Amber Archive Jul 2009: by date

Wednesday, 1 July 2009
- [AMBER] antechamber R. A.
- [AMBER] antechamber R. A.
- Re: [AMBER] antechamber Alan
- Re: [AMBER] antechamber case
- Re: [AMBER] antechamber gilbert.bluemarble.net
- [AMBER] The problem of restart file Jeffrey
- Re: [AMBER] antechamber FyD
- Re: [AMBER] Steps for NMR structure minimization case
- Re: [AMBER] The problem of restart file Carlos Simmerling
- [AMBER] amber9 in fedora10 Bala subramanian
- Re: [AMBER] The problem of restart file Jeffrey
- Re: [AMBER] Nonstandard molecules simulated with parm99EP ? Marek Maly
- Re: [AMBER] Nonstandard molecules simulated with parm99EP ? Marek Maly
- RE: [AMBER] amber9 in fedora10 Ross Walker
- [AMBER] pmemd/bintraj and ifort 10.1.0.21 Peter Varnai
- Re: [AMBER] pmemd/bintraj and ifort 10.1.0.21 Robert Duke
- [AMBER] default integration scheme in 7 vs. 10 Paul Brandt
- RE: [AMBER] default integration scheme in 7 vs. 10 Ross Walker
- Re: [AMBER] antechamber R. A.
- Re: [AMBER] antechamber FyD
Thursday, 2 July 2009
- Re: [AMBER] amber9 in fedora10 Bala subramanian
- Re: [AMBER] amber9 in fedora10 Bala subramanian
- Re: [AMBER] antechamber Alan
- Re: [AMBER] default integration scheme in 7 vs. 10 case
- [AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom suhaib sh
- Re: [AMBER] antechamber R. A.
- 回复： [AMBER] antechamber 廖青华
- 回复：回复： [AMBER] antechamber 廖青华
Friday, 3 July 2009
- [AMBER] MM-PBSA problem Giorgos Lamprinidis
- Re: [AMBER] MM-PBSA problem Rubben Torella
- [AMBER] Re: Error in REDIII FyD
- [AMBER] H-bond vs. VdW Taufik Al-Sarraj
- Re: [AMBER] H-bond vs. VdW FyD
Saturday, 4 July 2009
- [AMBER] calculation of the solvent accessibility Rilei Yu
- [AMBER] Boundary Condition Problem Pepe` Falahat
- Re: [AMBER] Boundary Condition Problem case
- [AMBER] Leap Questions... Cihan Aydin
- [AMBER] RED: Charge derivation of transtion state analogue manoj singh
Sunday, 5 July 2009
- [AMBER] Re: [q4md-fft] Charge calculation or non standard residue FyD
- Re: [AMBER] RED: Charge derivation of transtion state analogue FyD
Thursday, 2 July 2009
- 回复： [AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom 廖青华
Sunday, 5 July 2009
- [AMBER] RE: question about TUTORIAL A1 Ross Walker
- [AMBER] RE: ask for help (zn parameters) Ross Walker
- RE: [AMBER] Leap Questions... Ross Walker
- Re: [AMBER] RED: Charge derivation of transtion state analogue manoj singh
- Re: [AMBER] RED: Charge derivation of transtion state analogue FyD
- Re: [AMBER] RED: Charge derivation of transtion state analogue FyD
Monday, 6 July 2009
- [AMBER] non standard residue Neha Gandhi
- Re: [AMBER] MM-PBSA problem Giorgos Lamprinidis
- [AMBER] Re: non aminoacid Residue Neha Gandhi
- [AMBER] unable to read MM charges Vishal Maingi
- [AMBER] need charges of FE-S cluster subarna thakur
- Re: [AMBER] need charges of FE-S cluster case
- Re: [AMBER] H-bond vs. VdW Cihan Aydin
- RE: [AMBER] Re: non aminoacid Residue Ross Walker
- [AMBER] RE: question about TUTORIAL A1 Ross Walker
- Re: [AMBER] H-bond vs. VdW case
- [AMBER] unsolved verbosity when running minimization albert albert
- Re: [AMBER] unsolved verbosity when running minimization Carlos Simmerling
- [AMBER] Directory - GAFF Parameter File? Patrick Gedeon
- [AMBER] Re: Directory - GAFF Parameter File? Patrick Gedeon
- [AMBER] RE: suggestions Ross Walker
- [AMBER] Tleap input error, atom not found in residue template Brothers, Michael Charles
- Re: [AMBER] RE: suggestions Cihan Aydin
- [AMBER] unable to read MM charges (no reply yet) Vishal Maingi
- RE: [AMBER] Tleap input error, atom not found in residue template Ross Walker
Tuesday, 7 July 2009
- Re: [AMBER] non standard residue FyD
- [AMBER] Principle Questions s_bill36.yahoo.co.uk
- [AMBER] DCCM Raja Pandian
- [AMBER] Steered MD---more than one pair of atoms Hlengisizwe Ndlovu
- [AMBER] Zinc ion, help Mahmoud A. A. Ibrahim
- RE: [AMBER] Tleap input error, atom not found in residue template Brothers, Michael Charles
- [AMBER] rdparm bug? Paul Mortenson
- [AMBER] QMMM outupts Myeong Lee
- RE: [AMBER] Principle Questions Ross Walker
- AW: [AMBER] Steered MD---more than one pair of atoms Aust, Susanne
- [AMBER] amber10 installation problem Lan JIN
Wednesday, 8 July 2009
- [AMBER] Installing of amber10 Rilei Yu
- [AMBER] installing of amber10 problem Rilei Yu
- [AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT) Andrew Voronkov
- Re: [AMBER] Zinc ion, help FyD
- [AMBER] Is rmsd ~ 3 A reasonable for a 4ns simulation? Catein Catherine
- [AMBER] suitable force field Jio M
- Re: [AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT) Andrew Voronkov
- Re: [AMBER] unsolved verbosity when running minimization albert albert
- Re: [AMBER] unsolved verbosity when running minimization Carlos Simmerling
- Re: [AMBER] Installing of amber10 case
- Re: [AMBER] amber10 installation problem case
- [AMBER] ouput trajectory of only CA atom Bala subramanian
- [AMBER] ff parameters oguz gurbulak
- Re: [AMBER] ouput trajectory of only CA atom Carlos Simmerling
- Re: [AMBER] ouput trajectory of only CA atom Bala subramanian
- RE: [AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT) Ross Walker
- Re: [AMBER] ouput trajectory of only CA atom Vlad Cojocaru
- Re: [AMBER] ouput trajectory of only CA atom Jordan Monnet
- [AMBER] rmsd_dna balaji nagarajan
- [AMBER] bug in antechamber David Mobley
- [AMBER] suitable force field Jio M
- Re: [AMBER] rmsd_dna Carlos Simmerling
- [AMBER] MM-PBSA delphi.crg and delphi.siz Manish Kumar
- [AMBER] Acetylate and Amidate Alison Saunders
- Re: [AMBER] Acetylate and Amidate Carlos Simmerling
- Re: [AMBER] Acetylate and Amidate Alison Saunders
- Re: [AMBER] Acetylate and Amidate Bill Ross
- RE: [AMBER] rmsd_dna balaji nagarajan
- Re: [AMBER] amber10 installation problem Lan JIN
- [AMBER] rmsd_ptraj balaji nagarajan
- RE: [AMBER] rmsd_ptraj Ross Walker
- RE: [AMBER] rmsd_ptraj balaji nagarajan
Thursday, 9 July 2009
- RE: [AMBER] rmsd_ptraj Thomas Cheatham
- Re: [AMBER] Acetylate and Amidate Carlos Simmerling
- [AMBER] charged or not s. Bill
- Re: [AMBER] amber10 installation problem case
- Re: [AMBER] ff parameters case
- [AMBER] Antechamber prep question Andrew Olson
- Re: [AMBER] charged or not case
- Re: [AMBER] Antechamber prep question case
- Re: [AMBER] Antechamber prep question Andrew Olson
- [AMBER] Re: pls help and suggest Gustavo Seabra
- Re: [AMBER] Antechamber prep question case
- Re: [AMBER] QMMM outupts Gustavo Seabra
- Re: [AMBER] Antechamber prep question Andrew Olson
- [AMBER] reference re. determining size of timestep Paul Brandt
- Fw: [AMBER] Re: pls help and suggest Vishal Maingi
- Re: [AMBER] Antechamber prep question case
- [AMBER] AMBER windows version ? Siddharth Rastogi
- RE: [AMBER] AMBER windows version ? Ross Walker
- Re: [AMBER] AMBER windows version ? Siddharth Rastogi
- [AMBER] question of mm_pbsa 廖青华
- [AMBER] Re: MM-PBSA delphi.crg and delphi.siz Manish Kumar
- Re: [AMBER] Antechamber prep question FyD
Friday, 10 July 2009
- Re: [AMBER] amber10 installation problem Lan JIN
- [AMBER] unexplained blow-up at restart Sally Pias
- Re: [AMBER] question of mm_pbsa Hannes Kopitz
- Re: [AMBER] unexplained blow-up at restart Carlos Simmerling
- [AMBER] Restrained backbone conformation MD simulation" Prem Prakash Pathak
- Re: [AMBER] Restrained backbone conformation MD simulation" Carlos Simmerling
- Re: [AMBER] Antechamber prep question gilbert.bluemarble.net
- Re: [AMBER] unexplained blow-up at restart Simon Becker
- Re: [AMBER] Antechamber prep question Andrew Olson
- [AMBER] Manganese bondi radii Chunliyan
- [AMBER] Manganese Chunliyan
- [AMBER] manganese bondi radii for mm_pbsa calculation Chunliyan
- [AMBER] radius for Manganese ion Chunliyan
- [AMBER] Manganese bondi radii for mm/pbsa calculation Chunliyan
- [AMBER] EPtot for Alpha-L- methyl fucose Sushil Mishra
- Re: [AMBER] EPtot for Alpha-L- methyl fucose Carlos Simmerling
- Re: [AMBER] EPtot for Alpha-L- methyl fucose Sushil Mishra
- Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz suhaib sh
- Re: [AMBER] Antechamber prep question FyD
- [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Keith Van Nostrand
- Re: [AMBER] unexplained blow-up at restart Sally Pias
- [AMBER] implicit solvent (GB version2) MD simulation workalemahu berhanu
- Re: [AMBER] implicit solvent (GB version2) MD simulation Carlos Simmerling
- [AMBER] Need help for PMEMD 10 installation Jun Dong
- [AMBER] problem with energy calculations Thomas Lake
- Re: [AMBER] charges in topology file Jeffrey
- RE: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Ross Walker
- RE: [AMBER] Need help for PMEMD 10 installation Ross Walker
- Re: [AMBER] unexplained blow-up at restart Sally Pias
- Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz Ray Luo
- TMD: was: Re: [AMBER] charges in topology file Carlos Simmerling
- Re: [AMBER] question of mm_pbsa Ray Luo
- Re: [AMBER] unexplained blow-up at restart Carlos Simmerling
- Re: [AMBER] unexplained blow-up at restart Sally Pias
- RE: [AMBER] Need help for PMEMD 10 installation Jun Dong
- Re: [AMBER] unexplained blow-up at restart Carlos Simmerling
- Re: [AMBER] problem with energy calculations Carlos Simmerling
- Re: [AMBER] unexplained blow-up at restart Carlos Simmerling
- [AMBER] Peptide bond broken Syed Tarique Moin
- [AMBER] calculation of binding energy for lectin and fucuse.. Sushil Mishra
- RE: [AMBER] Need help for PMEMD 10 installation Ross Walker
- Re: [AMBER] unexplained blow-up at restart Sally Pias
- [AMBER] ligand/protein minimization Andrew Olson
- [AMBER] R.E.D intra-mcc and reorientation Ganesh Krishnan
- [AMBER] Syntax Bellymask Brothers, Michael Charles
- 回复： [AMBER] question of mm_pbsa 廖青华
- [AMBER] TMD: solvation and equilibration questions Jeffrey
- 回复： [AMBER] question of mm_pbsa 廖青华
- Re: [AMBER] Peptide bond broken FyD
Saturday, 11 July 2009
- Re: [AMBER] R.E.D intra-mcc and reorientation FyD
- [AMBER] How to fix specific atoms? (not residue) Myeong Lee
- Re: [AMBER] How to fix specific atoms? (not residue) Tom Joseph
- Re: [AMBER] R.E.D intra-mcc and reorientation Ganesh Krishnan
- [AMBER] problem with the energetics of the system Mahmoud A. A. Ibrahim
- Re: [AMBER] problem with the energetics of the system Ross Walker
- 回复： [AMBER] question of mm_pbsa 廖青华
Sunday, 12 July 2009
- Re: [AMBER] problem with the energetics of the system Mahmoud A. A. Ibrahim
- RE: [AMBER] problem with energy calculations Lake, Thomas
- Re: [AMBER] problem with energy calculations Carlos Simmerling
- [AMBER] amber dihedral format s. Bill
- Re: [AMBER] problem with energy calculations Thomas Lake
- Re: [AMBER] problem with energy calculations Carlos Simmerling
- [AMBER] help needed for HID s. Bill
- Re: [AMBER] help needed for HID Marius Retegan
- [AMBER] Amber10, Serial compilation with ifort Aldo Humberto Romero
- RE: [AMBER] Amber10, Serial compilation with ifort Ross Walker
- Re: [AMBER] amber dihedral format case
- Re: [AMBER] ligand/protein minimization case
- Re: [AMBER] Peptide bond broken case
- [AMBER] ptraj mask selection Patrick Gedeon
- Re: [AMBER] Peptide bond broken Shubhra Gupta
Monday, 13 July 2009
- Re: [AMBER] unexplained blow-up at restart Sally Pias
- Re: [AMBER] unexplained blow-up at restart Carlos Simmerling
- Re: [AMBER] Peptide bond broken Syed Tarique Moin
- [AMBER] Exclamation marks in trajectory Hugh Heldenbrand
- Re: [AMBER] ligand/protein minimization Andrew Olson
- Re: [AMBER] unexplained blow-up at restart Sally Pias
- Re: [AMBER] ligand/protein minimization case
- [AMBER] Re: reference re. size of dt case
- Re: [AMBER] unexplained blow-up at restart case
- [AMBER] Trouble saving amberparm files Alison Saunders
- Re: [AMBER] ligand/protein minimization Andrew Olson
- [AMBER] (no subject) Beale, John
- [AMBER] Re: bug in antechamber David Mobley
- Re: [AMBER] ptraj mask selection Jianyin Shao
- RE: [AMBER] Need help for PMEMD 10 installation Jun Dong
- Re: [AMBER] ptraj mask selection case
- RE: [AMBER] Exclamation marks in trajectory Ross Walker
- Re: [AMBER] Exclamation marks in trajectory Hugh Heldenbrand
- Re: [AMBER] ptraj mask selection Jianyin Shao
- RE: [AMBER] Need help for PMEMD 10 installation Ross Walker
- RE: [AMBER] Exclamation marks in trajectory Ross Walker
- Re: [AMBER] ptraj mask selection Patrick Gedeon
- Re: [AMBER] Trouble saving amberparm files Tom Joseph
- Re: [AMBER] help needed for HID FyD
- [AMBER] GAFF and NME, ACE terminal res Jio M
- [AMBER] Problem with amber9 installation moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] Trouble saving amberparm files Alison Saunders
- Re: [AMBER] Trouble saving amberparm files Tom Joseph
- Re: [AMBER] Trouble saving amberparm files Tom Joseph
- Re: [AMBER] Trouble saving amberparm files Alison Saunders
- RE: [AMBER] Problem with amber9 installation Ross Walker
- [AMBER] Re: Request to mailing list AMBER rejected E.M.
- Re: [AMBER] non standard residue FyD
Tuesday, 14 July 2009
- RE: [AMBER] Problem with amber9 installation moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] Need help for PMEMD 10 installation Giorgos Lamprinidis
- Re: [AMBER] GAFF and NME, ACE terminal res FyD
- [AMBER] mpirun noticed that process rank 1 ... on signal 1 (Hangup). Naser Alijabbari
- [AMBER] Re: mpirun noticed that process rank 1 ... on signal 1 (Hangup). Naser Alijabbari
- Re: [AMBER] Need help for PMEMD 10 installation Robert Duke
- [AMBER] RE: pmemd parallel Ross Walker
- RE: [AMBER] Re: mpirun noticed that process rank 1 ... on signal 1 (Hangup). Ross Walker
- [AMBER] Could not find bond parameter for O2 - ca Yogesh Aher
- [AMBER] Molecular Modeling Workshop and Model(l)ing'09 in Erlangen, Germany Harald Lanig
- [AMBER] Holding ligand rigid for minimization Andrew Olson
- [AMBER] Holding ligand rigid for minimization Andrew Olson
- Re: [AMBER] Re: mpirun noticed that process rank 1 ... on signal 1 (Hangup). Naser Alijabbari
- Re: [AMBER] Holding ligand rigid for minimization Andrew Olson
- [AMBER] PMEMD in a Cygwin Environment Hopkins, Robert
- Re: [AMBER] non standard residue FyD
- Re: [AMBER] PMEMD in a Cygwin Environment Robert Duke
- [AMBER] Counterion release and Free energy of binding ? Marek Maly
- Re: [AMBER] Counterion release and Free energy of binding ? case
- Re: [AMBER] Could not find bond parameter for O2 - ca case
Wednesday, 15 July 2009
- [AMBER] Equilibrium water density Myeong Lee
- [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" Sushil Mishra
- [AMBER] Please help me out bharat lakhani
- Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" Shubhra Gupta
- Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" Sushil Mishra
- [AMBER] R.E.D. help please s. Bill
- Re: [AMBER] RE: pmemd parallel Jun Dong
- RE: [AMBER] DCCM Duggan, Brendan M.
- Re: [AMBER] R.E.D. help please FyD
- Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" Bill Ross
- [AMBER] question of ibelly used in pmemd xiaoqin huang
- [AMBER] position v time graph Shozeb Haider
- Re: [AMBER] question of ibelly used in pmemd Robert Duke
- Re: [AMBER] Equilibrium water density case
- Re: [AMBER] Please help me out case
- RE: [AMBER] question of ibelly used in pmemd xiaoqin huang
- [AMBER] Can I get the torsion angle between base-pairs using ptraj ? Myeong Lee
- Re: [AMBER] question of ibelly used in pmemd Robert Duke
- [AMBER] different results for antechamber/mopac for the same input Alan
- Re: [AMBER] Can I get the torsion angle between base-pairs using ptraj ? Jordan Monnet
- RE: [AMBER] question of ibelly used in pmemd Ross Walker
- Re: [AMBER] GAFF and NME, ACE terminal res Jio M
- [AMBER] ptraj - cluster Cihan Aydin
- Re: [AMBER] GAFF and NME, ACE terminal res FyD
- [AMBER] ptraj-radial distribution function Nancy
- [AMBER] questions about RESP Jeffrey
Thursday, 16 July 2009
- [AMBER] carbonic anhydrase (CA) simulation vhakkim boy
- [AMBER] command for RESP fitting bharat lakhani
- [AMBER] query regarding FE4S4 subarna thakur
- Re: [AMBER] ptraj-radial distribution function Christof Jaeger
- [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, Zhongjie Liang
- Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, steinbrt.rci.rutgers.edu
- 答复: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, Zhongjie Liang
- Re: [AMBER] different results for antechamber/mopac for the same input case
- Re: [AMBER] carbonic anhydrase (CA) simulation case
- Re: [AMBER] query regarding FE4S4 case
- [AMBER] IDIVF and PN s. Bill
- [AMBER] production phase s. Bill
- [AMBER] vlimit exceeded....nscu_SMD!! Hlengisizwe Ndlovu
- [AMBER] Disappearing common atoms in Amber 10 with TI Khavrutskii, Ilja
- Re: [AMBER] Disappearing common atoms in Amber 10 with TI steinbrt.rci.rutgers.edu
- Re: [AMBER] questions about RESP FyD
- Re: [AMBER] command for RESP fitting FyD
- [AMBER] ntt=3 and ibelly=1 Kristina Furse
- [AMBER] amino acids caps for truncated proteins Andrew Voronkov
- Re: [AMBER] amino acids caps for truncated proteins FyD
- [AMBER] Umbrella Sampling Hemant Kumar
- Re: [AMBER] Umbrella Sampling case
- RE: [AMBER] Umbrella Sampling Seetin, Matthew
- Re: [AMBER] Disappearing common atoms in Amber 10 with TI Khavrutskii, Ilja
- Re: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Keith Van Nostrand
- [AMBER] amber10 parallel compiling error Nam Kim
- 回复： [AMBER] amber10 parallel compiling error 廖青华
- RE: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Ross Walker
- RE: [AMBER] IDIVF and PN Ross Walker
- RE: [AMBER] amber10 parallel compiling error Ross Walker
- RE: [AMBER] ntt=3 and ibelly=1 Ross Walker
- RE: [AMBER] production phase Ross Walker
- Re: [AMBER] Could not find bond parameter for O2 - ca Yogesh Aher
- [AMBER] File conversion for from Amber to Charmm Yogesh Aher
Friday, 17 July 2009
- [AMBER] diffusion coeficients felix
- [AMBER] Steered MD.....SHAKE error!! Hlengisizwe Ndlovu
- Re: [AMBER] Disappearing common atoms in Amber 10 with TI steinbrt.rci.rutgers.edu
- Re: [AMBER] Counterion release and Free energy of binding ? Marek Maly
- Re: [AMBER] Disappearing common atoms in Amber 10 with TI case
- Re: [AMBER] File conversion for from Amber to Charmm case
- Re: [AMBER] diffusion coeficients case
- Re: [AMBER] Steered MD.....SHAKE error!! case
- RE: [AMBER] ptraj - cluster Wei Huang
- Re: [AMBER] diffusion coeficients felix
- RE: [AMBER] ptraj - cluster Cihan Aydin
- [AMBER] vlimit error after heating restart AL Olson
- RE: [AMBER] question of ibelly used in pmemd xiaoqin huang
- RE: [AMBER] question of ibelly used in pmemd xiaoqin huang
- Re: [AMBER] question of ibelly used in pmemd Robert Duke
- [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? Marek Maly
- RE: [AMBER] ntt=3 and ibelly=1 Kristina Furse
- Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? Thomas Cheatham III
- Re: Fw: [AMBER] Re: pls help and suggest Gustavo Seabra
- Re: [AMBER] reference re. determining size of timestep Gustavo Seabra
- Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? Marek Maly
- [AMBER] RESP fit E.M.
- [AMBER] charge not zero on group: RESP Jio M
- Re: [AMBER] RESP fit FyD
Saturday, 18 July 2009
- Re: [AMBER] charge not zero on group: RESP Ben Roberts
- [AMBER] RE: charge not zero on group:''''.respin1 attached Jio M
- [AMBER] amber10 parallel compiling error nam kim
- RE: [AMBER] Umbrella Sampling Hemant Kumar
- [AMBER] Box shape change Hemant Kumar
- Re: [AMBER] Box shape change Carlos Simmerling
Sunday, 19 July 2009
- Re: [AMBER] RE: charge not zero on group:''''.respin1 attached FyD
- [AMBER] Different machines s. Bill
- [AMBER] -a flag :RESP Jio M
- Re: [AMBER] Box shape change Hemant Kumar
- Re: [AMBER] Box shape change Carlos Simmerling
- Re: [AMBER] Box shape change Hemant Kumar
- [AMBER] which keyword s. Bill
- Re: [AMBER] Box shape change Carlos Simmerling
- [AMBER] (no subject) gunajyoti das
- [AMBER] (no subject) gunajyoti das
- RE: [AMBER] Different machines Ross Walker
- Re: [AMBER] Box shape change Hemant Kumar
- [AMBER] Tutorial A3 s. Bill
- Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz Manish Kumar
- Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz Ray Luo
Monday, 20 July 2009
- Re: [AMBER] command for RESP fitting bharat lakhani
- Re: [AMBER] questions about RESP Jeffrey
- [AMBER] bugfix 10 failing for ambertools1.2 Alan
- [AMBER] Re: bugfix 10 failing for ambertools1.2 Alan
- [AMBER] nasty memory bug in calculatePrincipalAxis Hannes Loeffler
- [AMBER] MM-PBSA tail: equil.out: file truncated during equilibration of salivated complex Sushil Mishra
- [AMBER] Output file truncated during equilibration of salivated complex in MM-PBSA Sushil Mishra
- Re: [AMBER] Disappearing common atoms in Amber 10 with TI Khavrutskii, Ilja
- Re: [AMBER] Disappearing common atoms in Amber 10 with TI steinbrt.rci.rutgers.edu
- [AMBER] file truncated : Output file truncated during equilibration of salivated complex in MM-PBSA Sushil Mishra
- RE: [AMBER] question of ibelly used in pmemd xiaoqin huang
- [AMBER] RE: DCCM Duggan, Brendan M.
- Re: [AMBER] question of ibelly used in pmemd Robert Duke
- RE: [AMBER] question of ibelly used in pmemd xiaoqin huang
- Re: [AMBER] question of ibelly used in pmemd Robert Duke
- RE: [AMBER] question of ibelly used in pmemd xiaoqin huang
- Re: [AMBER] question of ibelly used in pmemd Robert Duke
- RE: [AMBER] question of ibelly used in pmemd Kristina Furse
- Re: [AMBER] question of ibelly used in pmemd Robert Duke
- RE: [AMBER] question of ibelly used in pmemd xiaoqin huang
- Re: [AMBER] amber10 parallel compiling error nam kim
- RE: [AMBER] question of ibelly used in pmemd Ross Walker
- RE: [AMBER] amber10 parallel compiling error Ross Walker
- RE: [AMBER] question of ibelly used in pmemd xiaoqin huang
- Re: [AMBER] question of ibelly used in pmemd Robert Duke
- Re: [AMBER] amber10 parallel compiling error nam kim
- Re: [AMBER] amber10 parallel compiling error nam kim
- RE: [AMBER] Tutorial A3 Ross Walker
- [AMBER] nonbon.f question Rizwan Tai
- Re: [AMBER] questions about RESP FyD
- Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz Manish Kumar
- [AMBER] RE: the copper paramter Ross Walker
- Re: [AMBER] amber10 parallel compiling error nam kim
- [AMBER] equivalent atoms Ye MEI
- Re: [AMBER] amber10 parallel compiling error Toshifumi Yui
Tuesday, 21 July 2009
- [AMBER] ptraj grid option Youn Kyeung Lee
- Re: [AMBER] question of ibelly used in pmemd Robert Duke
- Re: [AMBER] IGB=7 vs IGB=5 Carlos Simmerling
- RE: [AMBER] question of ibelly used in pmemd Kristina Furse
- Re: [AMBER] question of ibelly used in pmemd Robert Duke
- Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz Ray Luo
- RE: [AMBER] question of ibelly used in pmemd Kristina Furse
- Re: [AMBER] amber10 parallel compiling error nam kim
- Re: [AMBER] need charges of FE-S cluster Markus Kaukonen
- [AMBER] Output forces in Sander Frank X. Vázquez
- [AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0 David Watson
- [AMBER] RE: Questions about QMMM Ross Walker
- [AMBER] Patching terminal Manish Kumar
- Re: [AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0 vitor.felix
- [AMBER] ESP charges of Fe4S4 subarna thakur
- [AMBER] Regarding Hbond interactions aneesh cna
Wednesday, 22 July 2009
- [AMBER] Equilibration step Olotu Odunayo
- Re: [AMBER] Equilibration step Tom Joseph
- [AMBER] errors of PMEMD installation 廖青华
- [AMBER] saquinavir parameterization with antechamber Oliver Kuhn
- Re: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Keith Van Nostrand
- RE: [AMBER] Equilibration step Olotu Odunayo
- RE: [AMBER] Equilibration step Olotu Odunayo
- Re: [AMBER] saquinavir parameterization with antechamber FyD
- Re: [AMBER] Equilibration step Tom Joseph
- [AMBER] [ALERT]: It's the time to come out on streets and stop the complete nation on it's place - Take immediate actions at once with full force. Organization
- Re: [AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0 Scott Brozell
- [AMBER] how to launch XLEaP from SSH Secure Shell? Yana Berezovskaya
- Re: [AMBER] how to launch XLEaP from SSH Secure Shell? Robert Duke
- Re: [AMBER] how to launch XLEaP from SSH Secure Shell? Tom Joseph
- Re: [AMBER] how to launch XLEaP from SSH Secure Shell? David Watson
- Re: [AMBER] how to launch XLEaP from SSH Secure Shell? Thomas Patko
- Re: [AMBER] setting AMBERHOME case
- Re: [AMBER] amber10 parallel compiling error case
- RE: [AMBER] Equilibration step Olotu Odunayo
Thursday, 23 July 2009
- Re: [AMBER] saquinavir parameterization with antechamber Oliver Kuhn
- Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz Manish Kumar
- Re: [AMBER] saquinavir parameterization with antechamber FyD
- Re: [AMBER] saquinavir parameterization with antechamber Oliver Kuhn
- [AMBER] MM-PBSA cannot finish without error message. Catein Catherine
- Re: [AMBER] questions about RESP Jeffrey
- [AMBER] Replacing DNA base with analog amoreno.wesleyan.edu
- RE: [AMBER] Replacing DNA base with analog Kristina Furse
- Re: [AMBER] questions about RESP FyD
- Re: [AMBER] errors of PMEMD installation Mengjuei Hsieh
- [AMBER] Compiling AMBER 10 (parallel, MPICH2) on Mac OS X Intel w/gcc, ifort, icc David Watson
- RE: [Subject Filtered] Re: [AMBER] PMEMD in a Cygwin Environment 8% Hopkins, Robert
- [AMBER] Langevin Dynamics in AMBER10 Biswaranjan Meher
- Re: [AMBER] Langevin Dynamics in AMBER10 Carlos Simmerling
- Re: [AMBER] Regarding Hbond interactions Thomas Cheatham
- Re: [AMBER] Langevin Dynamics in AMBER10 Biswaranjan Meher
- 回复： [AMBER] errors of PMEMD installation 廖青华
- [AMBER] mailing list Qinghua Liao
- Re: [AMBER] amber10 parallel compiling error nam kim
Friday, 24 July 2009
- [AMBER] cpin error Rukman Hertadi
- [AMBER] radical simulation Jeffrey
- Re: [AMBER] radical simulation Manish Kumar
- Re: 回复： [AMBER] errors of PMEMD installation Mengjuei Hsieh
- Re: 回复： [AMBER] errors of PMEMD installation Qinghua Liao
- Re: 回复： [AMBER] errors of PMEMD installation Qinghua Liao
- Re: [AMBER] radical simulation FyD
- Re: [AMBER] Langevin Dynamics in AMBER10 Carlos Simmerling
- [AMBER] xleap facility to insert a residue Sergey Samsonov
- [AMBER] thymidine monophosphate parametrization Yvonne.Westermaier.unige.ch
- [AMBER] loading a mol2 file in xleap vallespardojl.chem.leidenuniv.nl
- Re: 回复： [AMBER] errors of PMEMD installation Mengjuei Hsieh
- Re: [AMBER] cpin error case
- Re: [AMBER] loading a mol2 file in xleap FyD
- [AMBER] DNA + intercalator Rodrigo Galindo
- Re: [AMBER] DNA + intercalator Bill Ross
- Re: 回复： [AMBER] errors of PMEMD installation Qinghua Liao
- Re: [AMBER] DNA + intercalator Ashish Runthala
Saturday, 25 July 2009
- Re: [AMBER] errors of PMEMD installation Mengjuei Hsieh
- [AMBER] Could not find type: MG Parameter file was not saved. Mannan
- [AMBER] Simulation with United atom force field in Implicit solvent. Manish Kumar
Sunday, 26 July 2009
- Re: [AMBER] Simulation with United atom force field in Implicit solvent. Ray Luo
- Re: [AMBER] radical simulation Jeffrey
- Re: [AMBER] Simulation with United atom force field in Implicit solvent. Manish Kumar
- [AMBER] Could not find type: MG Parameter file was not saved. though it was loaded Mannan
- Re: [AMBER] Could not find type: MG Parameter file was not saved. though it was loaded FyD
- [AMBER] Re: Ambertools 1.2 installation error Bokun Cho
- [AMBER] Removed proton in protein (Advanced Tutorials A1 old) albert albert
Monday, 27 July 2009
- [AMBER] How to read md trajectory for each time slice as an input coordinate Myeong Lee
- Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) Ashish Runthala
- [AMBER] error in antechamber Qinghua Liao
- Re: [AMBER] loading a mol2 file in xleap vallespardojl.chem.leidenuniv.nl
- [AMBER] Average structure over simulation Olotu Odunayo
- Re: [AMBER] loading a mol2 file in xleap FyD
- Re: [AMBER] Re: Ambertools 1.2 installation error case
- Re: [AMBER] thymidine monophosphate parametrization case
- [AMBER] RE: Average structure over simulation Niel Henriksen
- Re: [AMBER] Re: bugfix 10 failing for ambertools1.2 case
- Re: [AMBER] Output forces in Sander case
- RE: [AMBER] RE: Average structure over simulation Olotu Odunayo
- [AMBER] residues lacking connect0/connect1 Jio M
- Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) Bill Ross
- Re: [AMBER] residues lacking connect0/connect1 Bill Ross
- Re: [AMBER] only ff94 and ff99 for GBSA? Andrew Voronkov
- Re: [AMBER] only ff94 and ff99 for GBSA? case
- [AMBER] nonbon.f question Rizwan Tai
- Re: [AMBER] nonbon.f question Carlos Simmerling
- [AMBER] Using idecomp=3 with igb=10 (PB) Chris Whittleston
- Re: [AMBER] error in antechamber Mengjuei Hsieh
- Re: [AMBER] error in antechamber Qinghua Liao
- Re: [AMBER] error in antechamber case
- Re: [AMBER] error in antechamber Qinghua Liao
- RE: [AMBER] cpin error Rukman Hertadi
- Re: [AMBER] only ff94 and ff99 for GBSA? Andrew Voronkov
- [AMBER] QM/MM s. Bill
Tuesday, 28 July 2009
- Re: [AMBER] QM/MM steinbrt.rci.rutgers.edu
- Re: [AMBER] only ff94 and ff99 for GBSA? FyD
- [AMBER] PLUMED release 1.1.0 available Massimiliano Bonomi
- [AMBER] RE: MM-PBSA test jobs error messages Catein Catherine
- [AMBER] How to visualize PCA results without IED? Catein Catherine
- Re: [AMBER] How to visualize PCA results without IED? Vlad Cojocaru
- Re: [AMBER] Using idecomp=3 with igb=10 (PB) Hannes Kopitz
- Re: [AMBER] How to visualize PCA results without IED? Hannes Loeffler
- Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) Ashish Runthala
- Re: [AMBER] How to visualize PCA results without IED? Vlad Cojocaru
- Re: [AMBER] Using idecomp=3 with igb=10 (PB) Chris Whittleston
- Re: [AMBER] How to visualize PCA results without IED? Shozeb Haider
- Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) FyD
- [AMBER] pulling two atoms in SMD Santosh Mogurampelly
- Re: [AMBER] thymidine monophosphate parametrization Yvonne.Westermaier.unige.ch
- Re: [AMBER] Using idecomp=3 with igb=10 (PB) Hannes Kopitz
- Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) Ashish Runthala
- Re: [AMBER] Using idecomp=3 with igb=10 (PB) Ashish Runthala
- [AMBER] Error in Sander Output File Alison Saunders
- [AMBER] Am I doing the right thing nicholus bhattacharjee
- [AMBER] Question on REST and VALUE1 keywords hwu.clarku.edu
- Re: [AMBER] Question on REST and VALUE1 keywords Carlos Simmerling
- Re: [AMBER] Question on REST and VALUE1 keywords Ashish Runthala
- Re: [AMBER] Am I doing the right thing Ashish Runthala
- [AMBER] how to choose exclusion policy for GPCR xueqin pang
- Re: [AMBER] Am I doing the right thing Bill Ross
- Re: [AMBER] Am I doing the right thing Ashish Runthala
- Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? Andrew Voronkov
- Re: [AMBER] Am I doing the right thing nicholus bhattacharjee
- [AMBER] RE: MM-PBSA test jobs error messages (with bugfix.all) Catein Catherine
- [AMBER] pdb file no bond and charges Jio M
Wednesday, 29 July 2009
- [AMBER] RED.III: Invalid Optimization OUTPUT s. Bill
- [AMBER] Re: MM-PBSA test jobs error messages (Can i fix the problem without recompile the amber?) Catein Catherine
- [AMBER] MPI error vhakkim boy
- [AMBER] MM/PBSA, MM/GBSA and NMODE Analysis Matthias Negri
- Re: [AMBER] MPI error Robert Duke
- Re: Solved it thanks [AMBER] RED.III: Invalid Optimization OUTPUT s. Bill
- [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits Alan
- Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits David Watson
- [AMBER] Installing Amber10 on Ubuntu David Dubins
- [AMBER] Re: problem of installation of amber10 Mengjuei Hsieh
- Re: [AMBER] Installing Amber10 on Ubuntu Rodrigo Galindo
- Re: [AMBER] MM/PBSA, MM/GBSA and NMODE Analysis Ray Luo
Thursday, 30 July 2009
- [AMBER] Normal mode analysis of water bharat lakhani
- [AMBER] PCA analysis: the first vector is the movement of whole molecule. Catein Catherine
- Re: [AMBER] PCA analysis: the first vector is the movement of whole molecule. Hannes Loeffler
- Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits Alan
- Re: [AMBER] Normal mode analysis of water case
- Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits David Watson
- [AMBER] ambpdb problem Jio M
- Re: [AMBER] ambpdb problem Jordan Monnet
- [AMBER] Non-Standard Amino Acid Residue LEAP ERROR Brothers, Michael Charles
- Re: [AMBER] ambpdb problem Ashish Runthala
- Re: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR Ashish Runthala
- RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule. Catein Catherine
- [AMBER] What is the meaning of "rms first *" Catein Catherine
Friday, 31 July 2009
- Re: [AMBER] ambpdb problem Jio M
- RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule. Hannes Loeffler
- [AMBER] query bharat lakhani
- [AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits Nicolas SAPAY
- Re: [AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits Robert Duke
- Re: [AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits Nicolas SAPAY
- [AMBER] vertex atom mismatch Clark, Tiffany D
- Re: [AMBER] ambpdb problem Jordan Monnet
- Re: [AMBER] vertex atom mismatch Guillermo Mulliert Carlín
- [AMBER] problem from xleap Qinghua Liao
- Re: [AMBER] query Pansy Patel
- Re: [AMBER] problem from xleap Tom Joseph
- [AMBER] Protonated or not s. Bill
- Re: [AMBER] Protonated or not Adrian Roitberg
- RE: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR Brothers, Michael Charles
- [AMBER] Metalloproteins - Ligand Protonation s. Bill
- Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) albert albert

Last message date: Wed Aug 19 2009 - 19:59:29 PDT
Archived on: Mon Apr 22 2024 - 05:53:47 PDT

Amber Archive Jul 2009 by date