Amber Archive Nov 2012: by date

Wednesday, 31 October 2012
- Re: [AMBER] antechamber limitation on molecule size anyiphysics.gmail.com
- Re: [AMBER] error when Chamber dealing with DNA, RNA and ATP baogen duan
- Re: [AMBER] Problem in running parallel hari krishna
- Re: [AMBER] Problem in running parallel Terry
Thursday, 1 November 2012
- Re: [AMBER] antechamber limitation on molecule size FyD
- [AMBER] solvation free enrgy calculation using PB equation. baogen duan
- [AMBER] metal protein -regarding subramanian boopathi
- Re: [AMBER] Download problem of amber12 Sanjib Paul
- [AMBER] Best atom types for N-Oxides compounds like TMAO sa
- [AMBER] force field file problem Changqing Yan
- Re: [AMBER] Best atom types for N-Oxides compounds like TMAO Gustavo Seabra
- [AMBER] implementation of string method to find minimum free energy paths in Amber Tan Yaw Sing
- Re: [AMBER] Best atom types for N-Oxides compounds like TMAO sa
- Re: [AMBER] Best atom types for N-Oxides compounds like TMAO Gustavo Seabra
- Re: [AMBER] implementation of string method to find minimum free energy paths in Amber Christina Bergonzo
- Re: [AMBER] Best atom types for N-Oxides compounds like TMAO sa
- Re: [AMBER] Amber and P450 cytochromes Maximilian Ebert
- Re: [AMBER] solvation free enrgy calculation using PB equation. Ray Luo, Ph.D.
- Re: [AMBER] antechamber limitation on molecule size David A Case
- Re: [AMBER] solvation free enrgy calculation using PB equation. David A Case
- [AMBER] references ? JAIME RUBIO MARTINEZ
- Re: [AMBER] force field file problem David A Case
- Re: [AMBER] references ? Bill Miller III
- [AMBER] vlimit exceed for step 1- regarding subramanian boopathi
- [AMBER] Amber12 PETASCALE Benchmarking. BERGY
- Re: [AMBER] Amber12 PETASCALE Benchmarking. Ross Walker
- Re: [AMBER] vlimit exceed for step 1- regarding Ross Walker
Friday, 2 November 2012
- [AMBER] Cannot setting AMBERHOME on ubuntu 12.04 setyanto md
- Re: [AMBER] Cannot setting AMBERHOME on ubuntu 12.04 David A Case
- [AMBER] vlimit exceeded error regarding subramanian boopathi
- [AMBER] how to calculate binding energy of one receptor and two ligands? bin wang
- Re: [AMBER] vlimit exceeded error regarding Ross Walker
- Re: [AMBER] how to calculate binding energy of one receptor and two ligands? Jason Swails
- Re: [AMBER] Amber12 Parrell Installation Error BERGY
- Re: [AMBER] deprotonated serine BERGY
- Re: [AMBER] how to calculate binding energy of one receptor and two ligands? bin wang
- [AMBER] AMBER-Gaussian and Infrared marawan hussain
- Re: [AMBER] how to calculate binding energy of one receptor and two ligands? Jason Swails
Saturday, 3 November 2012
- [AMBER] Problem related to the RMSD Sindrila Dutta banik
- Re: [AMBER] Problem related to the RMSD Jason Swails
- Re: [AMBER] AMBER-Gaussian and Infrared Brian Radak
- Re: [AMBER] AMBER-Gaussian and Infrared Andreas Goetz
- [AMBER] Problem related to the RMSD Sindrila Dutta banik
Sunday, 4 November 2012
- Re: [AMBER] AMBER-Gaussian and Infrared Brent Krueger
- [AMBER] no leaprc in search path Fabian Glaser
- Re: [AMBER] Problem related to the RMSD Niel Henriksen
- Re: [AMBER] no leaprc in search path Jason Swails
- Re: [AMBER] no leaprc in search path Fabian Glaser
- Re: [AMBER] no leaprc in search path Jason Swails
- [AMBER] Problem related to RMSD Sindrila Dutta banik
- Re: [AMBER] Problem related to RMSD Niel Henriksen
- Re: [AMBER] Problem related to RMSD Jason Swails
- [AMBER] MMPBSA.py "timer: need to reset the time before start" Adelene Sim
- [AMBER] Problem related to RMSD Sindrila Dutta banik
- Re: [AMBER] Problem related to RMSD Niel Henriksen
- [AMBER] Clarifications in umbrella sampling Sajeewa Pemasinghe
- [AMBER] Problem related to RMSD Sindrila Dutta banik
- Re: [AMBER] Clarifications in umbrella sampling Aron Broom
- [AMBER] Problem related to the RMSD Sindrila Dutta banik
- Re: [AMBER] Problem related to RMSD Miguel Ortiz Lombardia
- Re: [AMBER] Clarifications in umbrella sampling Sajeewa Pemasinghe
Monday, 5 November 2012
- Re: [AMBER] Clarifications in umbrella sampling steinbrt.rci.rutgers.edu
- Re: [AMBER] Clarifications in umbrella sampling Sajeewa Pemasinghe
- Re: [AMBER] no leaprc in search path Fabian Glaser
- [AMBER] How to use q4md-CD? Liu Denis
- [AMBER] workstation . mirage
- Re: [AMBER] Clarifications in umbrella sampling Aron Broom
- Re: [AMBER] MMPBSA.py "timer: need to reset the time before start" Jason Swails
- [AMBER] tleap not recognizing Na+ David Condon
- Re: [AMBER] tleap not recognizing Na+ Aron Broom
- Re: [AMBER] tleap not recognizing Na+ Ilyas Yildirim
- Re: [AMBER] tleap not recognizing Na+ David A Case
- Re: [AMBER] [Private q4md] R.E.D. Server: Private assistance FyD
- [AMBER] Dipole from a mask Ismail, Mohd F.
- Re: [AMBER] How to use q4md-CD? FyD
- Re: [AMBER] workstation Ross Walker
- [AMBER] pmemd cuda MPI nmropt crashes Scott Brozell
- [AMBER] pmemd cuda MPI and PBS_GPUFILE Scott Brozell
- Re: [AMBER] pmemd cuda MPI nmropt crashes Ross Walker
- Re: [AMBER] pmemd cuda MPI nmropt crashes Scott Brozell
- Re: [AMBER] pmemd cuda MPI and PBS_GPUFILE Ross Walker
- Re: [AMBER] pmemd cuda MPI nmropt crashes Ross Walker
- Re: [AMBER] pmemd cuda MPI nmropt crashes Ross Walker
Tuesday, 6 November 2012
- Re: [AMBER] How to use q4md-CD? Liu Denis
- Re: [AMBER] pmemd cuda MPI nmropt crashes Scott Le Grand
- [AMBER] Cannot match namelist object name scee Esam Tolba
- [AMBER] best tutorials Fabian Glaser
- Re: [AMBER] Cannot match namelist object name scee Jason Swails
- Re: [AMBER] questions about thermodynamic integration atom name and order Yulin Huang
- Re: [AMBER] pmemd cuda MPI and PBS_GPUFILE Jason Swails
- [AMBER] compiler errors Brown, Paul
- Re: [AMBER] pmemd cuda MPI and PBS_GPUFILE Jodi Ann Hadden
- Re: [AMBER] compiler errors Jason Swails
- Re: [AMBER] pmemd cuda MPI nmropt crashes Scott Le Grand
- [AMBER] about angle restraint anyiphysics.gmail.com
- [AMBER] Image problems with IWRAP=1 Brown, Kyle
- Re: [AMBER] questions about thermodynamic integration atom name and order David A Case
- Re: [AMBER] about angle restraint David A Case
- Re: [AMBER] Image problems with IWRAP=1 David A Case
- Re: [AMBER] questions about thermodynamic integration atom name and order Yulin Huang
- Re: [AMBER] Dipole from a mask Daniel Roe
- Re: [AMBER] Image problems with IWRAP=1 Daniel Roe
- Re: [AMBER] about angle restraint anyiphysics.gmail.com
- [AMBER] questions about AMBER prep files Yulin Huang
- Re: [AMBER] questions about thermodynamic integration atom name and order Jason Swails
- Re: [AMBER] questions about AMBER prep files Jason Swails
- Re: [AMBER] questions about AMBER prep files Yulin Huang
- Re: [AMBER] Image problems with IWRAP=1 Brown, Kyle
- Re: [AMBER] Image problems with IWRAP=1 Daniel Roe
- Re: [AMBER] about angle restraint Marek Maly
- Re: [AMBER] about angle restraint anyiphysics.gmail.com
- [AMBER] error of MMPBSA calculation using the prmtop and inpcrd generated by Chamber program baogen duan
- Re: [AMBER] error of MMPBSA calculation using the prmtop and inpcrd generated by Chamber program Bill Miller III
- Re: [AMBER] best tutorials BERGY
- [AMBER] Energy Analysis from Trajectory Aron Broom
- Re: [AMBER] Energy Analysis from Trajectory Roitberg,Adrian E
- Re: [AMBER] Energy Analysis from Trajectory Aron Broom
- [AMBER] Umbrella sampling with pmemd Sajeewa Pemasinghe
- Re: [AMBER] Umbrella sampling with pmemd Roitberg,Adrian E
- [AMBER] Will Ptraj image the coordinates after rms fitting? Alan
- Re: [AMBER] Umbrella sampling with pmemd Sajeewa Pemasinghe
Wednesday, 7 November 2012
- Re: [AMBER] How to use q4md-CD? FyD
- Re: [AMBER] error of MMPBSA calculation using the prmtop and inpcrd generated by Chamber program baogen duan
- [AMBER] "vlimit exceeded for step ..." during SA protocol Baptiste Legrand
- [AMBER] NAMD failed to read Amber parm file Sneha Menon
- Re: [AMBER] questions about thermodynamic integration atom name and order David A Case
- Re: [AMBER] questions about thermodynamic integration atom name and order David A Case
- Re: [AMBER] questions about thermodynamic integration atom name and order Yulin Huang
- Re: [AMBER] "vlimit exceeded for step ..." during SA protocol David A Case
- Re: [AMBER] Umbrella sampling with pmemd Roitberg,Adrian E
- Re: [AMBER] NAMD failed to read Amber parm file Aron Broom
- Re: [AMBER] pmemd cuda MPI nmropt crashes Scott Brozell
- Re: [AMBER] pmemd cuda MPI and PBS_GPUFILE Scott Brozell
- Re: [AMBER] pmemd cuda MPI nmropt crashes Scott Brozell
- Re: [AMBER] pmemd cuda MPI and PBS_GPUFILE Scott Le Grand
- [AMBER] bond missing in phosphate group after antechamber run Krisztina Feher
- Re: [AMBER] Energy Analysis from Trajectory Jason Swails
- Re: [AMBER] error of MMPBSA calculation using the prmtop and inpcrd generated by Chamber program Jason Swails
- Re: [AMBER] NAMD failed to read Amber parm file Jason Swails
- [AMBER] problem with Ca2.lib manikanthan bhavaraju
- Re: [AMBER] problem with Ca2.lib Tim Travers
- Re: [AMBER] problem with Ca2.lib manikanthan bhavaraju
- Re: [AMBER] Image problems with IWRAP=1 Daniel Roe
- Re: [AMBER] bond missing in phosphate group after antechamber run Krisztina Feher
- Re: [AMBER] Dipole from a mask Ismail, Mohd F.
- Re: [AMBER] best tutorials Jason Swails
- Re: [AMBER] antechamber limitation on molecule size anyiphysics.gmail.com
- Re: [AMBER] antechamber limitation on molecule size Aron Broom
- Re: [AMBER] antechamber limitation on molecule size Yi An
- [AMBER] genMetalFF.sh and getCharges.sh not exist Jia Xu
Thursday, 8 November 2012
- [AMBER] Multi-protein simulation in a box Rajeswari A.
- Re: [AMBER] "vlimit exceeded for step ..." during SA protocol Baptiste Legrand
- Re: [AMBER] antechamber limitation on molecule size FyD
- [AMBER] using nudged elastic band method with explicit solvent Tan Yaw Sing
- [AMBER] Parameters for amide bond isosteres Cecilia Lindgren
- Re: [AMBER] compiler errors Brown, Paul
- Re: [AMBER] compiler errors Jason Swails
- Re: [AMBER] bond missing in phosphate group after antechamber run Krisztina Feher
- Re: [AMBER] genMetalFF.sh and getCharges.sh not exist Jason Swails
- [AMBER] Heme iron definition: Atom type missing Maximilian Ebert
- Re: [AMBER] bond missing in phosphate group after antechamber run David A Case
- [AMBER] different force fields for different molecules in leap Pecher, Josua
- Re: [AMBER] Multi-protein simulation in a box Aron Broom
- Re: [AMBER] Dipole from a mask Daniel Roe
- Re: [AMBER] different force fields for different molecules in leap Aron Broom
- Re: [AMBER] different force fields for different molecules in leap Pecher, Josua
- Re: [AMBER] Multi-protein simulation in a box Jason Swails
- Re: [AMBER] using nudged elastic band method with explicit solvent Christina Bergonzo
- Re: [AMBER] antechamber limitation on molecule size anyiphysics.gmail.com
- Re: [AMBER] Multi-protein simulation in a box Brian Radak
- Re: [AMBER] bond missing in phosphate group after antechamber run Krisztina Feher
- Re: [AMBER] genMetalFF.sh and getCharges.sh not exist Jia Xu
- [AMBER] Primary structur to 3D structure Sindrila Dutta banik
- [AMBER] AmberTools versions Maxier Acosta Santiago
- Re: [AMBER] AmberTools versions Jason Swails
- Re: [AMBER] Primary structur to 3D structure Aron Broom
- [AMBER] EHBOND values and RESTRAINT values in mdout file Pyle, Ronald
- Re: [AMBER] EHBOND values and RESTRAINT values in mdout file Jason Swails
- Re: [AMBER] EHBOND values and RESTRAINT values in mdout file tec3.utah.edu
- Re: [AMBER] using nudged elastic band method with explicit solvent Tan Yaw Sing
- Re: [AMBER] Dipole from a mask Ismail, Mohd F.
- Re: [AMBER] Dipole from a mask Ismail, Mohd F.
- [AMBER] Obtain trajectory coordinates from LMOD minimization Sangmin Lee
- Re: [AMBER] Multi-protein simulation in a box Rajeswari A.
Friday, 9 November 2012
- [AMBER] No radius found for Mg+ using mm_pbsa.pl script baogen duan
- Re: [AMBER] compiler errors Brown, Paul
- Re: [AMBER] Obtain trajectory coordinates from LMOD minimization David A Case
- Re: [AMBER] EHBOND values and RESTRAINT values in mdout file Pyle, Ronald
- [AMBER] Error at the end of entropy calculation via MMPBSA.py Miguel Ortiz Lombardía
- Re: [AMBER] Error at the end of entropy calculation via MMPBSA.py Jason Swails
- Re: [AMBER] EHBOND values and RESTRAINT values in mdout file Jason Swails
- Re: [AMBER] Dipole from a mask Daniel Roe
- Re: [AMBER] No radius found for Mg+ using mm_pbsa.pl script Ray Luo, Ph.D.
- [AMBER] Regarding Quadruplex Formation Souvik Sur
- Re: [AMBER] Heme iron definition: Atom type missing Maximilian Ebert
- Re: [AMBER] Dipole from a mask Ismail, Mohd F.
- Re: [AMBER] Heme iron definition: Atom type missing David A Case
- Re: [AMBER] Regarding Quadruplex Formation David A Case
- [AMBER] System blows up after several nanoseconds using Amber 12 Sasha Perkins
- Re: [AMBER] System blows up after several nanoseconds using Amber 12 Jason Swails
- Re: [AMBER] Heme iron definition: Atom type missing Maximilian Ebert
Saturday, 10 November 2012
- Re: [AMBER] System blows up after several nanoseconds using Amber 12 Sasha Perkins
- Re: [AMBER] System blows up after several nanoseconds using Amber 12 Roitberg,Adrian E
- Re: [AMBER] System blows up after several nanoseconds using Amber 12 Jason Swails
- Re: [AMBER] System blows up after several nanoseconds using Amber 12 Sasha Perkins
- Re: [AMBER] System blows up after several nanoseconds using Amber 12 Roitberg,Adrian E
Sunday, 11 November 2012
- [AMBER] Amber Error : Segmentation fault Sumra Wajid Abbasi 30-FBAS/MSBI/F09
- Re: [AMBER] Amber Error : Segmentation fault Ross Walker
- Re: [AMBER] Amber Error : Segmentation fault Sumra Wajid Abbasi 30-FBAS/MSBI/F09
- [AMBER] Urgent Faez Iqbal khan
- Re: [AMBER] Urgent Ross Walker
Monday, 12 November 2012
- Re: [AMBER] Amber Error : Segmentation fault Sumra Wajid Abbasi 30-FBAS/MSBI/F09
- Re: [AMBER] Amber Error : Segmentation fault Jason Swails
- [AMBER] Generating a solvent Box from organic solvent Mark Zottola
- Re: [AMBER] Generating a solvent Box from organic solvent Bill Ross
- [AMBER] Tleap crash while loading frcmod Daniel Sindhikara
- Re: [AMBER] Amber Error : Segmentation fault Sumra Wajid Abbasi 30-FBAS/MSBI/F09
- Re: [AMBER] Amber Error : Segmentation fault Sumra Wajid Abbasi 30-FBAS/MSBI/F09
- Re: [AMBER] Amber Error : Segmentation fault Sumra Wajid Abbasi 30-FBAS/MSBI/F09
- Re: [AMBER] Tleap crash while loading frcmod Bill Ross
- Re: [AMBER] Tleap crash while loading frcmod Daniel Sindhikara
Tuesday, 13 November 2012
- [AMBER] imaging namd-generated dcd trajectories with cpptraj Vlad Cojocaru
- [AMBER] problem for lipid GAFF Albert
- [AMBER] NOE calculation Meli Massimiliano
- [AMBER] cppparmstrip command provokes segmentation fault Vlad Cojocaru
- Re: [AMBER] Tleap crash while loading frcmod David A Case
- Re: [AMBER] Amber Error : Segmentation fault David A Case
- Re: [AMBER] NOE calculation David A Case
- Re: [AMBER] cppparmstrip command provokes segmentation fault Jason Swails
- Re: [AMBER] imaging namd-generated dcd trajectories with cpptraj Jason Swails
- Re: [AMBER] cppparmstrip command provokes segmentation fault Vlad Cojocaru
- Re: [AMBER] imaging namd-generated dcd trajectories with cpptraj Vlad Cojocaru
- Re: [AMBER] imaging namd-generated dcd trajectories with cpptraj Jason Swails
- Re: [AMBER] imaging namd-generated dcd trajectories with cpptraj Vlad Cojocaru
- Re: [AMBER] cppparmstrip command provokes segmentation fault Daniel Roe
- Re: [AMBER] imaging namd-generated dcd trajectories with cpptraj Daniel Roe
- Re: [AMBER] "vlimit exceeded for step ..." during SA protocol Baptiste Legrand
- Re: [AMBER] NOE calculation Meli Massimiliano
- Re: [AMBER] problem for lipid GAFF Dickson, Callum
- Re: [AMBER] problem for lipid GAFF Ross Walker
- Re: [AMBER] problem for lipid GAFF Albert
- Re: [AMBER] problem for lipid GAFF Ross Walker
- [AMBER] Problem with "make install" after "./configure intel" Su, Shiquan
- Re: [AMBER] Problem with "make install" after "./configure intel" Daniel Roe
- Re: [AMBER] Problem with "make install" after "./configure intel" Su, Shiquan
- Re: [AMBER] Problem with "make install" after "./configure intel" Su, Shiquan
- [AMBER] MM PBSA error calculating entropy Aron Broom
- Re: [AMBER] MM PBSA error calculating entropy Jason Swails
- Re: [AMBER] MM PBSA error calculating entropy Aron Broom
- [AMBER] Regarding RNA Duplex formation Souvik Sur
- Re: [AMBER] problem for lipid GAFF Albert
Wednesday, 14 November 2012
- [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE Dmitry Mukha
- [AMBER] Odp: Re: problem for lipid GAFF klechward.wp.pl
- [AMBER] Problem of atom typing for the LYN residue? FyD
- Re: [AMBER] Odp: Re: problem for lipid GAFF Albert
- [AMBER] Explicit 1-4 pairs Joakim Jämbeck
- [AMBER] Antechamber and GTP Fernando Martín García
- [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 vojtech.mlynsky.upol.cz
- [AMBER] mmpbsa restart Giulia
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 Gustavo Seabra
- Re: [AMBER] Explicit 1-4 pairs Jason Swails
- Re: [AMBER] mmpbsa restart Jason Swails
- Re: [AMBER] mmpbsa restart Giulia
- Re: [AMBER] mmpbsa restart Jason Swails
- Re: [AMBER] problem for lipid GAFF Ross Walker
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 vojtech.mlynsky.upol.cz
- Re: [AMBER] Regarding RNA Duplex formation David A Case
- Re: [AMBER] Antechamber and GTP David A Case
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE Ray Luo, Ph.D.
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE Dmitry Mukha
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 Gustavo Seabra
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 Brian Radak
- [AMBER] COM removed message and Energy Drift Ismail, Mohd F.
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 Marc van der Kamp
- Re: [AMBER] COM removed message and Energy Drift Ismail, Mohd F.
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 Andreas Goetz
- Re: [AMBER] Energy Analysis from Trajectory Kepa K. Burusco
- [AMBER] residuegen Osman, Roman
- [AMBER] AMBER/ORCA marawan hussain
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE Ray Luo, Ph.D.
- [AMBER] Error in script file while running mm_pbsa.pl Anogna
- [AMBER] AMBER-ORCA marawan hussain
Thursday, 15 November 2012
- Re: [AMBER] Antechamber and GTP fmgarcia.cbm.uam.es
- Re: [AMBER] Antechamber and GTP Alan
- Re: [AMBER] COM removed message and Energy Drift Jason Swails
- Re: [AMBER] Energy Analysis from Trajectory David A Case
- Re: [AMBER] AMBER/ORCA David A Case
- Re: [AMBER] Antechamber and GTP David A Case
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 vojtech.mlynsky.upol.cz
- [AMBER] very large value of "fglen" and "cglen" during MMPBSA.py calculatio using sander.APBS dbaogen
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 Gustavo Seabra
- Re: [AMBER] Energy Analysis from Trajectory Kepa K. Burusco
- Re: [AMBER] Energy Analysis from Trajectory Jason Swails
- [AMBER] Kepler II (K20) benchmark results? filip fratev
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 vojtech.mlynsky.upol.cz
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 Brian Radak
- Re: [AMBER] COM removed message and Energy Drift Ismail, Mohd F.
- Re: [AMBER] AMBER-ORCA Andreas Goetz
- [AMBER] AMBER-ORCA-Freq marawan hussain
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 Andreas Goetz
- Re: [AMBER] Kepler II (K20) benchmark results? Ross Walker
- [AMBER] Problem with the specification of the bellymask Sajeewa Pemasinghe
- [AMBER] large value of "fglen" and "cglen"of iAPBS initiation during MMPBSA python script calculation baogen duan
- Re: [AMBER] Problem with the specification of the bellymask Jason Swails
- Re: [AMBER] Problem with the specification of the bellymask Sajeewa Pemasinghe
- Re: [AMBER] large value of "fglen" and "cglen"of iAPBS initiation during MMPBSA python script calculation Robert Konecny
Friday, 16 November 2012
- [AMBER] WARNING: a parameter is 0.0 for atom Jacopo Sgrignani
- Re: [AMBER] WARNING: a parameter is 0.0 for atom Gustavo Seabra
- Re: [AMBER] WARNING: a parameter is 0.0 for atom Jacopo Sgrignani
- Re: [AMBER] WARNING: a parameter is 0.0 for atom Gustavo Seabra
- Re: [AMBER] Antechamber and GTP Fernando Martín García
- Re: [AMBER] Error in script file while running mm_pbsa.pl Jason Swails
- Re: [AMBER] Antechamber and GTP Fernando Martín García
- Re: [AMBER] Antechamber and GTP FyD
- Re: [AMBER] AMBER-ORCA-Freq Brian Radak
- [AMBER] Theorical ramachandran map/energy map of modified residues Baptiste Legrand
- Re: [AMBER] Theorical ramachandran map/energy map of modified residues Carlos Simmerling
- Re: [AMBER] Theorical ramachandran map/energy map of modified residues Jason Swails
- [AMBER] C-C-N angle parameters for benzonitrile Sharma, Purshotam
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE Ray Luo, Ph.D.
- [AMBER] QM/MM bugfix for semiempirical NDDO code available, soon Andreas Goetz
Saturday, 17 November 2012
- [AMBER] Antechamber Maxier Acosta Santiago
- Re: [AMBER] Antechamber Jason Swails
Sunday, 18 November 2012
- Re: [AMBER] Antechamber Maxier Acosta Santiago
- Re: [AMBER] questions about Accelerated MD Thomas Evangelidis
- [AMBER] Can I mix Glycam and Gaff in a small molecule? Liu Denis
- [AMBER] Amber radii of ions Devlina Chakravarty
- [AMBER] trajout command in ptraj rahul sarma
Monday, 19 November 2012
- [AMBER] mixing of scaling factor in amber 12 Subrata Paul
- Re: [AMBER] Can I mix Glycam and Gaff in a small molecule? David A Case
- Re: [AMBER] Amber radii of ions David A Case
- Re: [AMBER] mixing of scaling factor in amber 12 Jason Swails
- Re: [AMBER] trajout command in ptraj Daniel Roe
- Re: [AMBER] questions about Accelerated MD Romelia Salomon
- Re: [AMBER] questions about Accelerated MD Thomas Evangelidis
- Re: [AMBER] questions about Accelerated MD Romelia Salomon
- Re: [AMBER] mixing of scaling factor in amber 12 Subrata Paul
- Re: [AMBER] questions about Accelerated MD Thomas Evangelidis
- [AMBER] generate rst from mdcrd Yunjie Zhao
- Re: [AMBER] generate rst from mdcrd Jason Swails
- Re: [AMBER] questions about Accelerated MD Romelia Salomon
- Re: [AMBER] trajout command in ptraj rahul sarma
Tuesday, 20 November 2012
- [AMBER] unsubscribe Aust, Susanne
- [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Thomas Evangelidis
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Jason Swails
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Thomas Evangelidis
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Ross Walker
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Thomas Evangelidis
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Su, Shiquan
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Ross Walker
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Thomas Evangelidis
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Ross Walker
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Thomas Evangelidis
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Ross Walker
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Thomas Evangelidis
- Re: [AMBER] Can I mix Glycam and Gaff in a small molecule? Liu Denis
- [AMBER] Magnesium ion (Mg2+) simulation dbaogen
- [AMBER] is AMBER FF good enough for long time scaled MD? Albert
Wednesday, 21 November 2012
- [AMBER] Ligand appears broken after minimization Jitesh Doshi
- Re: [AMBER] Ligand appears broken after minimization Kshatresh Dutta Dubey
- [AMBER] selecting a gpu device in multiple gpu system 홍종희
- Re: [AMBER] selecting a gpu device in multiple gpu system Marc van der Kamp
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? francesco oteri
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? David A Case
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? Albert
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? Albert
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? Vlad Cojocaru
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? Albert
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? Vlad Cojocaru
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? Vlad Cojocaru
- Re: [AMBER] selecting a gpu device in multiple gpu system Jason Swails
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? Albert
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? Thomas Evangelidis
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? Vlad Cojocaru
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? Albert
- [AMBER] strange deprotonation in QM/MM Jacopo Sgrignani
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? Vlad Cojocaru
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? Thomas Evangelidis
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? Vlad Cojocaru
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Ross Walker
- Re: [AMBER] selecting a gpu device in multiple gpu system Ross Walker
- [AMBER] Forcefield Maxier Acosta Santiago
- Re: [AMBER] Forcefield Christina Bergonzo
Thursday, 22 November 2012
- [AMBER] Problem to run sander with more than 60 atom types Elise Duboué-Dijon
- Re: [AMBER] strange deprotonation in QM/MM Alex Rodriguez
- Re: [AMBER] strange deprotonation in QM/MM Jacopo Sgrignani
- Re: [AMBER] questions about Accelerated MD Thomas Evangelidis
- [AMBER] Heating process- amber 8 regarding subramanian boopathi
Friday, 23 November 2012
- [AMBER] GPU and ntpr Fernando Martín García
- [AMBER] INTER-molecular RDF only ? Marek Maly
- Re: [AMBER] Happy Thanksgiving!!!! Eliana Asciutto
- [AMBER] Sorry for the previous email Eliana Asciutto
- Re: [AMBER] INTER-molecular RDF only ? Ismail, Mohd F.
- Re: [AMBER] INTER-molecular RDF only ? Marek Maly
- Re: [AMBER] INTER-molecular RDF only ? Ismail, Mohd F.
- Re: [AMBER] INTER-molecular RDF only ? Marek Maly
- Re: [AMBER] GPU and ntpr Ross Walker
Sunday, 25 November 2012
- [AMBER] What nonbonded interactions cutoff to use in amber. Itamar Kass
Monday, 26 November 2012
- [AMBER] Porcupine_Plots_Script Jia Xu
- Re: [AMBER] Porcupine_Plots_Script monica.imtech.res.in
- [AMBER] definition of receptor_mask and ligand_mask using MMPBSA method dbaogen
- Re: [AMBER] definition of receptor_mask and ligand_mask using MMPBSA method Bill Miller III
- Re: [AMBER] Heating process- amber 8 regarding David A Case
- Re: [AMBER] Problem of atom typing for the LYN residue? David A Case
- [AMBER] ptraj clustering problem (segmentation fault) adarm.nencki.gov.pl
- Re: [AMBER] [PATCH 1/8] AmberTools: Fix buffer overflows in mdgx, nab and ptraj David A Case
- Re: [AMBER] What nonbonded interactions cutoff to use in amber. Jason Swails
- [AMBER] ptraj grid by center of mass Daniel Álvarez García
- Re: [AMBER] ptraj clustering problem (segmentation fault) Daniel Roe
- Re: [AMBER] ptraj grid by center of mass Daniel Roe
- Re: [AMBER] ptraj grid by center of mass Daniel Álvarez García
- Re: [AMBER] Porcupine_Plots_Script Jia Xu
- [AMBER] LMOD issues in Amber 12 Sarah Edwards
- Re: [AMBER] ptraj clustering problem (segmentation fault) adarm.nencki.gov.pl
- [AMBER] calculation of protein-DNA complex structure 丁鹏飞
Tuesday, 27 November 2012
- [AMBER] Xleap rotation in mac OS Hirdesh Kumar
- Re: [AMBER] MMPBSA.py - problem with complex.prmtop colvin
- [AMBER] complete bond energy list יוכבד
- [AMBER] Antechamber-- Creating inputs for Ammonium-Borane Ravi Tripathi
- Re: [AMBER] Problem to run sander with more than 60 atom types Elise Duboué-Dijon
- Re: [AMBER] GPU and ntpr Fernando Martín García
- Re: [AMBER] Xleap rotation in mac OS Jason Swails
- [AMBER] UTP and CTP amber force field parameters dbaogen
- Re: [AMBER] calculation of protein-DNA complex structure David A Case
- Re: [AMBER] Antechamber-- Creating inputs for Ammonium-Borane David A Case
- [AMBER] postdoc RNA/DNA computations Jiri Sponer
- Re: [AMBER] MMPBSA.py - problem with complex.prmtop Jason Swails
- Re: [AMBER] complete bond energy list Jason Swails
- Re: [AMBER] Problem to run sander with more than 60 atom types Jason Swails
- Re: [AMBER] Problem to run sander with more than 60 atom types Elise Duboué-Dijon
- Re: [AMBER] Problem to run sander with more than 60 atom types Jason Swails
- Re: [AMBER] Porcupine_Plots_Script monica.imtech.res.in
- Re: [AMBER] Porcupine_Plots_Script Jason Swails
- Re: [AMBER] calculation of protein-DNA complex structure Carlos Simmerling
- [AMBER] calculate the binding free energy of more than one ligand in MMPBSA Shuyi Cao
- Re: [AMBER] calculate the binding free energy of more than one ligand in MMPBSA Jason Swails
- Re: [AMBER] GPU and ntpr Ross Walker
- [AMBER] simulation for a protein + ligand system with polarizable force field Jagur Lambix
- [AMBER] Reading DESMOND MD trajectory files in CPPTRAJ... Shashidhar Rao
- [AMBER] Polarizable force field for protein + ligand system Jagur Lambix
- Re: [AMBER] Reading DESMOND MD trajectory files in CPPTRAJ... Daniel Roe
- Re: [AMBER] Reading DESMOND MD trajectory files in CPPTRAJ... Shashidhar Rao
- Re: [AMBER] UTP and CTP amber force field parameters FyD
- Re: [AMBER] MMPBSA.py - problem with complex.prmtop -rdparm: a parameter array overflowed colvin
- [AMBER] error in heating process subramanian boopathi
- Re: [AMBER] Antechamber-- Creating inputs for Ammonium-Borane FyD
- [AMBER] Antechamber - Problem with protonated oxygen Ravi Tripathi
- Re: [AMBER] Antechamber-- Creating inputs for Ammonium-Borane Ravi Tripathi
- Re: [AMBER] Ligand appears broken after minimization Jitesh Doshi
- Re: [AMBER] Antechamber - Problem with protonated oxygen FyD
- Re: [AMBER] Antechamber - Problem with protonated oxygen Ravi Tripathi
- Re: [AMBER] error in heating process Bill Ross
Wednesday, 28 November 2012
- Re: [AMBER] Ligand appears broken after minimization Hirdesh Kumar
- Re: [AMBER] complete bond energy list יוכבד
- [AMBER] R.E.D calculation cannot be used for CHARMM FF? Albert
- Re: [AMBER] Antechamber - Problem with protonated oxygen FyD
- Re: [AMBER] error in heating process David A Case
- [AMBER] Calculating volume of the ligand manikanthan bhavaraju
- [AMBER] sander.MPI Fabian Glaser
- Re: [AMBER] MMPBSA.py - problem with complex.prmtop -rdparm: a parameter array overflowed Jason Swails
- Re: [AMBER] sander.MPI David A Case
- Re: [AMBER] Calculating volume of the ligand João Ribeiro
- Re: [AMBER] Calculating volume of the ligand manikanthan bhavaraju
- [AMBER] Doubt about binding dissociation constant manikanthan bhavaraju
- Re: [AMBER] Doubt about binding dissociation constant InSuk Joung
- Re: [AMBER] Doubt about binding dissociation constant manikanthan bhavaraju
- Re: [AMBER] Doubt about binding dissociation constant Ignacio J. General
- [AMBER] Amber 12 and PGI compilers >= 12.5 Ben Roberts
- Re: [AMBER] sander.MPI Fabian Glaser
- Re: [AMBER] sander.MPI Daniel Sindhikara
Thursday, 29 November 2012
- [AMBER] Compiler for Amber12 with GTX680 kurisaki
- Re: [AMBER] sander.MPI Jason Swails
- [AMBER] Solvation in Amber Ravi Tripathi
- Re: [AMBER] Porcupine_Plots_Script monica.imtech.res.in
- Re: [AMBER] Porcupine_Plots_Script Jason Swails
- Re: [AMBER] Solvation in Amber Jason Swails
- Re: [AMBER] sander.MPI Fabian Glaser
- Re: [AMBER] sander.MPI Jason Swails
- Re: [AMBER] Compiler for Amber12 with GTX680 Jason Swails
- Re: [AMBER] sander.MPI Fabian Glaser
- Re: [AMBER] sander.MPI Fabian Glaser
- Re: [AMBER] Compiler for Amber12 with GTX680 kurisaki
- Re: [AMBER] sander.MPI Jason Swails
- Re: [AMBER] R.E.D calculation cannot be used for CHARMM FF? FyD
- [AMBER] is there a difference between the GTX 680 GPU's Jonathan Gough
- Re: [AMBER] is there a difference between the GTX 680 GPU's Jason Swails
- Re: [AMBER] MMPBSA.py - problem with complex.prmtop -rdparm: a parameter array overflowed colvin
- Re: [AMBER] is there a difference between the GTX 680 GPU's Jonathan Gough
- Re: [AMBER] is there a difference between the GTX 680 GPU's Marek Maly
- Re: [AMBER] is there a difference between the GTX 680 GPU's Jason Swails
- Re: [AMBER] is there a difference between the GTX 680 GPU's Marek Maly
- Re: [AMBER] is there a difference between the GTX 680 GPU's Ross Walker
- Re: [AMBER] is there a difference between the GTX 680 GPU's Jonathan Gough
- Re: [AMBER] is there a difference between the GTX 680 GPU's Marek Maly
- Re: [AMBER] is there a difference between the GTX 680 GPU's Ross Walker
- Re: [AMBER] is there a difference between the GTX 680 GPU's Jonathan Gough
- [AMBER] The differences of MMPBSA calculations between AT1.5 and AT12, especially in PBSA solvation model. 徐见容
- [AMBER] The differences of MMPBSA calculations between AT1.5 andAT12, especially in PBSA solvation model. 徐见容
- Re: [AMBER] The differences of MMPBSA calculations between AT1.5 and AT12, especially in PBSA solvation model. Ray Luo
- [AMBER] GPU compile TEST does not work. kurisaki
- [AMBER] 回复: Re: The differences of MMPBSA calculations between AT1.5and AT12, especially in PBSA solvation model. 徐见容
- Re: [AMBER] GPU compile TEST does not work. kurisaki
Friday, 30 November 2012
- Re: [AMBER] GPU and ntpr Fernando Martín García
- Re: [AMBER] Solvation in Amber Ravi Tripathi
- Re: [AMBER] GPU compile TEST does not work. Jason Swails
- Re: [AMBER] GPU compile TEST does not work. kurisaki
- [AMBER] imaging issues during RMSF Sangeetha B
- Re: [AMBER] Porcupine_Plots_Script monica.imtech.res.in
- Re: [AMBER] Porcupine_Plots_Script Jason Swails
- Re: [AMBER] 回复: Re: The differences of MMPBSA calculations between AT1.5and AT12, especially in PBSA solvation model. Ray Luo, Ph.D.
- [AMBER] problem in loading pdb in xleap Shubhadip Das

Last message date: Fri Nov 30 2012 - 23:30:03 PST
Archived on: Fri Nov 22 2024 - 05:54:37 PST

Amber Archive Nov 2012 by date