER] trying to use antechamber with -nc 0 for a molecule Alan
- Re: [AMBER] Amber11, pure QM PBC case
- Re: [AMBER] vacuum bubbles generated after heating Bill Ross
- Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Bill Ross
- [AMBER] How do you know when to include improper dihedrals???? Dean Cuebas
- Re: [AMBER] vacuum bubbles generated after heating Bill Ross
- [AMBER] Amber10 Cuda compile failure aapeters.ncsu.edu
- Re: [AMBER] Amber10 Cuda compile failure Robert Duke
- RE: [AMBER] Amber10 Cuda compile failure Ross Walker
- [AMBER] Is the variation of C-Cl bond length normal? Shulin Zhuang
- Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing
- Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing
- [AMBER] Regarding parameter files of dna-lig complex Asfa Ali
- [AMBER] how to pick certain water molecular from a .mdcrd pxq
Tuesday, 13 April 2010
- Re: [AMBER] vacuum bubbles generated after heating jani vinod
- [AMBER] loadmol2 Segmentation fault Rui Li
- Re: [AMBER] loadmol2 Segmentation fault FyD
- Re: [AMBER] loadmol2 Segmentation fault FyD
- Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Carlos Simmerling
- Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? case
- Re: [AMBER] how to pick certain water molecular from a .mdcrd Jason Swails
- Re: [AMBER] loadmol2 Segmentation fault case
- Re: [AMBER] loadmol2 Segmentation fault case
- [AMBER] How to prepare the two tolopogy files when doing TI calculation? fancy2012
- Re: [AMBER] How to prepare the two tolopogy files when doing TI calculation? steinbrt.rci.rutgers.edu
- Re: [AMBER] How to prepare the two tolopogy files when doing TIcalculation? Ramu Anandakrishnan
- Re: [AMBER] vacuum bubbles generated after heating Nicee
- Re:Re: [AMBER] How to prepare the two tolopogy files when doing TI calculation? fancy2012
- Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing
- Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing
- Re: [AMBER] Regarding parameter files of dna-lig complex Jason Swails
- [AMBER] Asking help for some analysis section nicholus bhattacharjee
- Re: [AMBER] Asking help for some analysis section case
- RE: [AMBER] Amber10 Cuda compile failure Ross Walker
- RE: [AMBER] Amber11, pure QM PBC Ross Walker
- RE: [AMBER] PROBLEM WITH PMEMD PERFORMANCE Ross Walker
- [AMBER] Automatic assignment of HID, HIP, HIE?? Dean Cuebas
- Re: [AMBER] Automatic assignment of HID, HIP, HIE?? case
- Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Bill Ross
- Re: [AMBER] Regarding parameter files of dna-lig complex Bill Ross
- [AMBER] amber <-> desmond conversion tools Parish, Carol
- Re: [AMBER] loadmol2 Segmentation fault FyD
- [AMBER] Re: Is the variation of C-Cl bond length normal? Shulin Zhuang
- [AMBER] regarding parameter file creation of dna-lig complex Asfa Ali
- RE: [AMBER] Is the variation of C-Cl bond length normal? Ross Walker
- Re: [AMBER] regarding parameter file creation of dna-lig complex Bill Ross
- [AMBER] About restart-job Rilei Yu
- Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing
- Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Carlos Simmerling
- Re: [AMBER] how to pick certain water molecular from a .mdcrd Thomas Cheatham
- Re: [AMBER] slightly off topic: suggestions for DNA single strand simulations Thomas Cheatham
- Re: [AMBER] slightly off topic: suggestions for DNA single strand simulations Asfa Ali
- Re: [AMBER] regarding parameter file creation of dna-lig complex Asfa Ali
- Re: [AMBER] amber <-> desmond conversion tools Cen Gao
- Re: [AMBER] loadmol2 Segmentation fault Rui Li
Wednesday, 14 April 2010
- [AMBER] Chirality of amines in GAFF Dmitry Nilov
- [AMBER] the volume is always getting bigger and bigger until crash Yunfen Wang
- [AMBER] periodic boundary condition juan zeng
- Re: [AMBER] the volume is always getting bigger and bigger until crash Carlos Simmerling
- [AMBER] 1-4 EEL Jio M
- Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing
- Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Carlos Simmerling
- Re: [AMBER] Chirality of amines in GAFF Jason Swails
- Re: [AMBER] About restart-job Matthias Wildauer
- Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing
- Re: [AMBER] Chirality of amines in GAFF Alan
- [AMBER] (no subject) Waad RHAIEM
- [AMBER] RAMD random number generator Waad RHAIEM
- [AMBER] Thole screening in sander Diddo Diddens
- Re: [AMBER] Thole screening in sander case
- [AMBER] NMR refinment issues rolandmarques.aol.com
- Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Bill Ross
- Re: [AMBER] slightly off topic: suggestions for DNA single strand simulations Bill Ross
- Re: [AMBER] slightly off topic: suggestions for DNA single strand simulations Asfa Ali
- Re: [AMBER] slightly off topic: suggestions for DNA single strand simulations Bill Ross
- Re: [AMBER] loadmol2 Segmentation fault Scott Brozell
- Re: [AMBER] Chirality of amines in GAFF FyD
- Re: [AMBER] loadmol2 Segmentation fault FyD
- Re: [AMBER] loadmol2 Segmentation fault Scott Brozell
- RE: [AMBER] Amber10 Cuda compile failure aapeters.ncsu.edu
- [AMBER] Entropy-problem Rilei Yu
- Re: [AMBER] Chirality of amines in GAFF Dean Cuebas
- Re: [AMBER] Entropy-problem Jason Swails
- Re: [AMBER] Chirality of amines in GAFF David A. Case
- Re:Re: [AMBER] the volume is always getting bigger and bigger until crash Yunfen Wang
- Re: Re: [AMBER] the volume is always getting bigger and bigger until crash Carlos Simmerling
- Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing
- Re: [AMBER] Entropy-problem Rilei Yu
- [AMBER] Trajectory Smoothing Ganesh Krishnan
- RE: [AMBER] Amber10 Cuda compile failure Ross Walker
- [AMBER] PMEMD.CUDA on GTX275 Levi Pierce
- [AMBER] periodic boundary condition juan zeng
- RE: [AMBER] PMEMD.CUDA on GTX275 Ross Walker
- RE: [AMBER] PMEMD.CUDA on GTX275 Peter Schmidtke
- RE: [AMBER] PMEMD.CUDA on GTX275 Ross Walker
- Re: [AMBER] loadmol2 Segmentation fault Rui Li
Thursday, 15 April 2010
- Re: [AMBER] loadmol2 Segmentation fault FyD
- [AMBER] 1-4 EEL Jio M
- Re: [AMBER] RAMD random number generator Vlad Cojocaru
- Re: [AMBER] loadmol2 Segmentation fault FyD
- RE: [AMBER] PROBLEM WITH PMEMD PERFORMANCE Juan Carlos
- Re: [AMBER] How do you know when to include improper dihedrals???? Dmitry Nilov
- Re: [AMBER] periodic boundary condition Jason Swails
- Re: [AMBER] Trajectory Smoothing Bill Miller III
- Re: [AMBER] How do you know when to include improper dihedrals???? Dmitry Nilov
- Re: [AMBER] How do you know when to include improper dihedrals???? Karl N. Kirschner
- Re: [AMBER] Trajectory Smoothing Bill Ross
- Re: [AMBER] 1-4 EEL Bill Ross
- Re: [AMBER] periodic boundary condition Bill Ross
- Re: [AMBER] loadmol2 Segmentation fault David A. Case
- Re: [AMBER] How do you know when to include improper dihedrals???? Dean Cuebas
- Re: [AMBER] How do you know when to include improper dihedrals???? Dean Cuebas
- [AMBER] Steered/Targeted MD Ahmad, Rafi
- Re: [AMBER] periodic boundary condition Jason Swails
- [AMBER] angle between DNA (vector) and a plane Taufik Al-Sarraj
- Re: [AMBER] loadmol2 Segmentation fault FyD
- Re: [AMBER] periodic boundary condition Bill Ross
- [AMBER] Unit of analyze modes with ptraj Samuel Genheden
- [AMBER] radius of gyration Ganesh Kamath
- Re: [AMBER] NMR refinment issues rolandmarques.aol.com
- Re: [AMBER] Unit of analyze modes with ptraj David A. Case
- [AMBER] BOND TYPE Homa Azizian
- Re: [AMBER] BOND TYPE Dean Cuebas
- Re: [AMBER] 1-4 EEL Jio M
- RE: [AMBER] PROBLEM WITH PMEMD PERFORMANCE Ross Walker
Friday, 16 April 2010
- Re: [AMBER] periodic boundary condition juan zeng
- [AMBER] Nucleic acid aperture Fernando Martín García
- [AMBER] chirality restraints for non-standard residue Jio M
- [AMBER] problem in MMPBSA zgong.hust
- [AMBER] PMEMD missing type? - bugfix Josh Berryman
- Re: [AMBER] PMEMD missing type? - bugfix Robert Duke
- Re: [AMBER] radius of gyration Taufik Al-Sarraj
- [AMBER] how is pH treated in Amber - other than constant pH simulations Andrew Voronkov
- RE: [AMBER] PMEMD missing type? - bugfix Ross Walker
- Re: [AMBER] PMEMD missing type? - bugfix Robert Duke
- Re: [AMBER] BOND TYPE corrections Dean Cuebas
- Re: [AMBER] how is pH treated in Amber - other than constant pH simulations Carlos Simmerling
- RE: [AMBER] PMEMD missing type? - bugfix Ross Walker
- Re: [AMBER] BOND TYPE Bill Ross
- Re: [AMBER] 1-4 EEL Bill Ross
- Re: [AMBER] how is pH treated in Amber - other than constant pH simulations Dean Cuebas
- [AMBER] QM/MM + PIMD aapeters.ncsu.edu
- Re: Re: [AMBER] how is pH treated in Amber - other than constant pH simulations Andrew Voronkov
- Re: [AMBER] how is pH treated in Amber - other than constant pH simulations Jason Swails
- Re: [AMBER] chirality restraints for non-standard residue Jason Swails
- Re: [AMBER] chirality restraints for non-standard residue Jio M
- Re: [AMBER] chirality restraints for non-standard residue Jio M
- Re: [AMBER] QM/MM + PIMD Gustavo Seabra
- Re: [AMBER] how is pH treated in Amber - other than constant pH simulations Dean Cuebas
- [AMBER] Fwd: Re: RE: question on section 2 of MM-PBSA tutorial Andrew Voronkov
- [AMBER] RE: RE: question on section 2 of MM-PBSA tutorial Ross Walker
Saturday, 17 April 2010
- [AMBER] analysis for solvation effect for protein Yunfen Wang
- Re: [AMBER] NMR refinment issues David A. Case
- [AMBER] error when running mmpbsa pxq
- Re: [AMBER] error when running mmpbsa Jason Swails
- [AMBER] problem in MMPBSA zgong.hust
- Re: [AMBER] Trajectory Smoothing Ganesh Krishnan
- Re: [AMBER] problem in MMPBSA Dima A Sabbah
- Re: [AMBER] Trajectory Smoothing Daniel Roe
- Re: [AMBER] problem in MMPBSA Jason Swails
- Re: [AMBER] Trajectory Smoothing Jason Swails
- Re: Re: [AMBER] problem in MMPBSA zgong.hust
- Re: [AMBER] Trajectory Smoothing Ganesh Krishnan
Sunday, 18 April 2010
- Re: [AMBER] Trajectory Smoothing David A. Case
- [AMBER] how do MM_PBSA without water geyan
- Re: [AMBER] chirality restraints for non-standard residue Jio M
- Re: Re: [AMBER] error when running mmpbsa pxq
- Re: [AMBER] how do MM_PBSA without water Bill Miller III
- Re: Re: [AMBER] error when running mmpbsa Bill Miller III
- Re: Re: [AMBER] how do MM_PBSA without water geyan
- Re: Re: [AMBER] how do MM_PBSA without water Bill Miller III
- [AMBER] Force constant William Flak
- Re: [AMBER] Force constant Nicholas Musolino
- Re: [AMBER] Force constant William Flak
- Re: [AMBER] Trajectory Smoothing Ganesh Krishnan
- Re: [AMBER] Trajectory Smoothing David A. Case
- Re: Re: [AMBER] problem in MMPBSA Dima A Sabbah
- Re: [AMBER] problem in MMPBSA Dima A Sabbah
- Re: [AMBER] Trajectory Smoothing Ganesh Krishnan
- Re: [AMBER] Trajectory Smoothing Bill Ross
- Re: [AMBER] Trajectory Smoothing Carlos Simmerling
- Re: [AMBER] Force constant Nicholas Musolino
- Re: [AMBER] Trajectory Smoothing Ganesh Krishnan
- Re: [AMBER] Trajectory Smoothing Ganesh Krishnan
- Re: Re: Re: [AMBER] error when running mmpbsa pxq
Monday, 19 April 2010
- [AMBER] make a new residue FAD-CYS 030081094
- Re: Re: Re: [AMBER] how do MM_PBSA without water geyan
- [AMBER] how to add a gradually reduced restraint Jianing
- [AMBER] regarding running Nudged Elastic Band Approach with amber10 jani vinod
- Re: [AMBER] problem in MMPBSA Jason Swails
- Re: Re: Re: [AMBER] how do MM_PBSA without water Bill Miller III
- Re: [AMBER] how to add a gradually reduced restraint Dmitry Nilov
- [AMBER] Simulation of complex Asfa Ali
- Re: [AMBER] Simulation of complex Shozeb Haider
- Re: [AMBER] Simulation of complex steinbrt.rci.rutgers.edu
- Re: [AMBER] Simulation of complex Bill Ross
- Re: [AMBER] Simulation of complex Dean Cuebas
- [AMBER] elevated temperature MD Steve Seibold
- Re: [AMBER] elevated temperature MD Carlos Simmerling
- Re: [AMBER] elevated temperature MD Nicholas Musolino
- RE: [AMBER] regarding running Nudged Elastic Band Approach with amber10 Ross Walker
- Re: [AMBER] regarding running Nudged Elastic Band Approach with amber10 jani vinod
Tuesday, 20 April 2010
- Re: Re: [AMBER] how is pH treated in Amber - other than constant pH simulations Andrew Voronkov
- Re:Re: [AMBER] how to add a gradually reduced restraint Jianing
- [AMBER] remove water from system Yunfen Wang
- Re: [AMBER] remove water from system Carlos Simmerling
- Re: [AMBER] regarding running Nudged Elastic Band Approach with amber10 Carlos Simmerling
- [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups? Andrew Voronkov
- [AMBER] Error: Sander output is missing values Hyma vathi
- Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups? Dmitry Nilov
- Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups? Andrew Voronkov
- Re: [AMBER] Error: Sander output is missing values Bill Miller III
- Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups? Carlos Simmerling
- Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups? Dmitry Nilov
- Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups? Dmitry Nilov
- [AMBER] mm-pbsa: self assembly vijayaraj.clri.res.in
- Re: [AMBER] mm-pbsa: self assembly Nicholas Musolino
- Re: [AMBER] remove water from system Jason Swails
- Re: Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups? Andrew Voronkov
- Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups? Carlos Simmerling
- [AMBER] Setup of defined salt concentrations Anselm Horn
- [AMBER] Strange atom charge in topology file pellegrini
- Re: Re: [AMBER] how is pH treated in Amber - other than constant pH simulations Andrew Voronkov
- Re: [AMBER] Strange atom charge in topology file Yi Shang
- [AMBER] Request for MD protocol George Tzotzos
- Re: [AMBER] Request for MD protocol steinbrt.rci.rutgers.edu
- Re: [AMBER] Strange atom charge in topology file Yi Shang
- Re: [AMBER] Setup of defined salt concentrations InSuk Joung
- Re: [AMBER] how is pH treated in Amber - other than constant pH simulations Dean Cuebas
- Re: [AMBER] Error: Sander output is missing values Hyma vathi
- Re: [AMBER] Strange atom charge in topology file pellegrini
- [AMBER] Printing the reaction field in pbsa steinbrt.rci.rutgers.edu
- Re: [AMBER] Error: Sander output is missing values Jason Swails
- Re: [AMBER] Setup of defined salt concentrations Dean Cuebas
- [AMBER] elevated Temperature MD Steve Seibold
- [AMBER] QM/MM cut problem aapeters.ncsu.edu
- Re: [AMBER] remove water from system Bill Ross
- Re: [AMBER] QM/MM cut problem M. L. Dodson
- Re: [AMBER] Error: Sander output is missing values Bill Ross
- Re: [AMBER] Setup of defined salt concentrations Bill Ross
- RE: [AMBER] QM/MM cut problem Ross Walker
- Re: [AMBER] Setup of defined salt concentrations Bill Ross
- [AMBER] mutate function in NAB Alessandro Nascimento
- RE: [AMBER] QM/MM cut problem aapeters.ncsu.edu
- [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ? Marek Maly
- RE: [AMBER] QM/MM cut problem Ross Walker
- Re:Re: [AMBER] remove water from system Yunfen Wang
- Re: [AMBER] regarding running Nudged Elastic Band Approach with amber10 jani vinod
- [AMBER] mm-pbsa *_com.all.out files moitrayee.mbu.iisc.ernet.in
Wednesday, 21 April 2010
- [AMBER] Simulation of complex Asfa Ali
- [AMBER] about parmjoin Alan
- Re: Re: Re: [AMBER] how do MM_PBSA without water geyan
- Re: [AMBER] Simulation of complex steinbrt.rci.rutgers.edu
- Re:Re: [AMBER] remove water from system Yunfen Wang
- Re: Re: [AMBER] remove water from system Carlos Simmerling
- Re: [AMBER] Simulation of complex Asfa Ali
- Re: [AMBER] Simulation of complex steinbrt.rci.rutgers.edu
- Re: [AMBER] Simulation of complex N.R. Jena
- Re: [AMBER] Simulation of complex N.R. Jena
- Re: Re: [AMBER] remove water from system Jason Swails
- Re: [AMBER] Simulation of complex Asfa Ali
- Re: Re: Re: [AMBER] how do MM_PBSA without water Jason Swails
- Re: [AMBER] mm-pbsa *_com.all.out files Jason Swails
- Re: [AMBER] regarding running Nudged Elastic Band Approach with amber10 Jason Swails
- Re: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ? Jason Swails
- [AMBER] Do molecular dynamics in the limited space Yunjie Zhao
- [AMBER] MOPAC2009 output results into antechamber Alex Boncheff
- Re: [AMBER] Error: Sander output is missing values Hyma vathi
- Re: [AMBER] Error: Sander output is missing values Bill Miller III
- Re: [AMBER] Simulation of complex Bill Ross
- Re: [AMBER] Do molecular dynamics in the limited space Bill Ross
- Re: [AMBER] MOPAC2009 output results into antechamber David A. Case
- Re: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ? Marek Maly
- Re: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ? Jason Swails
- [AMBER] effect of pre-processor flags on pmemd? Thomas Zeiser
- Re: [AMBER] effect of pre-processor flags on pmemd? Robert Duke
- Re: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ? Marek Maly
- [AMBER] vdW question. ros
- Re: [AMBER] vdW question. Jason Swails
- Re: [AMBER] vdW question. Kevin Hauser
- [AMBER] solvent accessible surface Yunfen Wang
- Re: [AMBER] solvent accessible surface Bill Miller III
- [AMBER] regarding sqm Asfa Ali
Thursday, 22 April 2010
- Re: [AMBER] vdW question. steinbrt.rci.rutgers.edu
- Re: Re: Re: [AMBER] how do MM_PBSA without water geyan
- Re: Re: Re: [AMBER] how do MM_PBSA without water Bill Miller III
- [AMBER] A possible pmemd bug Lijiang Yang
- Re: [AMBER] regarding sqm Jason Swails
- Re: [AMBER] regarding sqm Asfa Ali
- Re: [AMBER] A possible pmemd bug Robert Duke
- Re: [AMBER] vdW question. ros
- Re: [AMBER] vdW question. Bill Ross
- Re: Re: Re: Re: [AMBER] how do MM_PBSA without water Bill Ross
- Re: [AMBER] vdW question. Bill Ross
- Re: [AMBER] A possible pmemd bug Scott Brozell
- [AMBER] Compiling pmemd (Amber 10) with OpenMPI, pathscale, etc. Paul S. Nerenberg
- RE: [AMBER] Compiling pmemd (Amber 10) with OpenMPI, pathscale, etc. Ross Walker
- RE: [AMBER] A possible pmemd bug Ross Walker
- Re: [AMBER] Compiling pmemd (Amber 10) with OpenMPI, pathscale, etc. Paul S. Nerenberg
- [AMBER] bond command Siddharth Rastogi
- Re: [AMBER] bond command Jason Swails
- [AMBER] problem on running saveAmberParm tianyuan meng
- Re: [AMBER] Do molecular dynamics in the limited space Yunjie Zhao
- [AMBER] H-bond analysis in ptraj Yunfen Wang
- [AMBER] molecular surface area geyan
- Re: [AMBER] H-bond analysis in ptraj geyan
- Re: [AMBER] molecular surface area Balazs Jojart
- Re: [AMBER] H-bond analysis in ptraj Shulin Zhuang
Friday, 23 April 2010
- Re: [AMBER] Installation on sles11 on ibm-power6-cpus German Erlenkamp
- [AMBER] Hydrogen Bond Analysis - explanation needed Srivatsan
- [AMBER] question about Amber Tutorial-A1 Rui Li
- Re: [AMBER] Do molecular dynamics in the limited space case
- RE: [AMBER] question about Amber Tutorial-A1 Ross Walker
- Re: [AMBER] Do molecular dynamics in the limited space Bill Ross
- Re: [AMBER] H-bond analysis in ptraj Bill Ross
- Re: [AMBER] problem on running saveAmberParm Bill Ross
- Re: [AMBER] problem on running saveAmberParm case
- Re: [AMBER] problem on running saveAmberParm Bill Ross
- [AMBER] PMEMD compiling errors Dian Jiao
- RE: [AMBER] PMEMD compiling errors Ross Walker
- [AMBER] problem with paiwise energy decomposition using mm-pbsa moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] PMEMD compiling errors Dian Jiao
- [AMBER] Antechamber, GAFF and methylimidazole typing Ben Roberts
- Re:Re: [AMBER] H-bond analysis in ptraj Yunfen Wang
- [AMBER] about IGB geyan
- RE: [AMBER] question about Amber Tutorial-A1 Rui Li
- RE: [AMBER] about IGB Ross Walker
Saturday, 24 April 2010
- Re: Re: [AMBER] H-bond analysis in ptraj Jason Swails
- [AMBER] pmemd.cuda problem Levi Pierce
- RE: [AMBER] pmemd.cuda problem Ross Walker
- Re: [AMBER] pmemd.cuda problem Levi Pierce
Sunday, 25 April 2010
- Re: RE: [AMBER] about IGB geyan
- Re: RE: [AMBER] about IGB Carlos Simmerling
- [AMBER] RESP Iodine William Flak
- Re: [AMBER] pmemd.cuda problem case
- Re: Re: RE: [AMBER] about IGB geyan
Monday, 26 April 2010
- RE: [AMBER] pmemd.cuda problem Ross Walker
- [AMBER] The system has extended beyond the extent of the virtual box kamlesh sahu
- [AMBER] WARNING: There is a bond of 8.894214 angstroms between Hyma vathi
- Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between Dmitry Nilov
- Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between Hyma vathi
- Re: [AMBER] The system has extended beyond the extent of the virtual box Carlos Simmerling
- Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between Dmitry Nilov
- Re: Re: RE: [AMBER] about IGB Carlos Simmerling
- [AMBER] Announcement: release of Amber11 and AmberTools 1.4 case
- Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between case
- Re: [AMBER] pmemd.cuda problem Levi Pierce
- [AMBER] Comparing dihedral energy curves Lekpa Duukori
- [AMBER] new ambertools folder distribution and Makefile_at Alan
- Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between Hyma vathi
- Re: [AMBER] Comparing dihedral energy curves Ilyas Yildirim
- Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between Bill Ross
- Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between Bill Ross
- Re: [AMBER] Comparing dihedral energy curves Lekpa Duukori
- Re: [AMBER] new ambertools folder distribution and Makefile_at case
- Re: [AMBER] The system has extended beyond the extent of the virtual box kamlesh sahu
- [AMBER]Fortran runtime error: Bad value during integer read Ying Yang
Tuesday, 27 April 2010
- [AMBER] ambertools 1.4, tests Alan
- Re: [AMBER]Fortran runtime error: Bad value during integer read Jason Swails
- Fw: Fwd: Fw: Fw: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ? Ramu Anandakrishnan
- Re: [AMBER] ambertools 1.4, tests David Watson
- [AMBER] explicit water MMPBSA Cristina Sisu
- Re: Fw: Fwd: Fw: Fw: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ? Marek Maly
- [AMBER] Addions grid ? Marek Maly
- Re: [AMBER] ambertools 1.4, tests Alan
- Re: [AMBER] ambertools 1.4, tests Jason Swails
- Re: [AMBER] Addions grid ? Bill Ross
- [AMBER] about skinnb liu junjun
- [AMBER] Compiling AmberTools 1.4 on MacOS10.5 Dean Cuebas
- Re: [AMBER] about skinnb Robert Duke
- Re: [AMBER] Compiling AmberTools 1.4 on MacOS10.5 Jason Swails
- Re: [AMBER] Compiling AmberTools 1.4 on MacOS10.5 Alan
- Re: [AMBER] Addions grid ? Marek Maly
- Re: [AMBER] Addions grid ? Bill Ross
- Re: [AMBER] Addions grid ? Marek Maly
- Re: [AMBER] Addions grid ? Bill Ross
- Re: [AMBER] ambertools 1.4, tests Mengjuei Hsieh
- [AMBER] ff99SB-ILDN Titus, Jamie (bairdje)
- Re: [AMBER] Compiling AmberTools 1.4 on MacOS10.5 Dean Cuebas
- Re: [AMBER] Addions grid ? Marek Maly
- [AMBER] Constraint minimisation before MD simulation Amire-Brahimi Benjamin
- Re: [AMBER] Constraint minimisation before MD simulation Carlos Simmerling
- Re: [AMBER] Constraint minimisation before MD simulation Bill Ross
- [AMBER] how to load topology file Siddharth Rastogi
- Re: [AMBER] how to load topology file Bill Ross
- Re: [AMBER] how to load topology file Lachele Foley (Lists)
- [AMBER] Question about RMSD in AMBER Yingjie Lin
- Re: [AMBER] Question about RMSD in AMBER Carlos Simmerling
- Re: [AMBER]Fortran runtime error: Bad value during integer read Ying Yang
- [AMBER] question about cluster analysis Jianing
- Re: [AMBER]Fortran runtime error: Bad value during integer read Jason Swails
- Re: [AMBER]Fortran runtime error: Bad value during integer read Jason Swails
Wednesday, 28 April 2010
- [AMBER] A bugfix for thiazole-imidazole rings Hasan Alniss
- [AMBER] AMBER VS QM energy calculations for dihedrals Palermo Giulia
- Re: [AMBER] AMBER VS QM energy calculations for dihedrals Ilyas Yildirim
- Re: [AMBER] Question about RMSD in AMBER Yingjie Lin
- [AMBER] problem rejoining segmented out files in long simulation g t
- Re: [AMBER] problem rejoining segmented out files in long simulation Carlos Simmerling
- Re: [AMBER] problem rejoining segmented out files in long simulation Jason Swails
- Re: [AMBER] Question about RMSD in AMBER Yi Shang
- [AMBER] Fortran runtime error: Bad value during integer read João Henriques
- Re: [AMBER] problem rejoining segmented out files in long simulation g t
- [AMBER] sleap from AT 1.4 doesn't seem ok Alan
- Re: [AMBER] about skinnb liu junjun
- Re: [AMBER] about skinnb Robert Duke
- Re: [AMBER] about skinnb liu junjun
- Re: [AMBER] about skinnb liu junjun
- [AMBER] forcefield parameters for TiO2/peptides? Tom Williams
- Re: [AMBER] about skinnb Robert Duke
- [AMBER] Question: ptraj masks Yingjie Lin
- Re: [AMBER] about skinnb liu junjun
- Re: [AMBER] Question: ptraj masks Carlos Simmerling
- [AMBER] OT: GLYLIB C libraries for molecular data Lachele Foley (Lists)
- [AMBER] Tesla C2050 atom limit? ben rodriguez
- Re: [AMBER] Fortran runtime error: Bad value during integer read Mengjuei Hsieh
- [AMBER] joining out files Homa Azizian
Thursday, 29 April 2010
- RE: [AMBER] Tesla C2050 atom limit? Scott Le Grand
- [AMBER] to test nab with openmp Alan
- RE: [AMBER] Tesla C2050 atom limit? Ross Walker
- RE: [AMBER] QM/MM cut problem Ross Walker
- [AMBER] Re: to test nab with openmp Alan
- [AMBER] Re: to test nab with openmp Alan
- Re: [AMBER] joining out files Homa Azizian
- Re: [AMBER] joining out files Bill Miller III
- Re: [AMBER] Fortran runtime error: Bad value during integer read João Henriques
- RE: [AMBER] QM/MM cut problem aapeters.ncsu.edu
- Re: [AMBER] Fortran runtime error: Bad value during integer read Jason Swails
- Re: [AMBER] Fortran runtime error: Bad value during integer read João Henriques
- RE: [AMBER] QM/MM cut problem Ross Walker
- Re: [AMBER] Fortran runtime error: Bad value during integer read João Henriques
- Re: [AMBER] Fortran runtime error: Bad value during integer read Jason Swails
- Re: [AMBER] sleap from AT 1.4 doesn't seem ok case
- [AMBER] AmberTools.pdf (AT 1.4) Alan
- [AMBER] failed to compile Amber11 with mpi on Mac Alan
- Re: [AMBER] failed to compile Amber11 with mpi on Mac Jason Swails
- [AMBER] Re: failed to compile Amber11 with mpi on Mac Alan
- Re: [AMBER] failed to compile Amber11 with mpi on Mac David Watson
- Re: [AMBER] failed to compile Amber11 with mpi on Mac Alan
- Re: [AMBER] failed to compile Amber11 with mpi on Mac case
- Re: [AMBER] forcefield parameters for TiO2/peptides? Ben Roberts
- [AMBER] a possible typo bug while building pmemd with mpi Alan
- [AMBER] Re: a possible typo bug while building pmemd with mpi Alan
- Re: [AMBER] a possible typo bug while building pmemd with mpi Jason Swails
- Re: [AMBER] a possible typo bug while building pmemd with mpi Alan
- Re: [AMBER] a possible typo bug while building pmemd with mpi David Watson
- Re: [AMBER] a possible typo bug while building pmemd with mpi Alan
- Re: [AMBER] a possible typo bug while building pmemd with mpi Jason Swails
- Re: [AMBER] a possible typo bug while building pmemd with mpi Ben Roberts
- Re: [AMBER] Fortran runtime error: Bad value during integer read Piotr Cieplak
- Re: [AMBER] a possible typo bug while building pmemd with mpi Alan
- Re: [AMBER] Fortran runtime error: Bad value during integer read João Henriques
- [AMBER] AmberTool 1.4 with Intel 10.1.014 on snow leopard Yu Chen
- [AMBER] Stability Calculation Using MMPBSA.py? Hopkins, Robert
- Re: [AMBER] joining out files Bill Ross
- Re: [AMBER] Stability Calculation Using MMPBSA.py? Jason Swails
- Re: [AMBER] Fortran runtime error: Bad value during integer read FyD
- RE: [AMBER] Stability Calculation Using MMPBSA.py? Hopkins, Robert
- Re: [AMBER] Fortran runtime error: Bad value during integer read Piotr Cieplak
- Re: [AMBER] Fortran runtime error: Bad value during integer read Piotr Cieplak
- Re: [AMBER] forcefield parameters for TiO2/peptides? Tom Williams
- Re: [AMBER] joining out files Homa Azizian
- Re: [AMBER] joining out files Jason Swails
- [AMBER] question about mass card of frcmod file Jim Miller
- Re: [AMBER] forcefield parameters for TiO2/peptides? FyD
- Re: [AMBER] question about mass card of frcmod file Bill Ross
Friday, 30 April 2010
- [AMBER] how to write one ptraj file into several smaller files Yunfen Wang
- Re: [AMBER] how to write one ptraj file into several smaller files Jason Swails
- Re: [AMBER] Fortran runtime error: Bad value during integer read João Henriques
- Re: [AMBER] how to write one ptraj file into several smaller files monica.imtech.res.in
- [AMBER] "go" keyword in ptraj Ben Roberts
- RE: [AMBER] "go" keyword in ptraj Ross Walker
- [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more Yu Chen
- Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more David Watson
- [AMBER] Problem from ala scanning Rilei Yu
- Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more case
- [AMBER] distance mapping monica.imtech.res.in
- Re: [AMBER] Problem from ala scanning Bill Miller III
- [AMBER] xgrid in opempi 1.4.1 still broken Alan
- Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more Yu Chen
- RE: [AMBER] "go" keyword in ptraj Thomas Cheatham III
- Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more Yu Chen
- Re: [AMBER] xgrid in opempi 1.4.1 still broken case
- Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more Bill Ross
- [AMBER] freezing selected residues Senthil Natesan
- Re: [AMBER] a possible typo bug while building pmemd with mpi Dean Cuebas
- Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more Yu Chen
- Re: [AMBER] "go" keyword in ptraj Ben Roberts
- [AMBER] nmr order parameter and autocorrelation luzhenw1.msu.edu
- Re: [AMBER] nmr order parameter and autocorrelation Carlos Simmerling
- Re: [AMBER] nmr order parameter and autocorrelation luzhenw1.msu.edu
- [AMBER] MM parameters for TiO2 Piotr Cieplak
- Re: [AMBER] nmr order parameter and autocorrelation Paul S. Nerenberg
- Re: [AMBER] Problem from ala scanning Bill Miller III
- Re: [AMBER] a possible typo bug while building pmemd with mpi Jason Swails
- Re: [AMBER] TER dfinition at the middile of pdb file Jason Swails

Last message date: Fri Apr 30 2010 - 21:00:03 PDT
Archived on: Fri Nov 22 2024 - 05:53:59 PST

Amber Archive Apr 2010 by date