Amber Archive Jan 2013: by date

Tuesday, 1 January 2013
- [AMBER] not getting dipole moment values in pmemd.cuda Sanjib Paul
- Re: [AMBER] NPT and NVE Energy Ismail, Mohd F.
Wednesday, 2 January 2013
- [AMBER] Need assistance to generate forcefield for PYRIDOXAL-5'-PHOSPHATE BALA SUBRAMANI G L
- Re: [AMBER] Amber LES.MPI crash Kirill Nuzhdin
- Re: [AMBER] Amber LES.MPI crash Carlos Simmerling
- Re: [AMBER] Amber LES.MPI crash David A Case
- Re: [AMBER] Amber LES.MPI crash Kirill Nuzhdin
- Re: [AMBER] Amber LES.MPI crash Kirill Nuzhdin
- Re: [AMBER] Amber LES.MPI crash David A Case
- Re: [AMBER] Amber LES.MPI crash David A Case
- Re: [AMBER] Amber LES.MPI crash Kirill Nuzhdin
- [AMBER] MMPBSA error marawan hussain
Thursday, 3 January 2013
- [AMBER] Thermodynamic integration with iwrap=1 in SANDER Miroslav Krepl
- Re: [AMBER] MMPBSA error Jason Swails
- Re: [AMBER] MMPBSA error marawan hussain
- [AMBER] Problems creating topology file for Dfrom Giri tomp
- [AMBER] Issue with creating topology file due to atom type not being recognised in frcmod Giri tomp
- Re: [AMBER] MMPBSA error Jason Swails
- Re: [AMBER] MMPBSA error marawan hussain
Friday, 4 January 2013
- Re: [AMBER] [q4md-fft] Issue with creating topology file due to atom type not being recognised in frcmod FyD
- Re: [AMBER] MMPBSA error Jason Swails
- [AMBER] bad atom type: f Date, Mihir
- Re: [AMBER] [q4md-fft] Issue with creating topology file due to atom type not being recognised in frcmod David A Case
- [AMBER] Announcement: Release of DOCK 6.6 Scott Brozell
- Re: [AMBER] bad atom type: f Vaibhav Dixit
- [AMBER] REMD restart gargi borgohai
Saturday, 5 January 2013
- Re: [AMBER] [q4md-fft] Issue with creating topology file due to atom type not being recognised in frcmod Giri tomp
- [AMBER] positive DeltaEel and negative DeltaGsolv in MMPBSA Emilio Angelina
- [AMBER] rfree parsing error in group specification Joel Dockray
- Re: [AMBER] positive DeltaEel and negative DeltaGsolv in MMPBSA Ray Luo, Ph.D.
- Re: [AMBER] positive DeltaEel and negative DeltaGsolv in MMPBSA Emilio Angelina
Sunday, 6 January 2013
- Re: [AMBER] MMPBSA error marawan hussain
- Re: [AMBER] MMPBSA error Jason Swails
- [AMBER] GPUs and PBSPro Vijay Manickam Achari
- Re: [AMBER] GPUs and PBSPro Ross Walker
Monday, 7 January 2013
- [AMBER] how to assign atom types. Salma Zahir
- Re: [AMBER] MMPBSA error marawan hussain
- Re: [AMBER] how to assign atom types. Jason Swails
- Re: [AMBER] MMPBSA error Jason Swails
- [AMBER] AMBER parameter problem osalo.abo.fi
- Re: [AMBER] AMBER parameter problem David A Case
- [AMBER] Group specification for energy decomposition in thermodynamic integration Joel Dockray
- [AMBER] Group specification for energy decomposition in thermodynamic integration (Corrected spacing) Joel Dockray
- [AMBER] bugfix.31 Norah Schlacter
- Re: [AMBER] bugfix.31 Jason Swails
- Re: [AMBER] MMPBSA error marawan hussain
- [AMBER] AMBER12 Installation failed Udaysankar Midya
Tuesday, 8 January 2013
- Re: [AMBER] how to assign atom types. FyD
- [AMBER] frcmod file dihedrals -phase shift question osalo.abo.fi
- Re: [AMBER] frcmod file dihedrals -phase shift question Carlos Simmerling
- Re: [AMBER] AMBER12 Installation failed Jason Swails
- [AMBER] Error with TIP4P Chandrasekaran, Suryanarayanan
- [AMBER] Query regarding GB calculation on a protein with FE using MMPBSA.py Prajwal Nandekar
- Re: [AMBER] Query regarding GB calculation on a protein with FE using MMPBSA.py Jason Swails
- [AMBER] GAFFlipid FF concern jfloresc.andrew.cmu.edu
- [AMBER] Is AM1-BCC charges ok for ligands with idodine atoms Shulin Zhuang
Wednesday, 9 January 2013
- Re: [AMBER] Is AM1-BCC charges ok for ligands with idodine atoms FyD
- [AMBER] hybrid imlicit/explicit system Алексей Раевский
- Re: [AMBER] Is AM1-BCC charges ok for ligands with idodine atoms FyD
- Re: [AMBER] hybrid imlicit/explicit system case
- Re: [AMBER] Query regarding GB calculation on a protein with FE using MMPBSA.py Prajwal Nandekar
- Re: [AMBER] Error with TIP4P case
- Re: [AMBER] GAFFlipid FF concern Dickson, Callum
- Re: [AMBER] GAFFlipid FF concern David A Case
- Re: [AMBER] GAFFlipid FF concern Ganesh Kamath
- [AMBER] problem with identifying Zn ion in Amber11 Agnieszka Dybala-Defratyka
- [AMBER] cudaMemcpyToSymbol: SetSim copy to Sim failed for K20x using JAC and Cellulose benchmarks Mohammad Ashraf Bhuiyan
- Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to Sim failed for K20x using JAC and Cellulose benchmarks Ross Walker
Thursday, 10 January 2013
- Re: [AMBER] problem with identifying Zn ion in Amber11 Jason Swails
- [AMBER] bug in sander nmr.F90, amber12? Fabian Zeller
- [AMBER] Problems using NAB and GCC Roberto Vera
- Re: [AMBER] Error with TIP4P George M Giambasu
- Re: [AMBER] Problems using NAB and GCC David A Case
- Re: [AMBER] bad atom type: f Date, Mihir
- Re: [AMBER] AMBER12 Installation failed Tru Huynh
- [AMBER] AMBER bonded parameters Dr. Vitaly Chaban
- [AMBER] antechamber problem Changqing Yan
- Re: [AMBER] antechamber problem Ravi Tripathi
- Re: [AMBER] bad atom type: f Vaibhav Dixit
- [AMBER] amber12 Bio Learner
- [AMBER] Simulating Folic Acid JD John
- Re: [AMBER] amber12 Daniel Sindhikara
Friday, 11 January 2013
- [AMBER] how to construct new molecule Bio Learner
- Re: [AMBER] how to construct new molecule Maxier Acosta Santiago
- [AMBER] Glycam_06 in amber12 Subrata Paul
- [AMBER] AMD pooja chahal
- Re: [AMBER] Glycam_06 in amber12 Urszula Uciechowska
- [AMBER] installation problem Tanmoy Paul
- Re: [AMBER] antechamber problem Jason Swails
- Re: [AMBER] bad atom type: f Jason Swails
- Re: [AMBER] AMD Jason Swails
- Re: [AMBER] installation problem Jason Swails
- Re: [AMBER] antechamber problem M. L. Dodson
- Re: [AMBER] Simulating Folic Acid M. L. Dodson
- Re: [AMBER] AMBER bonded parameters David A Case
- Re: [AMBER] Glycam_06 in amber12 Lachele Foley (Lists)
- Re: [AMBER] bug in sander nmr.F90, amber12? David A Case
- Re: [AMBER] installation problem JD John
- [AMBER] dnaiontracker command in cpptraj Le,Huy Tuan
- [AMBER] question about force fields and external QM program Kirill Nuzhdin
- Re: [AMBER] dnaiontracker command in cpptraj Daniel Roe
- Re: [AMBER] question about force fields and external QM program Jason Swails
- Re: [AMBER] AMD pooja chahal
- Re: [AMBER] Glycam_06 in amber12 Subrata Paul
- Re: [AMBER] AMD Daniel Sindhikara
- Re: [AMBER] AMD Bill Ross
- Re: [AMBER] AMD Ganesh Kamath
- Re: [AMBER] antechamber problem Changqing Yan
Saturday, 12 January 2013
- Re: [AMBER] AMD Hirdesh Kumar
- [AMBER] RMS2D Syed Tarique Moin
- Re: [AMBER] AMD Jason Swails
- [AMBER] Fwd: Query regarding umbrella sampling minhazul arfeen
- Re: [AMBER] RMS2D Daniel Roe
- Re: [AMBER] Glycam_06 in amber12 Lachele Foley (Lists)
Sunday, 13 January 2013
- Re: [AMBER] Fwd: Query regarding umbrella sampling Brian Radak
- [AMBER] Software announcement: Release of PUPIL 2.0 Joan Torras
- Re: [AMBER] Glycam_06 in amber12 Subrata Paul
Monday, 14 January 2013
- [AMBER] command used to upload pdb Bio Learner
- Re: [AMBER] command used to upload pdb Prajwal Nandekar
- [AMBER] installation error Bio Learner
- Re: [AMBER] RMS2D Syed Tarique Moin
- [AMBER] amber organic box 纪晓峰
- [AMBER] Citrate ion (-3) parameters moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] amber organic box David A Case
- [AMBER] Problem with Identification of bonds Volker Lesch
- Re: [AMBER] installation error Daniel Roe
- Re: [AMBER] installation error Jason Swails
- Re: [AMBER] Glycam_06 in amber12 Lachele Foley (Lists)
- Re: [AMBER] amber organic box Bill Ross
- [AMBER] density for PBC system; addles error Kirill Nuzhdin
- [AMBER] Getting AmberTools12 to work in Ubuntu 12.04? David Dubins
- [AMBER] vlimit exceeded and distorted bonds Chris Chris
- Re: [AMBER] Getting AmberTools12 to work in Ubuntu 12.04? Jason Swails
- [AMBER] Membrane-protein simulation using amber12 Manikanthan Bhavaraju
- Re: [AMBER] installation error Bio Learner
Tuesday, 15 January 2013
- Re: [AMBER] AMD pooja chahal
- Re: [AMBER] installation error Jason Swails
- Re: [AMBER] AMD Jason Swails
- Re: [AMBER] AMD pooja chahal
- [AMBER] xlead aentrena
- [AMBER] Atom reordering for TI Thomas Exner
- Re: [AMBER] density for PBC system; addles error David A Case
- Re: [AMBER] xlead David A Case
- Re: [AMBER] Atom reordering for TI David A Case
- [AMBER] umbrella sampling Elisa Frezza
- Re: [AMBER] umbrella sampling Adrian Roitberg
- Re: [AMBER] umbrella sampling Elisa Frezza
- [AMBER] Getting total dipole moment of molecules in periodic box. 강현아
- Re: [AMBER] Getting total dipole moment of molecules in periodic box. Jason Swails
- [AMBER] Is it possible to do TI calculations with pmemd? Anna Bauß
- Re: [AMBER] umbrella sampling Elisa Frezza
- Re: [AMBER] umbrella sampling Aron Broom
- Re: [AMBER] umbrella sampling Elisa Frezza
- Re: [AMBER] umbrella sampling Aron Broom
- Re: [AMBER] umbrella sampling Elisa Frezza
- Re: [AMBER] umbrella sampling Ross Walker
- Re: [AMBER] Is it possible to do TI calculations with pmemd? steinbrt.rci.rutgers.edu
- Re: [AMBER] Is it possible to do TI calculations with pmemd? Ross Walker
- Re: [AMBER] Atom reordering for TI Thomas Exner
- Re: [AMBER] AMD Ross Walker
- [AMBER] atom type definition mm_pbsa Andrew Anighoro
- Re: [AMBER] umbrella sampling Elisa Frezza
- Re: [AMBER] umbrella sampling ros
- Re: [AMBER] atom type definition mm_pbsa Jason Swails
- Re: [AMBER] umbrella sampling Elisa Frezza
- Re: [AMBER] Membrane-protein simulation using amber12 Benjamin D Madej
- [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM
- Re: [AMBER] Membrane-protein simulation using amber12 manikanthan bhavaraju
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Benjamin D Madej
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) manikanthan bhavaraju
- Re: [AMBER] Membrane-protein simulation using amber12 Benjamin D Madej
- [AMBER] using image command in cpptraj... Shashidhar Rao
- Re: [AMBER] Membrane-protein simulation using amber12 manikanthan bhavaraju
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Benjamin D Madej
- Re: [AMBER] using image command in cpptraj... Daniel Roe
- Re: [AMBER] using image command in cpptraj... Shashidhar Rao
- Re: [AMBER] umbrella sampling Adrian Roitberg
- [AMBER] MMPBSA/Disulfide bond error Divi
- [AMBER] parameters for deoxyADP Jorgen Simonsen
- [AMBER] How to choose the boost for aMD when using restraints Thomas Evangelidis
- Re: [AMBER] umbrella sampling Elisa Frezza
- Re: [AMBER] umbrella sampling Adrian Roitberg
- Re: [AMBER] umbrella sampling Elisa Frezza
- Re: [AMBER] umbrella sampling Aron Broom
- Re: [AMBER] MMPBSA/Disulfide bond error Jason Swails
- Re: [AMBER] MMPBSA/Disulfide bond error Jason Swails
- Re: [AMBER] density for PBC system; addles error Kirill Nuzhdin
- Re: [AMBER] AMD Bill Ross
- Re: [AMBER] density for PBC system; addles error case
- Re: [AMBER] parameters for deoxyADP FyD
- Re: [AMBER] Citrate ion (-3) parameters FyD
Wednesday, 16 January 2013
- Re: [AMBER] Is it possible to do TI calculations with pmemd? Anna Bauß
- [AMBER] A link atoms between protein and sugar! john Kerk
- Re: [AMBER] Citrate ion (-3) parameters moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] umbrella sampling Elisa Frezza
- Re: [AMBER] xlead Antonio Entrena Guadix
- Re: [AMBER] xlead Jan-Philip Gehrcke
- Re: [AMBER] xlead Jason Swails
- [AMBER] LJ parameters for Ho in GLYCAM06 changes ABEL Stephane 175950
- [AMBER] Structure refinement protocol on the AMPS-NMR portal Baptiste Legrand
- [AMBER] xtc to mdcrd box coords Federica Chiappori
- Re: [AMBER] xtc to mdcrd box coords Daniel Roe
- Re: [AMBER] xlead Daniel Roe
- Re: [AMBER] density for PBC system; addles error Kirill Nuzhdin
- Re: [AMBER] LJ parameters for Ho in GLYCAM06 changes Jason Swails
- Re: [AMBER] xtc to mdcrd box coords Federica Chiappori
- Re: [AMBER] xtc to mdcrd box coords Daniel Roe
- [AMBER] RE : LJ parameters for Ho in GLYCAM06 changes ABEL Stephane 175950
- Re: [AMBER] density for PBC system; addles error Kirill Nuzhdin
- Re: [AMBER] density for PBC system; addles error David A Case
- Re: [AMBER] RE : LJ parameters for Ho in GLYCAM06 changes Lachele Foley (Lists)
- [AMBER] Errors while reading a MOL2 file with "parm" in cpptraj... Shashidhar Rao
- Re: [AMBER] xtc to mdcrd box coords Bill Ross
- Re: [AMBER] density for PBC system; addles error Kirill Nuzhdin
- Re: [AMBER] density for PBC system; addles error Kirill Nuzhdin
- Re: [AMBER] Errors while reading a MOL2 file with "parm" in cpptraj... Daniel Roe
- [AMBER] generating restart file with velocity information Vijay Manickam Achari
- [AMBER] Simulating one molecule in the gas phase Volker Lesch
- Re: [AMBER] xlead Antonio Entrena Guadix
- Re: [AMBER] A link atoms between protein and sugar! FyD
Thursday, 17 January 2013
- Re: [AMBER] Citrate ion (-3) parameters FyD
- Re: [AMBER] A link atoms between protein and sugar! john Kerk
- Re: [AMBER] A link atoms between protein and sugar! FyD
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM
- [AMBER] H-bond analysis of backbone atoms HM
- [AMBER] SHAKE error with dt=0.002 DEBOSTUTI GHOSHDASTIDAR
- [AMBER] velocity information lost in traj files when select frames Vijay Manickam Achari
- Re: [AMBER] density for PBC system; addles error David A Case
- Re: [AMBER] SHAKE error with dt=0.002 David A Case
- Re: [AMBER] generating restart file with velocity information Jason Swails
- Re: [AMBER] velocity information lost in traj files when select frames Jason Swails
- [AMBER] Amoeba water model parameters Kirill Nuzhdin
- Re: [AMBER] SHAKE error with dt=0.002 DEBOSTUTI GHOSHDASTIDAR
- Re: [AMBER] SHAKE error with dt=0.002 David A Case
- [AMBER] difficulty with basic tutorial 1 mhclewett.msn.com
- Re: [AMBER] difficulty with basic tutorial 1 Daniel Roe
- Re: [AMBER] SHAKE error with dt=0.002 Jason Swails
- Re: [AMBER] difficulty with basic tutorial 1 Brian Radak
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Benjamin D Madej
- [AMBER] pmemd.amoeba.MPI run error 旭东肖
- [AMBER] Query regarding Amber atom type Shubhadip Das
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Thomas Evangelidis
Friday, 18 January 2013
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Thomas Evangelidis
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Ross Walker
- Re: [AMBER] Query regarding Amber atom type FyD
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Aldo Segura
- [AMBER] PMEMD and cutoff Urszula Uciechowska
- Re: [AMBER] PMEMD and cutoff Ross Walker
- [AMBER] problem starting amber Ayesha Fatima
- Re: [AMBER] problem starting amber Ross Walker
- Re: [AMBER] problem starting amber Ayesha Fatima
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Thomas Evangelidis
- Re: [AMBER] difficulty with basic tutorial 1 mhclewett.msn.com
- [AMBER] Using multiple CPU cores with pmemd.cuda Filippo Pullara
- Re: [AMBER] Using multiple CPU cores with pmemd.cuda Ross Walker
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Benjamin D Madej
- [AMBER] RRES and LRES card not recognized when using idecomp with sander WenJuan Huang
Saturday, 19 January 2013
- Re: [AMBER] Citrate ion (-3) parameters moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] [AMBER: gauche effect in OS-CT-CT-F Steven M. Graham
Sunday, 20 January 2013
- [AMBER] Minimum distance between the protein and membrane Manikanthan Bhavaraju
- Re: [AMBER] Minimum distance between the protein and membrane Aron Broom
- Re: [AMBER] Minimum distance between the protein and membrane Manikanthan Bhavaraju
Monday, 21 January 2013
- Re: [AMBER] Citrate ion (-3) parameters FyD
- Re: [AMBER] [AMBER: gauche effect in OS-CT-CT-F Karl N. Kirschner
- [AMBER] amber11 installation test files Mary Varughese
- [AMBER] Bug in amber12, pmemd ch2int function Ake Sandgren
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM
- Re: [AMBER] Bug in amber12, pmemd ch2int function Jason Swails
- [AMBER] Defining a dihedral torsional energy for non-serial atoms. Negar Ashari Astani
- Re: [AMBER] Defining a dihedral torsional energy for non-serial atoms. Carlos Simmerling
- [AMBER] Dihedral energy for non-serial atoms Negar Ashari Astani
- [AMBER] Query regarding rms2d with cpptraj HM
- Re: [AMBER] Query regarding rms2d with cpptraj Daniel Roe
- [AMBER] Charge relocation CHAMI F.
- Re: [AMBER] Query regarding rms2d with cpptraj HM
- Re: [AMBER] Dihedral energy for non-serial atoms Jason Swails
- Re: [AMBER] amber11 installation test files Jason Swails
- Re: [AMBER] amber11 installation test files Daniel Roe
- Re: [AMBER] Citrate ion (-3) parameters moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] solvent accessible volume vs Daniel Roe
- Re: [AMBER] Dihedral energy for non-serial atoms Negar Ashari Astani
- Re: [AMBER] [AMBER: gauche effect in OS-CT-CT-F Steven M. Graham
- Re: [AMBER] [AMBER: gauche effect in OS-CT-CT-F Jason Swails
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Ross Walker
- [AMBER] question on the latest manifestation of AMBER force field... Shashidhar Rao
- Re: [AMBER] Citrate ion (-3) parameters FyD
Tuesday, 22 January 2013
- [AMBER] Amber ff03w/tip4p2005 Neha Gandhi
- [AMBER] mmpbsa-with and without entropy colvin
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM
- [AMBER] Minimization failure of a ligand Sun
- Re: [AMBER] Minimization failure of a ligand Hirdesh Kumar
- [AMBER] multi pmemd and REMD Neha Gandhi
- Re: [AMBER] Minimization failure of a ligand Sun
- Re: [AMBER] mmpbsa-with and without entropy Kshatresh Dutta Dubey
- Re: [AMBER] multi pmemd and REMD Neha Gandhi
- [AMBER] 27th Molecular Modelling Workshop 2013 Feb., 25th-27th in Erlangen, Germany Harald Lanig
- Re: [AMBER] Amber ff03w/tip4p2005 David A Case
- Re: [AMBER] multi pmemd and REMD Jason Swails
- Re: [AMBER] mmpbsa-with and without entropy David A Case
- Re: [AMBER] Minimization failure of a ligand David A Case
- Re: [AMBER] multi pmemd and REMD David A Case
- [AMBER] Steered MD in Specific Direction Kyle Roberts
- Re: [AMBER] Steered MD in Specific Direction Jason Swails
- [AMBER] Building a new structure! Ibrahim Said
- [AMBER] Amber12 Cuda installation issues Vivek Shankar Bharadwaj
- Re: [AMBER] Minimization failure of a ligand Bill Ross
- [AMBER] Theoretical explanation of adding ions to make the system neutral Mahendra B Thapa
- Re: [AMBER] Theoretical explanation of adding ions to make the system neutral Aron Broom
- [AMBER] glibc detected in ptraj Jagur Lambix
- Re: [AMBER] glibc detected in ptraj Daniel Roe
Wednesday, 23 January 2013
- Re: [AMBER] Amber12 Cuda installation issues Ross Walker
- [AMBER] Analyzing AMBER10 trajectories using AmberTools1.4 Kamali Sripathi
- Re: [AMBER] Analyzing AMBER10 trajectories using AmberTools1.4 Jason Swails
- Re: [AMBER] Building a new structure! David A Case
- Re: [AMBER] Charge relocation CHAMI F.
- Re: [AMBER] Theoretical explanation of adding ions to make the system neutral Brian Radak
- Re: [AMBER] Analyzing AMBER10 trajectories using AmberTools1.4 Daniel Roe
- Re: [AMBER] glibc detected in ptraj Jagur Lambix
- Re: [AMBER] Building a new structure! Ibrahim Said
- Re: [AMBER] glibc detected in ptraj Jason Swails
- [AMBER] Problem compatibility pdb in tleap Stefan Knippenberg
- Re: [AMBER] Problem compatibility pdb in tleap Daniel Roe
- Re: [AMBER] Problem compatibility pdb in tleap David A Case
- Re: [AMBER] Building a new structure! David A Case
- [AMBER] KCl crystals with Dang parameters ? Vlad Cojocaru
- Re: [AMBER] KCl crystals with Dang parameters ? Daniel Roe
- [AMBER] error in running a minimization job.... Shashidhar Rao
- Re: [AMBER] KCl crystals with Dang parameters ? Vlad Cojocaru
- Re: [AMBER] Problem compatibility pdb in tleap Stefan Knippenberg
- Re: [AMBER] Problem compatibility pdb in tleap Daniel Roe
- [AMBER] how to keep the previous restart file when saving the current one Thomas Evangelidis
- Re: [AMBER] how to keep the previous restart file when saving the current one Aron Broom
- Re: [AMBER] error in running a minimization job.... case
- Re: [AMBER] Analyzing AMBER10 trajectories using AmberTools1.4 Kamali Sripathi
- Re: [AMBER] Analyzing AMBER10 trajectories using AmberTools1.4 Daniel Roe
- Re: [AMBER] Analyzing AMBER10 trajectories using AmberTools1.4 Jason Swails
- Re: [AMBER] KCl crystals with Dang parameters ? InSuk Joung
- Re: [AMBER] how to keep the previous restart file when saving the current one Jason Swails
- Re: [AMBER] how to keep the previous restart file when saving the current one case
- Re: [AMBER] KCl crystals with Dang parameters ? Thomas Cheatham
- [AMBER] minimization problem Sanjib Paul
- Re: [AMBER] Building a new structure! FyD
Thursday, 24 January 2013
- Re: [AMBER] KCl crystals with Dang parameters ? Vlad Cojocaru
- [AMBER] Cpptraj: distance does not work with center of mass Vlastimil Zíma
- Re: [AMBER] Problem compatibility pdb in tleap Stefan Knippenberg
- Re: [AMBER] minimization problem Sanjib Paul
- Re: [AMBER] how to keep the previous restart file when saving the current one Thomas Evangelidis
- Re: [AMBER] Problem compatibility pdb in tleap David A Case
- Re: [AMBER] how to keep the previous restart file when saving the current one Jason Swails
- Re: [AMBER] Cpptraj: distance does not work with center of mass Daniel Roe
- Re: [AMBER] error in running a minimization job.... Shashidhar Rao
- Re: [AMBER] minimization problem Daniel Roe
- [AMBER] Error running sander.MPI "rfree: End of file on unit 5 " Urszula Uciechowska
- [AMBER] Dihedral angle PCA Sergey Samsonov
- Re: [AMBER] Error running sander.MPI "rfree: End of file on unit 5 " Daniel Roe
- Re: [AMBER] Dihedral angle PCA Daniel Roe
- Re: [AMBER] Error running sander.MPI "rfree: End of file on unit 5 " Jason Swails
- Re: [AMBER] Dihedral angle PCA Jian Yin
- Re: [AMBER] Problem compatibility pdb in tleap Stefan Knippenberg
- [AMBER] RMSD of globular proteins Anselm Horn
- Re: [AMBER] RMSD of globular proteins Aron Broom
Friday, 25 January 2013
- Re: [AMBER] KCl crystals with Dang parameters ? Vlad Cojocaru
- Re: [AMBER] KCl crystals with Dang parameters ? Jason Swails
- Re: [AMBER] KCl crystals with Dang parameters ? Vlad Cojocaru
- [AMBER] TI alpha-beta glucose Glycam06h Kepa K. Burusco
- Re: [AMBER] KCl crystals with Dang parameters ? Jason Swails
- Re: [AMBER] KCl crystals with Dang parameters ? Vlad Cojocaru
- Re: [AMBER] TI alpha-beta glucose Glycam06h steinbrt.rci.rutgers.edu
- Re: [AMBER] RMSD of globular proteins Julio Dominguez
Saturday, 26 January 2013
- [AMBER] Mixing Small Organic + Water Ismail, Mohd F.
- Re: [AMBER] Analyzing AMBER10 trajectories using AmberTools1.4 Kamali Sripathi
- [AMBER] Generating Electrostatic Potential Maps Kamali Sripathi
- Re: [AMBER] Generating Electrostatic Potential Maps Ray Luo, Ph.D.
- Re: [AMBER] Mixing Small Organic + Water case
- Re: [AMBER] Mixing Small Organic + Water Ismail, Mohd F.
Sunday, 27 January 2013
- [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file Jonathan Saboury
- [AMBER] about iwrap=1 and ntxo=2 Thomas Evangelidis
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file Jason Swails
- Re: [AMBER] about iwrap=1 and ntxo=2 Jason Swails
- [AMBER] distance restraints between the primary molecule and its periodic image Thomas Evangelidis
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file Jonathan Saboury
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file Jason Swails
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file Jonathan Saboury
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file Jonathan Saboury
- [AMBER] cudaMemcpyToSymbol Lars Skjærven
- [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file (2) Jonathan Saboury
- Re: [AMBER] distance restraints between the primary molecule and its periodic image Daniel Roe
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file case
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Ross Walker
- Re: [AMBER] distance restraints between the primary molecule and its periodic image Ross Walker
- Re: [AMBER] cudaMemcpyToSymbol Ross Walker
- [AMBER] installation of amber10 in cluster fails Jorgen Simonsen
Monday, 28 January 2013
- [AMBER] amber 12 patch for cuda-5.0 Asmita Gupta
- Re: [AMBER] distance restraints between the primary molecule and its periodic image Thomas Evangelidis
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file FyD
- Re: [AMBER] cudaMemcpyToSymbol Lars Skjærven
- Re: [AMBER] TI alpha-beta glucose Glycam06h Kepa K. Burusco
- Re: [AMBER] installation of amber10 in cluster fails Jason Swails
- Re: [AMBER] amber 12 patch for cuda-5.0 Jason Swails
- Re: [AMBER] TI alpha-beta glucose Glycam06h steinbrt.rci.rutgers.edu
- [AMBER] Explicit ions in GB solvent Debayan Chakraborty
- Re: [AMBER] Explicit ions in GB solvent Aron Broom
- Re: [AMBER] Explicit ions in GB solvent Jason Swails
- Re: [AMBER] Explicit ions in GB solvent manikanthan bhavaraju
- Re: [AMBER] TI alpha-beta glucose Glycam06h Kepa K. Burusco
- [AMBER] Sigmoidal dielectric functions in AMBER Debayan Chakraborty
- Re: [AMBER] Sigmoidal dielectric functions in AMBER case
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file(case) Jonathan Saboury
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file(jason) Jonathan Saboury
- [AMBER] patching problem amber12 Vaibhav Dixit
Tuesday, 29 January 2013
- [AMBER] How to calculate PMF using Jarzynski’s equality? Cuiyl
- [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters Sanjib Paul
- [AMBER] Fwd: Regarding the problem with ligand conformation aneesh cna
- [AMBER] Pocket Volume Calculation Soumya Lipsa Rath
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file(case) David A Case
- Re: [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters David A Case
- Re: [AMBER] Pocket Volume Calculation João Ribeiro
- Re: [AMBER] Fwd: Regarding the problem with ligand conformation Karl N. Kirschner
- [AMBER] CPPTRAJ Parmstrip error HM
- Re: [AMBER] How to calculate PMF using Jarzynski’s equality? Brian Radak
- Re: [AMBER] How to calculate PMF using Jarzynski’s equality? Adrian Roitberg
- Re: [AMBER] CPPTRAJ Parmstrip error Jason Swails
- [AMBER] AMBER 4.1 Manual Romelia Salomon
- Re: [AMBER] AMBER 4.1 Manual Gerald Monard
- [AMBER] coexisting nab and nab openmp Scott Brozell
- Re: [AMBER] coexisting nab and nab openmp Jason Swails
- Re: [AMBER] Explicit ions in GB solvent Bill Ross
- Re: [AMBER] coexisting nab and nab openmp David A Case
- Re: [AMBER] patching problem amber12 Vaibhav Dixit
- Re: [AMBER] Pocket Volume Calculation Soumya Lipsa Rath
- Re: [AMBER] patching problem amber12 Daniel Sindhikara
- Re: [AMBER] patching problem amber12 Vaibhav Dixit
- Re: [AMBER] patching problem amber12 Daniel Sindhikara
- Re: [AMBER] patching problem amber12 Vaibhav Dixit
- Re: [AMBER] Fwd: Regarding the problem with ligand conformation aneesh cna
- Re: [AMBER] Fwd: Regarding the problem with ligand conformation Bill Ross
- Re: [AMBER] coexisting nab and nab openmp Scott Brozell
- Re: [AMBER] Fwd: Regarding the problem with ligand conformation aneesh cna
Wednesday, 30 January 2013
- Re: [AMBER] RMSD of globular proteins Anselm Horn
- [AMBER] saving PDB with chain ID in leap aneesh cna
- [AMBER] error while running mmpbsa.py in amber12 Alessandro Contini
- Re: [AMBER] patching problem amber12 Jason Swails
- Re: [AMBER] error while running mmpbsa.py in amber12 Jason Swails
- Re: [AMBER] saving PDB with chain ID in leap Jason Swails
- Re: [AMBER] patching problem amber12 Daniel Sindhikara
- Re: [AMBER] error while running mmpbsa.py in amber12 Alessandro Contini
- Re: [AMBER] patching problem amber12 Vaibhav Dixit
- Re: [AMBER] patching problem amber12 Jason Swails
- Re: [AMBER] patching problem amber12 Vaibhav Dixit
- Re: [AMBER] patching problem amber12 Jason Swails
- Re: [AMBER] error while running mmpbsa.py in amber12 Jason Swails
- Re: [AMBER] CPPTRAJ Parmstrip error HM
- [AMBER] How to save secondary structure gnuplot as image HM
- Re: [AMBER] How to save secondary structure gnuplot as image steinbrt.rci.rutgers.edu
- Re: [AMBER] error while running mmpbsa.py in amber12 Alessandro Contini
- Re: [AMBER] error while running mmpbsa.py in amber12 Alessandro Contini
- Re: [AMBER] error while running mmpbsa.py in amber12 Jason Swails
- Re: [AMBER] error while running mmpbsa.py in amber12 Alessandro Contini
- [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead Marko Wehle
- Re: [AMBER] error while running mmpbsa.py in amber12 Jason Swails
- Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead Jason Swails
- Re: [AMBER] Fwd: Regarding the problem with ligand conformation Bill Ross
- Re: [AMBER] distance restraints between the primary molecule and its periodic image Thomas Evangelidis
- Re: [AMBER] AMBER 4.1 Manual Romelia Salomon
- Re: [AMBER] distance restraints between the primary molecule and its periodic image Jason Swails
- Re: [AMBER] How to save secondary structure gnuplot as image Daniel Roe
- Re: [AMBER] amber11 installation test files Mary Varughese
- Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead Marko Wehle
- [AMBER] mmPBSA.py: mmGBSA and solute dielectric constant psu4.uic.edu
- Re: [AMBER] mmPBSA.py: mmGBSA and solute dielectric constant Jason Swails
- Re: [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters Sanjib Paul
- Re: [AMBER] patching problem amber12 Vaibhav Dixit
- Re: [AMBER] patching problem amber12 Daniel Sindhikara
- Re: [AMBER] patching problem amber12 Vaibhav Dixit
- [AMBER] two fold difference between MMPBSA.py and NAMDenergy plugin in vmd 1.9.1 dbaogen
- Re: [AMBER] patching problem amber12 Vaibhav Dixit
Thursday, 31 January 2013
- Re: [AMBER] Fwd: Regarding the problem with ligand conformation Karl N. Kirschner
- Re: [AMBER] Fwd: Regarding the problem with ligand conformation aneesh cna
- Re: [AMBER] two fold difference between MMPBSA.py and NAMDenergy plugin in vmd 1.9.1 Jason Swails
- [AMBER] does iwrap=1 work with dodecahedra ? Thomas Evangelidis
- Re: [AMBER] does iwrap=1 work with dodecahedra ? David A Case
- Re: [AMBER] Fwd: Regarding the problem with ligand conformation Karl N. Kirschner
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Alessandro Contini
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Jason Swails
- Re: [AMBER] How to save secondary structure gnuplot as image HM
- Re: [AMBER] How to save secondary structure gnuplot as image HM
Wednesday, 30 January 2013
- Re: [AMBER] AMBER 4.1 Manual David A Case
Thursday, 31 January 2013
- Re: [AMBER] How to save secondary structure gnuplot as image ros
- [AMBER] Sampling of a point by a molecule while keeping the relative position of the molecule unchanged in TMD Sajeewa Pemasinghe
- Re: [AMBER] AMBER 4.1 Manual Romelia Salomon
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Ross Walker
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Scott Le Grand
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Alessandro Contini
- Re: [AMBER] does iwrap=1 work with dodecahedra ? Thomas Evangelidis
- Re: [AMBER] does iwrap=1 work with dodecahedra ? Brian Radak
- [AMBER] Fwd: Sampling of a point by a molecule while keeping the relative position of the molecule unchanged in TMD Sajeewa Pemasinghe
- Re: [AMBER] does iwrap=1 work with dodecahedra ? Thomas Evangelidis
- Re: [AMBER] does iwrap=1 work with dodecahedra ? Jason Swails
- Re: [AMBER] does iwrap=1 work with dodecahedra ? Daniel Roe
- Re: [AMBER] does iwrap=1 work with dodecahedra ? Thomas Evangelidis
- [AMBER] pmemd.cuda compilation with amber12 Vivek Shankar Bharadwaj
- [AMBER] mmPBSA and restraint energy decreasing psu4.uic.edu
- Re: [AMBER] Problem using solvatebox for large, linear peptide David A Case
- Re: [AMBER] scaling problem in RADIAL of CPPTRAJ Daniel Roe

Last message date: Thu Jan 31 2013 - 21:00:02 PST
Archived on: Mon Nov 03 2025 - 05:54:43 PST

Amber Archive Jan 2013 by date