Amber Archive Sep 2011: by date

Wednesday, 31 August 2011
- Re: [AMBER] problem in installing xleap sonali dhindwal
- [AMBER] cpptraj-segmentation fault Praapti Jayaswal
- Re: [AMBER] problem in installing xleap Ismail, Mohd F.
Thursday, 1 September 2011
- Re: [AMBER] problem in installing xleap David A Case
- [AMBER] CCA-Phe terminal using Antechamber Sindrila Dutta banik
- Re: [AMBER] CCA-Phe terminal using Antechamber David A Case
- Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system Keith Yarem
- Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system Keith Yarem
- Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system InSuk Joung
- Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system Jason Swails
- [AMBER] PTRAJ strange behavior peker milas
- [AMBER] Energy change KIRTANA S
- [AMBER] solvateBox Ismail, Mohd F.
- Re: [AMBER] solvateBox Jason Swails
- Re: [AMBER] solvateBox Jason Swails
- Re: [AMBER] solvateBox Ismail, Mohd F.
- Re: [AMBER] solvateBox Jason Swails
- Re: [AMBER] solvateBox Ismail, Mohd F.
- Re: [AMBER] solvateBox Jason Swails
- Re: [AMBER] Energy change steinbrt.rci.rutgers.edu
Friday, 2 September 2011
- [AMBER] Non standard residue parameterization madhumita das
- Re: [AMBER] problem in installing xleap sonali dhindwal
- [AMBER] writing box info to pdb file extracted from an mdcrd trajectory CHAMI F.
- Re: [AMBER] solvateBox Ismail, Mohd F.
- Re: [AMBER] problem in installing xleap Ismail, Mohd F.
- Re: [AMBER] problem in installing xleap peker milas
- [AMBER] Energy of solute molecule Mattei, Alessandra
- Re: [AMBER] Energy of solute molecule Jason Swails
- Re: [AMBER] Energy change KIRTANA S
- Re: [AMBER] Energy change Jason Swails
- [AMBER] Run Amber on a system with multiple GPUs peter.stauffert.boehringer-ingelheim.com
- [AMBER] some questions on GAFF su He
- Re: [AMBER] some questions on GAFF Chirag Vora
- Re: [AMBER] some questions on GAFF su He
- Re: [AMBER] cpptraj-segmentation fault Daniel Roe
- Re: [AMBER] Run Amber on a system with multiple GPUs Sasha Buzko
- [AMBER] SHAKE error help tsurma.umich.edu
- Re: [AMBER] Non standard residue parameterization Jason Swails
- Re: [AMBER] SHAKE error help Bill Ross
Saturday, 3 September 2011
- [AMBER] antechamber error Soonmin Jang
- Re: [AMBER] problem in installing xleap sonali dhindwal
- [AMBER] MM_PBSA triple trajectory approch Sangita Kachhap
- Re: [AMBER] MM_PBSA triple trajectory approch Bill Miller III
- Re: [AMBER] SHAKE error help case
- Re: [AMBER] problem in installing xleap case
- Re: [AMBER] antechamber error case
- Re: [AMBER] MM_PBSA triple trajectory approch Sangita Kachhap
- Re: [AMBER] MM_PBSA triple trajectory approch Bill Miller III
- Re: [AMBER] problem in installing xleap sonali dhindwal
- Re: [AMBER] MM_PBSA triple trajectory approch Jason Swails
- Re: [AMBER] antechamber error Jason Swails
- Re: [AMBER] SHAKE error help tsurma.umich.edu
- Re: [AMBER] SHAKE error help case
- Re: [AMBER] SHAKE error help tsurma.umich.edu
- [AMBER] Amber tools KIRTANA S
- Re: [AMBER] Amber tools manikanthan bhavaraju
- Re: [AMBER] Amber tools Jason Swails
Sunday, 4 September 2011
- Re: [AMBER] MM_PBSA triple trajectory approch Sangita Kachhap
Monday, 5 September 2011
- [AMBER] NAB Module compilation error cpp failed Rajesh Raju
- [AMBER] NAB Module compilation error cpp failed Rajesh Raju
- [AMBER] Energy kirtana S
- Re: [AMBER] Energy Bill Miller III
- Re: [AMBER] SHAKE error help case
Sunday, 4 September 2011
- [AMBER] MMPBSA Ala scan error Jesper Sørensen
Monday, 5 September 2011
- Re: [AMBER] Energy kirtana S
- Re: [AMBER] MMPBSA Ala scan error Bill Miller III
Sunday, 4 September 2011
- Re: [AMBER] Energy change kirtana S
- [AMBER] replace unit in leap tsurma.umich.edu
- [AMBER] replace unit in leap tsurma.umich.edu
Monday, 5 September 2011
- Re: [AMBER] SHAKE error help tsurma.umich.edu
- Re: [AMBER] Energy change manikanthan bhavaraju
- Re: [AMBER] Energy change Bill Miller III
- [AMBER] Sleap : amoeba and gaff Guenegou, Guillaume [JRDFR]
- Re: [AMBER] Sleap : amoeba and gaff Wei Zhang
- Re: [AMBER] Non standard residue parameterization madhumita das
- [AMBER] problem while using Antechamber sonali dhindwal
- Re: [AMBER] Energy of solute molecule Ignacio J. General
- Re: [AMBER] NAB Module compilation error cpp failed Jason Swails
- Re: [AMBER] Energy of solute molecule Jason Swails
Sunday, 4 September 2011
- Re: [AMBER] cpptraj-segmentation fault Praapti Jayaswal
- Re: [AMBER] Amber tools kirtana S
Monday, 5 September 2011
- Re: [AMBER] how to fill in missing parameters in tleap? Yun Shi
- Re: [AMBER] replace unit in leap case
- Re: [AMBER] Amber tools case
- Re: [AMBER] problem while using Antechamber case
- Re: [AMBER] Non standard residue parameterization case
- Re: [AMBER] cpptraj-segmentation fault Daniel Roe
- [AMBER] velocity modification in PMEMD, CUDA version Chen, Changjun
- Re: [AMBER] Non standard residue parameterization Bill Ross
- [AMBER] antechamber am1bcc stops with no error message Danny Xu
- Re: [AMBER] problem while using Antechamber sonali dhindwal
- Re: [AMBER] Non standard residue parameterization madhumita das
- Re: [AMBER] Non standard residue parameterization madhumita das
- [AMBER] Creating prmtop and inpcrd files Chidambar Kulkarni
Tuesday, 6 September 2011
- [AMBER] Is there any module which can calculate interaction energy, as ANAL in Amber 8? wrong string
- Re: [AMBER] MMPBSA Ala scan error Jesper Sørensen
- [AMBER] problem with MM-PBSA Maryam Hamzehee
- Re: [AMBER] how to fill in missing parameters in tleap? Astrid Maaß
- [AMBER] hydrogen boding and PBC Vijay Manickam Achari
- Re: [AMBER] MMPBSA Ala scan error Bill Miller III
- Re: [AMBER] problem with MM-PBSA Bill Miller III
- [AMBER] Amber for GPUs Baker D.J.
- Re: [AMBER] Non standard residue parameterization case
- Re: [AMBER] Creating prmtop and inpcrd files case
- Re: [AMBER] Is there any module which can calculate interaction energy, as ANAL in Amber 8? case
- Re: [AMBER] Creating prmtop and inpcrd files Chidambar Kulkarni
- [AMBER] How to Generate Structure with Correct Valence for an Unnatural Amino Acid in Position 1 George A. Khoury
- Re: [AMBER] Amber tools manikanthan bhavaraju
- Re: [AMBER] antechamber error Soonmin Jang
- [AMBER] How to use WHAM to analysis Replica Exchange Simulations Catein Catherine
- Re: [AMBER] How to Generate Structure with Correct Valence for an Unnatural Amino Acid in Position 1 FyD
- Re: [AMBER] how to fill in missing parameters in tleap? Yun Shi
- Re: [AMBER] replace unit in leap tsurma.umich.edu
- Re: [AMBER] SHAKE error help tsurma.umich.edu
- Re: [AMBER] Creating prmtop and inpcrd files Jason Swails
- Re: [AMBER] How to use WHAM to analysis Replica Exchange Simulations Brian Radak
- [AMBER] mbondi3 Peter Varnai
- Re: [AMBER] how to fill in missing parameters in tleap? Yun Shi
- [AMBER] moment of inertia John S
- Re: [AMBER] mbondi3 Carlos Simmerling
- Re: [AMBER] moment of inertia peker milas
- Re: [AMBER] MMPBSA Ala scan error Jesper Sørensen
- [AMBER] umbrella sampling with amber10 Qian Wang
- Re: [AMBER] How to use WHAM to analysis Replica Exchange Simulations Daniel Sindhikara
- Re: [AMBER] How to use WHAM to analysis Replica Exchange Simulations Andrew Jewett
- [AMBER] results from independent simulations Wu Xu
- Re: [AMBER] velocity modification in PMEMD, CUDA version Ross Walker
- Re: [AMBER] velocity modification in PMEMD, CUDA version Chen, Changjun
- [AMBER] Some question regarding force field for periodic system jun kit
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi
- Re: [AMBER] velocity modification in PMEMD, CUDA version Jason Swails
- Re: [AMBER] mbondi3 Jason Swails
Wednesday, 7 September 2011
- [AMBER] Minimum distance RANAJIT SHINDE
- [AMBER] Residence time aiswarya pawar
- Re: [AMBER] how to fill in missing parameters in tleap? Astrid Maaß
- [AMBER] Restrain of atoms during MD simulation Sindrila Dutta banik
- Re: [AMBER] results from independent simulations Jason Swails
- Re: [AMBER] results from independent simulations Simon Becker
- Re: [AMBER] Residence time Carlos Simmerling
- Re: [AMBER] Some question regarding force field for periodic system Carlos Simmerling
- Re: [AMBER] Residence time aiswarya pawar
- Re: [AMBER] writing box info to pdb file extracted from an mdcrd trajectory Mark Williamson
- Re: [AMBER] results from independent simulations Wu Xu
- Re: [AMBER] results from independent simulations Jason Swails
- Re: [AMBER] writing box info to pdb file extracted from an mdcrd trajectory CHAMI F.
- [AMBER] libmkl_ia32.a missing from MKL em64t Aaron Greenwood
- Re: [AMBER] mbondi3 Peter Varnai
- Re: [AMBER] problem with MM-PBSA Maryam Hamzehee
- [AMBER] Proble related to correlation function Sindrila Dutta banik
- Re: [AMBER] problem with MM-PBSA Bill Miller III
- [AMBER] Format conversion aiswarya.pawar.gmail.com
- Re: [AMBER] Proble related to correlation function InSuk Joung
- Re: [AMBER] Residence time Carlos Simmerling
- Re: [AMBER] How to Generate Structure with Correct Valence for an Unnatural Amino Acid in Position 1 case
- Re: [AMBER] mbondi3 Jason Swails
- Re: [AMBER] libmkl_ia32.a missing from MKL em64t case
- [AMBER] false positive on too large QM region? Brian Radak
- Re: [AMBER] false positive on too large QM region? Gustavo Seabra
- Re: [AMBER] results from independent simulations Daniel Sindhikara
Thursday, 8 September 2011
- [AMBER] MPI version of MMPBSA Siavoush Dastmalchi
Wednesday, 7 September 2011
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD
Thursday, 8 September 2011
- Re: [AMBER] MPI version of MMPBSA Siavoush Dastmalchi
- [AMBER] Hydrogen Bonding Sara Ahmadi
- [AMBER] Parameters for Boron containing molecules gal.fradin.live.biu.ac.il
- Re: [AMBER] results from independent simulations Wu Xu
- [AMBER] Fwd: false positive on too large QM region? Brian Radak
- Re: [AMBER] MPI version of MMPBSA Jason Swails
- Re: [AMBER] Parameters for Boron containing molecules Jason Swails
- [AMBER] Water density/potential visualization Abhishek Mukhopadhyay
- [AMBER] turning on 1-2 and 1-3 interactions Steven Burger
- Re: [AMBER] turning on 1-2 and 1-3 interactions Bill Ross
- Re: [AMBER] Water density/potential visualization Ozen, Aysegul
- Re: [AMBER] Fwd: false positive on too large QM region? Gustavo Seabra
- Re: [AMBER] Fwd: false positive on too large QM region? Brian Radak
- Re: [AMBER] turning on 1-2 and 1-3 interactions Jason Swails
- Re: [AMBER] Fwd: false positive on too large QM region? Ross Walker
- [AMBER] intermolecular interaction su He
- Re: [AMBER] Fwd: false positive on too large QM region? Gustavo Seabra
- Re: [AMBER] Fwd: false positive on too large QM region? Brian Radak
- Re: [AMBER] how to fill in missing parameters in tleap? Yun Shi
- Re: [AMBER] Fwd: false positive on too large QM region? Qiantao Wang
- Re: [AMBER] intermolecular interaction Jason Swails
- Re: [AMBER] PBS script Bruno Rodrigues
- Re: [AMBER] PBS script Bruno Rodrigues
- Re: [AMBER] how to fill in missing parameters in tleap? Astrid Maaß
- Re: [AMBER] How to interpret GLYCAM prep file? Yun Shi
- Re: [AMBER] how to fill in missing parameters in tleap? Yun Shi
- Re: [AMBER] Water density/potential visualization Daniel Sindhikara
Friday, 9 September 2011
- Re: [AMBER] velocity modification in PMEMD, CUDA version Chen, Changjun
- Re: [AMBER] how to fill in missing parameters in tleap? Astrid Maaß
- [AMBER] SMD: restraints on the pulled apart interacting proteins Sergey Samsonov
- Re: [AMBER] How to interpret GLYCAM prep file? Lachele Foley (Lists)
- Re: [AMBER] intermolecular interaction su He
- Re: [AMBER] SHAKE error help tsurma.umich.edu
- Re: [AMBER] SHAKE error help case
- Re: [AMBER] how to fill in missing parameters in tleap? Yun Shi
- [AMBER] problems with prmtops & MMGBSA Irene Newhouse
- Re: [AMBER] problems with prmtops & MMGBSA Romelia Salomon
- Re: [AMBER] problems with prmtops & MMGBSA Jason Swails
Saturday, 10 September 2011
- [AMBER] the result of pseudorotation angle clwg
- Re: [AMBER] the result of pseudorotation angle case
- Re: [AMBER] SHAKE error help tsurma.umich.edu
- Re: [AMBER] SHAKE error help case
- Re: [AMBER] Parameters for Boron containing molecules gal.fradin.live.biu.ac.il
Sunday, 11 September 2011
- Re: [AMBER] antechamber am1bcc stops with no error message case
- [AMBER] residue list kirtana S
- Re: [AMBER] residue list Jason Swails
- [AMBER] Why cut=999.9 was used in Tutorial A7 for REMD calculation? Catein Catherine
- [AMBER] vlimit exeeding problem Aparna P
- Re: [AMBER] cpptraj-segmentation fault Praapti Jayaswal
Monday, 12 September 2011
- [AMBER] QM-MM atoms input Shruti Koulgi
- Re: [AMBER] QM-MM atoms input Shruti Koulgi
- [AMBER] Aromatic bonds disappear during sdf creation with sleap Guenegou, Guillaume [JRDFR]
- Re: [AMBER] QM-MM atoms input Marc van der Kamp
- Re: [AMBER] cpptraj-segmentation fault Daniel Roe
- Re: [AMBER] Why cut=999.9 was used in Tutorial A7 for REMD calculation? Jason Swails
- Re: [AMBER] Aromatic bonds disappear during sdf creation with sleap Jason Swails
- Re: [AMBER] QM-MM atoms input Jason Swails
- Re: [AMBER] how to fill in missing parameters in tleap? Astrid Maaß
- [AMBER] ptraj clustering George Tzotzos
- Re: [AMBER] vlimit exeeding problem manikanthan bhavaraju
- [AMBER] pbsa kirtana S
- Re: [AMBER] pbsa Ray Luo, Ph.D.
- Re: [AMBER] pbsa kirtana S
- [AMBER] Amber 11 configure error with openmpi Lianhu Wei
- Re: [AMBER] Amber 11 configure error with openmpi Jason Swails
- [AMBER] Fwd: pbsa Ray Luo, Ph.D.
- Re: [AMBER] Why cut=999.9 was used in Tutorial A7 for REMD calculation? Catein Catherine
- Re: [AMBER] pbsa kirtana S
- Re: [AMBER] ptraj clustering Thomas Cheatham
- Re: [AMBER] pbsa Jason Swails
- Re: [AMBER] ptraj clustering George Tzotzos
- Re: [AMBER] Amber 11 configure error with openmpi David A Case
- Re: [AMBER] Amber 11 configure error with openmpi Jason Swails
- Re: [AMBER] ptraj clustering Thomas Cheatham III
- [AMBER] Residue transformation Fabrício Bracht
- Re: [AMBER] pbsa kirtana S
- [AMBER] error using saveamberparm on pdb with nonstandard residues Darren Jindal
- Re: [AMBER] Residue transformation Bruno Rodrigues
- Re: [AMBER] Residue transformation M. L. Dodson
- Re: [AMBER] cpptraj-segmentation fault Praapti Jayaswal
- Re: [AMBER] vlimit exeeding problem Aparna P
- [AMBER] Parameters from Jaguar output Kshatresh Dutta Dubey
- Re: [AMBER] vlimit exeeding problem Ross Walker
- Re: [AMBER] vlimit exeeding problem Aparna P
- Re: [AMBER] vlimit exeeding problem Ross Walker
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi
Tuesday, 13 September 2011
- [AMBER] visualization of secstruc with e.g. gnuplot Nadine Utz
- Re: [AMBER] vlimit exeeding problem Aparna P
- Re: [AMBER] error using saveamberparm on pdb with nonstandard residues David A Case
- [AMBER] Problem with mmpbsa Devlina Chakravarty
- [AMBER] undefined reference Lars Skjærven
- Re: [AMBER] Problem with mmpbsa Bill Miller III
- Re: [AMBER] visualization of secstruc with e.g. gnuplot steinbrt.rci.rutgers.edu
- Re: [AMBER] Problem with mmpbsa dhilip kumar ramalingam
- Re: [AMBER] undefined reference David A Case
- [AMBER] Fwd: amber Gustavo Seabra
- Re: [AMBER] undefined reference Lars Skjærven
- [AMBER] Global Minimum in Simulated Annealing using SANDER Julian Zachmann
- Re: [AMBER] Fwd: amber steinbrt.rci.rutgers.edu
- Re: [AMBER] Global Minimum in Simulated Annealing using SANDER steinbrt.rci.rutgers.edu
- [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? dhilip kumar ramalingam
- Re: [AMBER] Amber 11 configure error with openmpi Lianhu Wei
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Ross Walker
- Re: [AMBER] undefined reference David A Case
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Ross Walker
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly
- [AMBER] October 20 deadline for ACS COMP division awards for junior faculty and graduate students Carlos Simmerling
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? peter.stauffert.boehringer-ingelheim.com
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Gould, Ian R
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Scott Le Grand
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly
- Re: [AMBER] visualization of secstruc with e.g. gnuplot Anselm Horn
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Ross Walker
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Ross Walker
- Re: [AMBER] pbsa Ray Luo, Ph.D.
- Re: [AMBER] Fwd: false positive on too large QM region? Brian Radak
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly
- [AMBER] Compiling Amber11 on Blue Gene/P Garo Garabedyan
- [AMBER] Run amber on Cluster Lianhu Wei
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Scott Le Grand
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly
- Re: [AMBER] Compiling Amber11 on Blue Gene/P Jed W Pitera
- Re: [AMBER] Run amber on Cluster Jason Swails
- [AMBER] MMGBSA binding free energy shows large change with saltcon parameter, but not for MMPBSA binding free energy value Rajesh Raju
- Re: [AMBER] MMGBSA binding free energy shows large change with saltcon parameter, but not for MMPBSA binding free energy value David Case
- [AMBER] TI and MM-GBSA results manikanthan bhavaraju
- Re: [AMBER] MMGBSA binding free energy shows large change with saltcon parameter, but not for MMPBSA binding free energy value Jason Swails
- Re: [AMBER] MMGBSA binding free energy shows large change with saltcon parameter, but not for MMPBSA binding free energy value Rajesh Raju
- Re: [AMBER] MMGBSA binding free energy shows large change with saltcon parameter, but not for MMPBSA binding free energy value Jason Swails
- Re: [AMBER] Compiling Amber11 on Blue Gene/P Garo Garabedyan
Wednesday, 14 September 2011
- [AMBER] AMBER Shesh Nath
- [AMBER] Error in computing entropy! problem with number of frames in NMODE hongphuc nguyen
- Re: [AMBER] How to avoid Zn parametrization? Andrew Voronkov
- [AMBER] Running amber v11 over multiple gpus/nodes Baker D.J.
- Re: [AMBER] Error in computing entropy! problem with number of frames in NMODE Bill Miller III
- Re: [AMBER] Running amber v11 over multiple gpus/nodes peter.stauffert.boehringer-ingelheim.com
- [AMBER] hello Linda catherine
- [AMBER] pulling DNA amir abbasi
- Re: [AMBER] hello steinbrt.rci.rutgers.edu
- [AMBER] How to extract time angle, time, Energy from for MBAR analysis? Catein Catherine
- [AMBER] Need Help! (TMD - NSCM - IWRAP reg!) Fredrick Devadoss
- Re: [AMBER] How to extract time angle, time, Energy from for MBAR analysis? Brian Radak
- Re: [AMBER] Need Help! (TMD - NSCM - IWRAP reg!) Jason Swails
- Re: [AMBER] Run amber on Cluster Lianhu Wei
- [AMBER] energy kirtana S
- Re: [AMBER] Running amber v11 over multiple gpus/nodes Baker D.J.
- Re: [AMBER] SHAKE error help tsurma.umich.edu
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Jodi Ann Hadden
- Re: [AMBER] energy Bill Miller III
- Re: [AMBER] energy kirtana S
- [AMBER] attachment for my previous mail Fredrick Devadoss
- Re: [AMBER] Run amber on Cluster Ross Walker
- Re: [AMBER] AMBER Jason Swails
- Re: [AMBER] TI and MM-GBSA results Ray Luo, Ph.D.
- Re: [AMBER] TI and MM-GBSA results manikanthan bhavaraju
- Re: [AMBER] TI and MM-GBSA results Jason Swails
- [AMBER] Can we extract information from out file for MBAR analysis? Catein Catherine
- Re: [AMBER] Running amber v11 over multiple gpus/nodes Ross Walker
- Re: [AMBER] Run amber on Cluster Lianhu Wei
- Re: [AMBER] Can we extract information from out file for MBAR analysis? Brian Radak
- Re: [AMBER] Compiling Amber11 on Blue Gene/P Garo Garabedyan
- Re: [AMBER] Can we extract information from out file for MBAR analysis for PMF analysis? Catein Catherine
- [AMBER] benchmarking Tesla S2050 1U system Sidney Elmer
- Re: [AMBER] Compiling Amber11 on Blue Gene/P Ross Walker
- Re: [AMBER] Can we extract information from out file for MBAR analysis for PMF analysis? Brian Radak
- Re: [AMBER] benchmarking Tesla S2050 1U system Ross Walker
- [AMBER] Bond command using xleap or tleap Fabrício Bracht
- [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Yun Shi
- Re: [AMBER] benchmarking Tesla S2050 1U system Sidney Elmer
- Re: [AMBER] How to interpret GLYCAM prep file? Yun Shi
Tuesday, 13 September 2011
- [AMBER] inpcrd file fatahiya
Wednesday, 14 September 2011
- Re: [AMBER] inpcrd file Emmanuel Baribefe Naziga
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly
- [AMBER] Electrpostatic interaction vs Coulombic interaction Rilei Yu
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Scott Le Grand
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly
- Re: [AMBER] Electrpostatic interaction vs Coulombic interaction David Case
- [AMBER] MMPBSA.py 3DRISM error Jesper Soerensen
- Re: [AMBER] MMPBSA.py 3DRISM error Jason Swails
- Re: [AMBER] MMPBSA.py 3DRISM error Jason Swails
- [AMBER] help ! zinc parameters Kk Zhu
- [AMBER] Print Dipole Moment in Centriod MD Wei Lin
- [AMBER] tleap command "set default Dielectric constant" not valid? Yongmei Wang (ywang)
- Re: [AMBER] how to fill in missing parameters in tleap? Yun Shi
- Re: [AMBER] Electrpostatic interaction vs Coulombic interaction Rilei Yu
Thursday, 15 September 2011
- Re: [AMBER] How to avoid Zn parametrization? FyD
- Re: [AMBER] help ! zinc parameters FyD
- Re: [AMBER] How to interpret GLYCAM prep file? FyD
- [AMBER] AMOEBA potentials Neha Gandhi
- [AMBER] MMPBSA.py energy decomposition inconsistencies Antje Wolf
- [AMBER] X-PLOR formatted .psf in CHAMBER Marc van der Kamp
- Re: [AMBER] X-PLOR formatted .psf in CHAMBER Thomas Cheatham
- [AMBER] radial distribution function Massimiliano Porrini
- Re: [AMBER] cpptraj-segmentation fault Daniel Roe
- Re: [AMBER] X-PLOR formatted .psf in CHAMBER Marc van der Kamp
- Re: [AMBER] X-PLOR formatted .psf in CHAMBER Marc van der Kamp
- [AMBER] Dihedral parameters Chidambar Kulkarni
- Re: [AMBER] MMPBSA.py energy decomposition inconsistencies Jason Swails
- Re: [AMBER] How to interpret GLYCAM prep file? Lachele Foley (Lists)
- Re: [AMBER] Dihedral parameters Jason Swails
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Lachele Foley (Lists)
- Re: [AMBER] MMPBSA.py energy decomposition inconsistencies Antje Wolf
- Re: [AMBER] Dihedral parameters Chidambar Kulkarni
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Yun Shi
- Re: [AMBER] MMPBSA.py energy decomposition inconsistencies Jason Swails
- Re: [AMBER] Dihedral parameters Jason Swails
- [AMBER] Effect of SLI for Amber GPU calculations - AMD Bulldozers ? Marek Maly
- Re: [AMBER] Effect of SLI for Amber GPU calculations - AMD Bulldozers ? Ross Walker
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Lachele Foley (Lists)
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Yun Shi
- Re: [AMBER] Effect of SLI for Amber GPU calculations - AMD Bulldozers ? Marek Maly
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Lachele Foley (Lists)
- Re: [AMBER] Bond command using xleap or tleap David A Case
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Matthew Tessier
- Re: [AMBER] tleap command "set default Dielectric constant" not valid? David A Case
- Re: [AMBER] Effect of SLI for Amber GPU calculations - AMD Bulldozers ? Scott Le Grand
- Re: [AMBER] AMOEBA potentials David A Case
- Re: [AMBER] tleap command "set default Dielectric constant" not valid? Yongmei Wang (ywang)
- Re: [AMBER] Effect of SLI for Amber GPU calculations - AMD Bulldozers ? Marek Maly
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Lachele Foley (Lists)
- Re: [AMBER] Dihedral parameters Dean Cuebas
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Yun Shi
- Re: [AMBER] benchmarking Tesla S2050 1U system Sidney Elmer
- Re: [AMBER] Bond command using xleap or tleap Sidney Elmer
- Re: [AMBER] Bond command using xleap or tleap Bill Ross
- Re: [AMBER] Error in computing entropy! problem with number of frames in NMODE hongphuc nguyen
- Re: [AMBER] cpptraj-segmentation fault Praapti Jayaswal
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi
- Re: [AMBER] cpptraj-segmentation fault Daniel Roe
- Re: [AMBER] Dihedral parameters Chidambar Kulkarni
- [AMBER] help ! zinc parameters Kk Zhu
- Re: [AMBER] MMPBSA.py energy decomposition inconsistencies Antje Wolf
Friday, 16 September 2011
- Re: [AMBER] Running amber v11 over multiple gpus/nodes Baker D.J.
- [AMBER] Grid Aparna P
- [AMBER] FATAL: allocation failure in vector(), please help me to fix that problem hongphuc nguyen
- Re: [AMBER] Grid Thomas Cheatham
- [AMBER] Problems with parsing .PSF files by ptraj Marc van der Kamp
- [AMBER] Initial plateau of the radial distribution function Massimiliano Porrini
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD
- Re: [AMBER] FATAL: allocation failure in vector(), please help me to fix that problem Bill Miller III
- [AMBER] ptraj Linda catherine
- Re: [AMBER] radial distribution function Thomas Cheatham
- Re: [AMBER] ptraj Thomas Cheatham
- [AMBER] How to start with aiswarya.pawar.gmail.com
- Re: [AMBER] MMPBSA.py energy decomposition inconsistencies Jason Swails
- [AMBER] help!!zinc parameters zhukk
- Re: [AMBER] help!!zinc parameters steinbrt.rci.rutgers.edu
- Re: [AMBER] help ! zinc parameters Bill Ross
- Re: [AMBER] help ! zinc parameters Oteri Francesco
- Re: [AMBER] MMPBSA.py energy decomposition inconsistencies Antje Wolf
- Re: [AMBER] help ! zinc parameters Ross Walker
- Re: [AMBER] Bond command using xleap or tleap Sidney Elmer
- Re: [AMBER] Running amber v11 over multiple gpus/nodes Ross Walker
- Re: [AMBER] MMPBSA.py energy decomposition inconsistencies Jason Swails
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Yun Shi
- [AMBER] unsubscribe Yongmei Wang (ywang)
- Re: [AMBER] How to start with Jason Swails
- [AMBER] Radial distribution kirtana S
- [AMBER] Serial Version of libFpbsa.a Aaron Greenwood
- Re: [AMBER] Serial Version of libFpbsa.a Ross Walker
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Jodi Ann Hadden
- [AMBER] AMBER expense David Condon
- [AMBER] How to mutate nucleobases Rajesh Raju
- Re: [AMBER] Bond command using xleap or tleap Bill Ross
- [AMBER] Difference between serial and parallel MMPBSA Osman, Roman
- Re: [AMBER] AMBER expense steinbrt.rci.rutgers.edu
- Re: [AMBER] AMBER expense David Condon
- Re: [AMBER] Difference between serial and parallel MMPBSA Ray Luo, Ph.D.
- [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights Himanshu Joshi
- Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights Himanshu Joshi
Saturday, 17 September 2011
- Re: [AMBER] Bond command using xleap or tleap case
- Re: [AMBER] Difference between serial and parallel MMPBSA Osman, Roman
- Re: [AMBER] How to mutate nucleobases Sangita Kachhap
- Re: [AMBER] How to mutate nucleobases Rajesh Raju
- [AMBER] Dihedral Rotation David Condon
- [AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis.. Rajesh Raju
- Re: [AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis.. Bill Miller III
- Re: [AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis.. Rajesh Raju
- [AMBER] scaling factors in carbohydrate-protein interaction Yun Shi
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly
- Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights Ross Walker
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Ross Walker
- Re: [AMBER] scaling factors in carbohydrate-protein interaction Lachele Foley (Lists)
- Re: [AMBER] scaling factors in carbohydrate-protein interaction FyD
Sunday, 18 September 2011
- Re: [AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis.. Jason Swails
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly
- Re: [AMBER] radial distribution function Massimiliano Porrini
- Re: [AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis.. Rajesh Raju
- Re: [AMBER] scaling factors in carbohydrate-protein interaction Lachele Foley (Lists)
- Re: [AMBER] scaling factors in carbohydrate-protein interaction Ross Walker
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi
- [AMBER] rst or mdcrd file to view the structures? Chinh Su Tran To
- [AMBER] Glycam06g and ff99SB cause the difference of DIHED (not attributed to the scaling factor) d944286.oz.nthu.edu.tw
- Re: [AMBER] Glycam06g and ff99SB cause the difference of DIHED (not attributed to the scaling factor) mish
Monday, 19 September 2011
- Re: [AMBER] rst or mdcrd file to view the structures? steinbrt.rci.rutgers.edu
- Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights Himanshu Joshi
- [AMBER] ptraj: problem with distance and multi-atom masks Marc van der Kamp
- Re: [AMBER] rst or mdcrd file to view the structures? Chinh Su Tran To
- Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights Himanshu Joshi
- Re: [AMBER] rst or mdcrd file to view the structures? steinbrt.rci.rutgers.edu
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD
- Re: [AMBER] help!!zinc parameters zhukk
- Re: [AMBER] help ! zinc parameters zhukk
- Re: [AMBER] help ! zinc parameters zhukk
- Re: [AMBER] help ! zinc parameters zhukk
- [AMBER] help! zinc parameters Kk Zhu
- Re: [AMBER] Glycam06g and ff99SB cause the difference of DIHED (not attributed to the scaling factor) Lachele Foley (Lists)
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Matthew Tessier
- Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights Ross Walker
- Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights Ross Walker
- Re: [AMBER] ptraj: problem with distance and multi-atom masks Daniel Roe
- [AMBER] force field of molecular crystals jun kit
- [AMBER] Unit of the partial charge as given in the topology file Sindrila Dutta banik
- Re: [AMBER] Unit of the partial charge as given in the topology file Jason Swails
- Re: [AMBER] force field of molecular crystals David A Case
- Re: [AMBER] force field of molecular crystals jun kit
- Re: [AMBER] help ! zinc parameters Bill Ross
- [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Kenneth Tussey
- [AMBER] Self-Diffusion coefficient Bruno Rodrigues
- [AMBER] How to build the surface of crystalline cellulose? bin wang
- Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Jason Swails
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Yun Shi
- Re: [AMBER] Self-Diffusion coefficient Thomas Cheatham III
- Re: [AMBER] radial distribution function Thomas Cheatham III
- Re: [AMBER] force field of molecular crystals case
- Re: [AMBER] Dihedral Rotation Niel Henriksen
- Re: [AMBER] rst or mdcrd file to view the structures? Chinh Su Tran To
- [AMBER] How to build the surface of crystalline cellulose? bin wang
- Re: [AMBER] rst or mdcrd file to view the structures? Bill Ross
- [AMBER] new residue parameters transfer Yao Yao
- Re: [AMBER] rst or mdcrd file to view the structures? Chinh Su Tran To
- Re: [AMBER] cpptraj-segmentation fault Praapti Jayaswal
- [AMBER] charges on ligand kamlesh sahu
Tuesday, 20 September 2011
- Re: [AMBER] rst or mdcrd file to view the structures? steinbrt.rci.rutgers.edu
- Re: [AMBER] charges on ligand steinbrt.rci.rutgers.edu
- Re: [AMBER] scaling factors in carbohydrate-protein interaction FyD
- Re: [AMBER] rst or mdcrd file to view the structures? Chinh Su Tran To
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage FyD
- Re: [AMBER] help ! zinc parameters FyD
- Re: [AMBER] ptraj: problem with distance and multi-atom masks Marc van der Kamp
- [AMBER] Automatic creation of charge and radius files for Delphi Jan-Philip Gehrcke
- [AMBER] topology and coordinate files madhumita das
- Re: [AMBER] cpptraj-segmentation fault Daniel Roe
- Re: [AMBER] ptraj: problem with distance and multi-atom masks Daniel Roe
- Re: [AMBER] new residue parameters transfer David A Case
- Re: [AMBER] new residue parameters transfer Yong Duan
- [AMBER] Instantaneous temperature in TI simulation Brian Radak
- Re: [AMBER] ptraj: problem with distance and multi-atom masks Marc van der Kamp
- Re: [AMBER] Instantaneous temperature in TI simulation David A Case
- Re: [AMBER] Instantaneous temperature in TI simulation Brian Radak
- Re: [AMBER] Glycam06g and ff99SB cause the difference of DIHED (notattributed to the scaling factor) d944286.oz.nthu.edu.tw
- [AMBER] tx/LEaP numlock. Ross Walker
- Re: [AMBER] rst or mdcrd file to view the structures? Bill Ross
- Re: [AMBER] Self-Diffusion coefficient Bruno Rodrigues
- Re: [AMBER] Instantaneous temperature in TI simulation Brian Radak
- [AMBER] problem with TI calculations Victor Ma
- Re: [AMBER] Instantaneous temperature in TI simulation Qiantao Wang
- Re: [AMBER] Instantaneous temperature in TI simulation Jason Swails
- Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Kenneth Tussey
- Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Jason Swails
- Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Kenneth Tussey
- Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Jason Swails
- [AMBER] Xleap Installation Yao Yao
- Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Robert Konecny
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi
- Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Jason Swails
- Re: [AMBER] rst or mdcrd file to view the structures? Chinh Su Tran To
- [AMBER] Help needed for Amber SCC-DFTB code 杨立江
- [AMBER] Error: peek_ewald_inpcrd: SHOULD NOT BE HERE Hirdesh Kumar
Wednesday, 21 September 2011
- Re: [AMBER] help ! zinc parameters Kk Zhu
- [AMBER] bug in respgen ? thomas.fox.boehringer-ingelheim.com
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD
- [AMBER] Grid and SDF Lorenzo Gontrani
- [AMBER] Sleap and TIP4P BOX Guenegou, Guillaume [JRDFR]
- Re: [AMBER] problem with TI calculations David A Case
- Re: [AMBER] Instantaneous temperature in TI simulation David A Case
Tuesday, 20 September 2011
- [AMBER] Difficulties trying to derive charge for new acetylated serine Fabrício Bracht
Wednesday, 21 September 2011
- Re: [AMBER] How to build the surface of crystalline cellulose? Lachele Foley (Lists)
- Re: [AMBER] Difficulties trying to derive charge for new acetylated serine M. L. Dodson
- [AMBER] Grid and SDF Lorenzo Gontrani
- Re: [AMBER] Sleap and TIP4P BOX David A Case
- Re: [AMBER] Instantaneous temperature in TI simulation Brian Radak
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Matthew Tessier
- Re: [AMBER] Xleap Installation Ben Roberts
- Re: [AMBER] Sleap and TIP4P BOX Guenegou, Guillaume [JRDFR]
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi
- Re: [AMBER] help ! zinc parameters FyD
- Re: [AMBER] Difficulties trying to derive charge for new acetylated serine FyD
- [AMBER] SASA calculation in Amber Horacio Pérez-Sánchez
- Re: [AMBER] SASA calculation in Amber Jason Swails
- [AMBER] Different Temps Coupling Yao Yao
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Jodi Ann Hadden
- [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Marek Maly
- Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Jason Swails
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly
- Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Marek Maly
- Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Jason Swails
- Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Bill Ross
- Re: [AMBER] Different Temps Coupling Ross Walker
- Re: [AMBER] Instantaneous temperature in TI simulation Qiantao Wang
- Re: [AMBER] Instantaneous temperature in TI simulation Brian Radak
- Re: [AMBER] Instantaneous temperature in TI simulation Qiantao Wang
- Re: [AMBER] Help needed for Amber SCC-DFTB code Qiantao Wang
- Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Marek Maly
- Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Marek Maly
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Matthew Tessier
- Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Jason Swails
- [AMBER] RMSD fatahiya
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage FyD
Thursday, 22 September 2011
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD
- Re: [AMBER] bug in respgen ? FyD
- [AMBER] GRID and SDF Lorenzo Gontrani
- [AMBER] Amber parmbsc0 souvik sur
- [AMBER] Grid and SDF Lorenzo Gontrani
- Re: [AMBER] Amber parmbsc0 Nadine Utz
- [AMBER] Model building Aparna P
- [AMBER] ICST truongco nguyen
- Re: [AMBER] RMSD Aparna P
- Re: [AMBER] RMSD Daniel Roe
- Re: [AMBER] Model building Daniel Roe
- Re: [AMBER] Amber parmbsc0 Daniel Roe
- Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Marek Maly
- Re: [AMBER] Sleap and TIP4P BOX David A Case
- [AMBER] help ! zinc parameters Bruno Luís Pinto de Oliveira
- [AMBER] Restart-Files in Sander Julian Zachmann
- Re: [AMBER] ICST David A Case
- Re: [AMBER] Restart-Files in Sander Brian Radak
- [AMBER] Amber parmbsc0 vs ff99 souvik sur
- Re: [AMBER] Amber parmbsc0 vs ff99 Brian Radak
- Re: [AMBER] help ! zinc parameters Baldoni Hector Armando
- Re: [AMBER] Amber parmbsc0 vs ff99 Hugh Heldenbrand
- Re: [AMBER] Amber parmbsc0 vs ff99 Marek Maly
- Re: [AMBER] Amber parmbsc0 vs ff99 Thomas Cheatham
- Re: [AMBER] Amber parmbsc0 vs ff99 Jason Swails
- Re: [AMBER] Amber parmbsc0 vs ff99 Brian Radak
- [AMBER] GB protocol problems for large RNAs Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] Amber parmbsc0 vs ff99 Marek Maly
- Re: [AMBER] Amber parmbsc0 vs ff99 Jason Swails
- Re: [AMBER] Amber parmbsc0 vs ff99 Marek Maly
- Re: [AMBER] GB protocol problems for large RNAs Ross Walker
- [AMBER] sander/amoeba parameter format Andrew Petersen
- [AMBER] error when installing parallel sander / AmberTools1.5 Amber11 matheus froeyen
- Re: [AMBER] error when installing parallel sander / AmberTools1.5 Amber11 Ross Walker
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Matthew Tessier
- Re: [AMBER] Grid and SDF Thomas Cheatham III
- Re: [AMBER] Amber parmbsc0 vs ff99 Jiri Sponer
- Re: [AMBER] Difference between serial and parallel MMPBSA Mengjuei Hsieh
- Re: [AMBER] Difference between serial and parallel MMPBSA Osman, Roman
- [AMBER] Large pressure fluctuations over the whole run Hernán Meier
- [AMBER] XH/pi (X=C, O, N) interactions and stacking interactions in AMBER Rajesh Raju
- Re: [AMBER] XH/pi (X=C, O, N) interactions and stacking interactions in AMBER Jason Swails
- Re: [AMBER] error when installing parallel sander / AmberTools1.5 Amber11 K T
- Re: [AMBER] error when installing parallel sander / AmberTools1.5 Amber11 Jason Swails
- [AMBER] AmberTools Parallel Compilation Issue Matteo Guglielmi
- Re: [AMBER] AmberTools Parallel Compilation Issue Jason Swails
- Re: [AMBER] Large pressure fluctuations over the whole run Jason Swails
- [AMBER] how to generate a correlation matrix for both protein and substrate atoms sunxi.comcast.net
- Re: [AMBER] Grid and SDF - sorry for the mail spamming Lorenzo Gontrani
Friday, 23 September 2011
- Re: [AMBER] Sleap and TIP4P BOX Guenegou, Guillaume [JRDFR]
- Re: [AMBER] Model building Aparna P
- Re: [AMBER] error when installing parallel sander / AmberTools1.5 Amber11 matheus froeyen
- Re: [AMBER] AmberTools Parallel Compilation Issue Matteo Guglielmi
- [AMBER] problem with nmodes calculation-260-residue protein hongphuc nguyen
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage FyD
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Karl N. Kirschner
- [AMBER] RESP charge fitting shome sankar bhunia
- Re: [AMBER] Model building Daniel Roe
- Re: [AMBER] how to generate a correlation matrix for both protein and substrate atoms Daniel Roe
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage FyD
- [AMBER] hydrogen bonding Vijay Manickam Achari
- Re: [AMBER] RESP charge fitting FyD
- Re: [AMBER] bug in respgen ? thomas.fox.boehringer-ingelheim.com
- Re: [AMBER] AmberTools Parallel Compilation Issue David A Case
- Re: [AMBER] Sleap and TIP4P BOX David A Case
- [AMBER] load parmbsc0 and X-Ol for RNA David Condon
- Re: [AMBER] Sleap and TIP4P BOX Guenegou, Guillaume [JRDFR]
- Re: [AMBER] AmberTools Parallel Compilation Issue Carlos Sosa
- Re: [AMBER] bug in respgen ? FyD
- Re: [AMBER] XH/pi (X=C, O, N) interactions and stacking interactions in AMBER Qiantao Wang
- Re: [AMBER] hydrogen bonding Daniel Roe
- Re: [AMBER] AmberTools Parallel Compilation Issue Matteo Guglielmi
- Re: [AMBER] AmberTools Parallel Compilation Issue Carlos Sosa
- Re: [AMBER] XH/pi (X=C, O, N) interactions and stacking interactions in AMBER Jiri Sponer
- Re: [AMBER] MMPBSA.py 3DRISM error Jesper Soerensen
- [AMBER] Antechamber Zachary Davis
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Matthew Tessier
- Re: [AMBER] AmberTools Parallel Compilation Issue Matteo Guglielmi
- Re: [AMBER] Instantaneous temperature in TI simulation Qiantao Wang
- Re: [AMBER] Instantaneous temperature in TI simulation Qiantao Wang
- Re: [AMBER] AmberTools Parallel Compilation Issue Ross Walker
- Re: [AMBER] Instantaneous temperature in TI simulation Brian Radak
- Re: [AMBER] load parmbsc0 and X-Ol for RNA David A Case
- [AMBER] nmode calculations kirtana S
- Re: [AMBER] load parmbsc0 and X-Ol for RNA Catein Catherine
- [AMBER] How to recover rst or can I readin mdcrd for a MD by -c? Catein Catherine
- Re: [AMBER] hydrogen bonding Vijay Manickam Achari
- [AMBER] Amber parmbsc0 force field souvik sur
- Re: [AMBER] Amber parmbsc0 force field Bruno Rodrigues
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Yun Shi
Saturday, 24 September 2011
- [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6 George Tzotzos
- Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6 George Tzotzos
- Re: [AMBER] How to recover rst or can I readin mdcrd for a MD by -c? Bruno Rodrigues
- Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6 Daniel Roe
- Re: [AMBER] Instantaneous temperature in TI simulation case
- Re: [AMBER] problem with nmodes calculation-260-residue protein case
- Re: [AMBER] Amber parmbsc0 force field case
- Re: [AMBER] Amber parmbsc0 force field souvik sur
- Re: [AMBER] MMPBSA.py 3DRISM error Jason Swails
- Re: [AMBER] Amber parmbsc0 force field Jason Swails
- Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6 Jason Swails
- Re: [AMBER] AmberTools Parallel Compilation Issue Matteo Guglielmi
- Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6 Mengjuei Hsieh
- Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6 Daniel Roe
- Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6 Jason Swails
- Re: [AMBER] nmode calculations Jason Swails
- Re: [AMBER] Model building Aparna P
- Re: [AMBER] How to recover rst or can I readin mdcrd for a MD by -c? Catein Catherine
Sunday, 25 September 2011
- Re: [AMBER] Instantaneous temperature in TI simulation Qiantao Wang
- [AMBER] fixing rmsd values Massimiliano Porrini
- Re: [AMBER] fixing rmsd values Niel Henriksen
- Re: [AMBER] nmode calculations kirtana S
- Re: [AMBER] nmode calculations case
- Re: [AMBER] load parmbsc0 and X-Ol for RNA David Condon
- Re: [AMBER] Error: peek_ewald_inpcrd: SHOULD NOT BE HERE case
- Re: [AMBER] Antechamber case
- [AMBER] Problems of Hbond calculation qiao xue
- Re: [AMBER] RMSD fatahiya
- [AMBER] Regarding Force field souvik sur
- [AMBER] Solvent model charges off by factor of 18.2223 or typo? Daniel Sindhikara
Monday, 26 September 2011
- Re: [AMBER] bug in respgen ? thomas.fox.boehringer-ingelheim.com
- Re: [AMBER] bug in respgen ? FyD
- [AMBER] GAMESS to RESP input file shome sankar bhunia
- Re: [AMBER] bug in respgen ? FyD
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage FyD
- Re: [AMBER] GAMESS to RESP input file FyD
- Re: [AMBER] Regarding Force field David A Case
- Re: [AMBER] RMSD Bruno Rodrigues
- Re: [AMBER] Problems of Hbond calculation Bruno Rodrigues
- Re: [AMBER] Instantaneous temperature in TI simulation Brian Radak
- Re: [AMBER] fixing rmsd values Massimiliano Porrini
- Re: [AMBER] fixing rmsd values Bruno Rodrigues
- Re: [AMBER] fixing rmsd values Massimiliano Porrini
- Re: [AMBER] fixing rmsd values Niel Henriksen
- Re: [AMBER] fixing rmsd values InSuk Joung
- [AMBER] ambertool question !!! Алексей Раевский
- [AMBER] ambertool question !!! Алексей Раевский
- Re: [AMBER] ambertool question !!! Brian Radak
- Re: [AMBER] ambertool question !!! Dmitry Nilov
- [AMBER] MM/GBSA question - pairwise decomposition Anselm Horn
- [AMBER] Some common doubts about MMPBSA.py decomposition Rajesh Raju
- [AMBER] dihedral parameters kirtana S
- Re: [AMBER] Large pressure fluctuations over the whole run Hernán Meier
- Re: [AMBER] Large pressure fluctuations over the whole run Adrian Roitberg
- [AMBER] thermodynamic integration on protein mutation Jorge Iulek
- Re: [AMBER] Some common doubts about MMPBSA.py decomposition Jason Swails
- Re: [AMBER] dihedral parameters Jason Swails
- [AMBER] Some common doubts about MMPBSA.py decomposition Rajesh Raju
- Re: [AMBER] RMSD fatahiya
- Re: [AMBER] Large pressure fluctuations over the whole run case
- Re: [AMBER] thermodynamic integration on protein mutation case
- Re: [AMBER] dihedral parameters Chidambar Kulkarni
- [AMBER] Mol2 file creation Chidambar Kulkarni
- Re: [AMBER] Model building Aparna P
Tuesday, 27 September 2011
- [AMBER] non-bond interaction Anglea A.
- Re: [AMBER] non-bond interaction steinbrt.rci.rutgers.edu
- Re: [AMBER] Model building Daniel Roe
- Re: [AMBER] Mol2 file creation David A Case
- Re: [AMBER] dihedral parameters Jason Swails
- Re: [AMBER] RMSD Daniel Roe
- [AMBER] GB protocol problems for large RNAs (follow-up) Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] Mol2 file creation Chidambar Kulkarni
- Re: [AMBER] dihedral parameters Chidambar Kulkarni
- Re: [AMBER] thermodynamic integration on protein mutation Jorge Iulek
- Re: [AMBER] GB protocol problems for large RNAs (follow-up) Ross Walker
- Re: [AMBER] GB protocol problems for large RNAs (follow-up) Carlos Simmerling
- Re: [AMBER] GB protocol problems for large RNAs (follow-up) Niel Henriksen
- Re: [AMBER] GB protocol problems for large RNAs (follow-up) Thomas Gaillard
- [AMBER] giving acceptor mask in ptraj for hbond utility Bala subramanian
- Re: [AMBER] giving acceptor mask in ptraj for hbond utility Daniel Roe
- [AMBER] Fwd: fixing rmsd values (follow-up) Massimiliano Porrini
- Re: [AMBER] Fwd: fixing rmsd values (follow-up) Carlos Simmerling
- [AMBER] Chromophore Building Yao Yao
- Re: [AMBER] GB protocol problems for large RNAs (follow-up) David A Case
- Re: [AMBER] Chromophore Building M. L. Dodson
- [AMBER] Failure building Amber 11 parallel on AmberTools1.5 George Tzotzos
- Re: [AMBER] Fwd: fixing rmsd values (follow-up) Thomas Cheatham III
- Re: [AMBER] Fwd: fixing rmsd values (follow-up) Carlos Simmerling
- Re: [AMBER] Fwd: fixing rmsd values (follow-up) Bruno Rodrigues
- Re: [AMBER] dihedral parameters kirtana S
- Re: [AMBER] Failure building Amber 11 parallel on AmberTools1.5 Jason Swails
- [AMBER] Parallel compile error of Amber11 kurisaki
- Re: [AMBER] Parallel compile error of Amber11 Jason Swails
- Re: [AMBER] Parallel compile error of Amber11 kurisaki
- [AMBER] solvateBox or setBox or set box Neha Gandhi
Wednesday, 28 September 2011
- [AMBER] PMEMD job was aborted kurisaki
- Re: [AMBER] PMEMD job was aborted Ross Walker
- Re: [AMBER] PMEMD job was aborted kurisaki
- [AMBER] sander outout using mdin=5 and idecomp=2 kurisaki
- Re: [AMBER] Fwd: fixing rmsd values (follow-up) Massimiliano Porrini
- [AMBER] PCA Linda catherine
- Re: [AMBER] solvateBox or setBox or set box David A Case
- Re: [AMBER] sander outout using mdin=5 and idecomp=2 Jason Swails
- [AMBER] MMPBSA.py discrepancies in results George Tzotzos
- Re: [AMBER] MMPBSA.py discrepancies in results Bill Miller III
- Re: [AMBER] MMPBSA.py discrepancies in results George Tzotzos
- Re: [AMBER] sander outout using mdin=5 and idecomp=2 kurisaki
- Re: [AMBER] sander outout using mdin=5 and idecomp=2 kurisaki
- Re: [AMBER] bug in respgen ? David A Case
- Re: [AMBER] MMPBSA.py discrepancies in results Jason Swails
- Re: [AMBER] MMPBSA.py discrepancies in results George Tzotzos
- Re: [AMBER] MMPBSA.py discrepancies in results Jason Swails
- Re: [AMBER] MMPBSA.py discrepancies in results George Tzotzos
- Re: [AMBER] MMPBSA.py discrepancies in results Bill Miller III
- Re: [AMBER] bug in respgen ? FyD
- Re: [AMBER] MMPBSA.py discrepancies in results George Tzotzos
- Re: [AMBER] Fwd: fixing rmsd values (follow-up) Massimiliano Porrini
- Re: [AMBER] MMPBSA.py discrepancies in results Jason Swails
- Re: [AMBER] Instantaneous temperature in TI simulation Qiantao Wang
- [AMBER] Announcing the NVIDIA MD SimCluster Program (Free test drives available) Ross Walker
- Re: [AMBER] MMPBSA.py discrepancies in results George Tzotzos
- Re: [AMBER] MMPBSA.py discrepancies in results Jason Swails
- [AMBER] 1st DNA tutorial cannot save parameter Yao Yao
- [AMBER] Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021) Ross Walker
- [AMBER] PNEB on GPUs William Cantara
- [AMBER] Parallel limit? Hu Ge
- Re: [AMBER] Parallel limit? Ross Walker
- Re: [AMBER] PNEB on GPUs Ross Walker
- Re: [AMBER] PNEB on GPUs Jason Swails
- Re: [AMBER] PNEB on GPUs Jason Swails
- Re: [AMBER] Parallel limit? Jason Swails
- Re: [AMBER] PNEB on GPUs Ross Walker
- Re: [AMBER] Parallel limit? Ross Walker
- [AMBER] Parameter files :problem to save souvik sur
- Re: [AMBER] PNEB on GPUs Jason Swails
- Re: [AMBER] Parameter files :problem to save Jason Swails
- Re: [AMBER] Parameter files :problem to save Ross Walker
- [AMBER] Query regarding MMPBSA in Amber11 Hirdesh Kumar
- Re: [AMBER] Parameter files :problem to save Ross Walker
- Re: [AMBER] 1st DNA tutorial cannot save parameter Ross Walker
- Re: [AMBER] PCA Jason Swails
- Re: [AMBER] Query regarding MMPBSA in Amber11 Jason Swails
- Re: [AMBER] Fwd: fixing rmsd values (follow-up) Mariano Rech
Thursday, 29 September 2011
- [AMBER] Chirality restraints Rajeswari A.
- [AMBER] sander mpi error when unfolding the protein Chinh Su Tran To
- [AMBER] GBSW AMBER Cindy Pembroke
- Re: [AMBER] sander mpi error when unfolding the protein steinbrt.rci.rutgers.edu
- Re: [AMBER] sander mpi error when unfolding the protein Chinh Su Tran To
- Re: [AMBER] Query regarding MMPBSA in Amber11 Hirdesh Kumar
- Re: [AMBER] sander mpi error when unfolding the protein steinbrt.rci.rutgers.edu
- Re: [AMBER] On Cationic Dummy Atom francesco oteri
- Re: [AMBER] MMPBSA.py discrepancies in results George Tzotzos
- Re: [AMBER] sander mpi error when unfolding the protein Chinh Su Tran To
- Re: [AMBER] Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021) Jan-Philip Gehrcke
- Re: [AMBER] MMPBSA.py discrepancies in results Bill Miller III
- Re: [AMBER] Model building Aparna P
- Re: [AMBER] PNEB on GPUs Christina Bergonzo
- Re: [AMBER] Parallel limit? David A Case
- Re: [AMBER] Chirality restraints David A Case
- Re: [AMBER] GBSW AMBER David A Case
- Re: [AMBER] Chirality restraints Rajeswari A.
- Re: [AMBER] PNEB on GPUs William Cantara
- Re: [AMBER] PNEB on GPUs Jason Swails
- Re: [AMBER] Query regarding MMPBSA in Amber11 Jason Swails
- [AMBER] AmberTools1.5 parallel implementation of mmpbsa.py - Incomplete installation? George Tzotzos
- Re: [AMBER] AmberTools1.5 parallel implementation of mmpbsa.py - Incomplete installation? Bill Miller III
- Re: [AMBER] AmberTools1.5 parallel implementation of mmpbsa.py - Incomplete installation? George Tzotzos
- Re: [AMBER] AmberTools1.5 parallel implementation of mmpbsa.py - Incomplete installation? Jason Swails
- Re: [AMBER] Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021) Ross Walker
- [AMBER] force field modification kirtana S
- Re: [AMBER] Parallel limit? Scott Le Grand
- Re: [AMBER] Model building Sangita Kachhap
- [AMBER] how NOT to label terminal residue Victor Ma
- Re: [AMBER] how NOT to label terminal residue Jason Swails
- Re: [AMBER] how NOT to label terminal residue Victor Ma
- [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Marek Maly
- Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Jason Swails
- Re: [AMBER] Fwd: fixing rmsd values (follow-up) Jason Swails
- Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Marek Maly
- Re: [AMBER] Query regarding MMPBSA in Amber11 Hirdesh Kumar
- Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Jason Swails
- Re: [AMBER] Query regarding MMPBSA in Amber11 Jason Swails
- Re: [AMBER] On Cationic Dummy Atom Jason Swails
Friday, 30 September 2011
- Re: [AMBER] Compiling Amber11 on Blue Gene/P Garo Garabedyan
- [AMBER] From amber to gromacs madhumita das
- [AMBER] Failure to compile AmberTools 1.5 on linux Francesco Pietra
- Re: [AMBER] From amber to gromacs Ivan Gladich
- Re: [AMBER] Failure to compile AmberTools 1.5 on linux FyD
- Re: [AMBER] how NOT to label terminal residue David A Case
- Re: [AMBER] Failure to compile AmberTools 1.5 on linux David A Case
- [AMBER] Amber 10/ambertool Installation error Kshatresh Dutta Dubey
- Re: [AMBER] Compiling Amber11 on Blue Gene/P Jason Swails
- Re: [AMBER] Amber 10/ambertool Installation error Jason Swails
- [AMBER] Quick initial impressions of PNY water cooled GTX 580 and some numbers for the usual GPU benchmarks Gould, Ian R
- Re: [AMBER] Failure to compile AmberTools 1.5 on linux Francesco Pietra
- Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Marek Maly
- Re: [AMBER] Quick initial impressions of PNY water cooled GTX 580 and some numbers for the usual GPU benchmarks Scott Le Grand
- Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Jason Swails
- Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Marek Maly
- [AMBER] MMPBSA: how to include only some residues Victor Ma
- Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Jason Swails
- Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Marek Maly
- Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Jason Swails
- Re: [AMBER] MMPBSA: how to include only some residues Jason Swails
- [AMBER] Parameters kirtana S

Last message date: Fri Sep 30 2011 - 19:30:02 PDT
Archived on: Mon Nov 03 2025 - 05:54:26 PST

Amber Archive Sep 2011 by date