Amber Archive Apr 2016: by date

Thursday, 31 March 2016
- [AMBER] mmpbsa_py_energy failed with prmtop lig_tleap.prm sunita gupta
- [AMBER] Problems running MD simulation using residual dipolar couplings as restraints Francisco Corzana López
Friday, 1 April 2016
- [AMBER] aMD ruins membrane structure Michael Shokhen
- Re: [AMBER] Periodicity box Eiros Zamora, Juan
- [AMBER] Introducing the exciting next step in MD software development Jason Swails
- Re: [AMBER] Introducing the exciting next step in MD software development ABEL Stephane 175950
- Re: [AMBER] Introducing the exciting next step in MD software development Brent Krueger
- Re: [AMBER] Introducing the exciting next step in MD software development Adrian Roitberg
- Re: [AMBER] mmpbsa_py_energy failed with prmtop lig_tleap.prm Bill Miller III
- Re: [AMBER] Introducing the exciting next step in MD software development Thomas Pochapsky
- Re: [AMBER] Introducing the exciting next step in MD software development Chris Moth
- Re: [AMBER] Problems running MD simulation using residual dipolar couplings as restraints David A Case
- [AMBER] Problems with periodic boundaries Luke Presson
- Re: [AMBER] Introducing the exciting next step in MD software development Bill Ross
- Re: [AMBER] Introducing the exciting next step in MD software development Adrian Roitberg
- Re: [AMBER] Relation between binding affinity and free enegy Carlos Simmerling
- Re: [AMBER] Problems running MD simulation using residual dipolar couplings as restraints Francisco Corzana López
- [AMBER] hoogsteen base pair Martina Devi
- Re: [AMBER] hoogsteen base pair Martina Devi
- [AMBER] A contrarian note about gravity potentials in MD David A Case
- Re: [AMBER] hoogsteen base pair David A Case
- Re: [AMBER] Problems with periodic boundaries Daniel Roe
- Re: [AMBER] Problems with periodic boundaries Luke Presson
- Re: [AMBER] Problems with periodic boundaries Carlos Simmerling
- Re: [AMBER] Problems with periodic boundaries Luke Presson
- Re: [AMBER] Problems with periodic boundaries Carlos Simmerling
- [AMBER] QM calculation mohammad r
Saturday, 2 April 2016
- Re: [AMBER] Hydrophobic solution environment ??? Mijiddorj Batsaikhan
- Re: [AMBER] Problems with periodic boundaries David A Case
- Re: [AMBER] QM calculation David A Case
- Re: [AMBER] Hydrophobic solution environment ??? David A Case
Sunday, 3 April 2016
- [AMBER] Run Stage 2 of the RESP fit yhzahsc
- Re: [AMBER] QM calculation mohammad r
- Re: [AMBER] QM calculation David A Case
- [AMBER] How to use tiMerge properly in pmemd TI calculation jfliu.itcs.ecnu.edu.cn
- Re: [AMBER] How to use tiMerge properly in pmemd TI calculation hannes.loeffler.stfc.ac.uk
- Re: [AMBER] Run Stage 2 of the RESP fit Brent Krueger
- Re: [AMBER] How to use tiMerge properly in pmemd TI calculation jfliu.itcs.ecnu.edu.cn
- Re: [AMBER] How to use tiMerge properly in pmemd TI calculation hannes.loeffler.stfc.ac.uk
- Re: [AMBER] How to use tiMerge properly in pmemd TI calculation jfliu.itcs.ecnu.edu.cn
- Re: [AMBER] QM calculation mohammad r
- Re: [AMBER] Run Stage 2 of the RESP fit yhzahsc
- [AMBER] how to prepare a pdb file of a protein being phosphorylated at specific residues 欧阳艳华
- [AMBER] how to run a MD of a phosphorylated protein using amber 欧阳艳华
- Re: [AMBER] how to run a MD of a phosphorylated protein using amber Mijiddorj Batsaikhan
- Re: [AMBER] how to prepare a pdb file of a protein being phosphorylated at specific residues Mijiddorj Batsaikhan
- [AMBER] General question Sreemol G
- Re: [AMBER] General question David Cerutti
- Re: [AMBER] General question hannes.loeffler.stfc.ac.uk
- Re: [AMBER] how to run a MD of a phosphorylated protein using amber YanhuaOuyang
- Re: [AMBER] General question Sreemol G
Monday, 4 April 2016
- Re: [AMBER] how to prepare a pdb file of a protein being phosphorylated at specific residues YanhuaOuyang
- Re: [AMBER] General question hannes.loeffler.stfc.ac.uk
- [AMBER] build a phosphorylated protein structure pdb file YanhuaOuyang
- [AMBER] turning of non-bonded interactions with addExclusions Batuhan Kav
- Re: [AMBER] General question Sreemol G
- Re: [AMBER] build a phosphorylated protein structure pdb file Carlos Simmerling
- Re: [AMBER] General question hannes.loeffler.stfc.ac.uk
- Re: [AMBER] General question Sreemol G
- Re: [AMBER] General question hannes.loeffler.stfc.ac.uk
- Re: [AMBER] General question Sreemol G
- Re: [AMBER] mmpbsa_py_energy failed with prmtop lig_tleap.prm sunita gupta
- Re: [AMBER] General question hannes.loeffler.stfc.ac.uk
- Re: [AMBER] QM calculation David A Case
- Re: [AMBER] General question David A Case
- [AMBER] MD simulations of deprotonated tyrosine residue with AMBER ABEL Stephane 175950
- Re: [AMBER] MD simulations of deprotonated tyrosine residue with AMBER Adrian Roitberg
- Re: [AMBER] mmpbsa_py_energy failed with prmtop lig_tleap.prm Jason Swails
- Re: [AMBER] MD simulations of deprotonated tyrosine residue with AMBER ABEL Stephane 175950
- Re: [AMBER] aMD ruins membrane structure Dickson, Callum J
- Re: [AMBER] MD simulations of deprotonated tyrosine residue with AMBER Jason Swails
- Re: [AMBER] turning of non-bonded interactions with addExclusions Jason Swails
- [AMBER] spherical restraint flatwell potentials Kenneth McGuinness
- Re: [AMBER] spherical restraint flatwell potentials David Cerutti
- Re: [AMBER] spherical restraint flatwell potentials Kenneth McGuinness
- Re: [AMBER] QM calculation mohammad r
- Re: [AMBER] spherical restraint flatwell potentials David Cerutti
- Re: [AMBER] spherical restraint flatwell potentials Kenneth McGuinness
- Re: [AMBER] build a phosphorylated protein structure pdb file YanhuaOuyang
- Re: [AMBER] build a phosphorylated protein structure pdb file YanhuaOuyang
- Re: [AMBER] build a phosphorylated protein structure pdb file Bill Ross
- Re: [AMBER] build a phosphorylated protein structure pdb file David A Case
Tuesday, 5 April 2016
- [AMBER] sander number of atoms limit TERREUX RAPHAEL
- Re: [AMBER] sander number of atoms limit Gould, Ian R
- Re: [AMBER] sander number of atoms limit TERREUX RAPHAEL
- Re: [AMBER] sander number of atoms limit Bill Ross
- Re: [AMBER] sander number of atoms limit Gould, Ian R
- Re: [AMBER] sander number of atoms limit Gould, Ian R
- Re: [AMBER] build a phosphorylated protein structure pdb file YanhuaOuyang
- Re: [AMBER] sander number of atoms limit Jason Swails
- [AMBER] The question about SMD wjli
- Re: [AMBER] The question about SMD Adrian Roitberg
- Re: [AMBER] sander number of atoms limit David A Case
- [AMBER] cpptraj: reading in previously created covariance matrix Vlad Cojocaru
- Re: [AMBER] QM calculation Gustavo Seabra
- Re: [AMBER] cpptraj: reading in previously created covariance matrix Daniel Roe
- Re: [AMBER] QM calculation Marc van der Kamp
- [AMBER] 回复： The question about SMD wjli
- [AMBER] 回复： The question about SMD wjli
- Re: [AMBER] General question Sreemol G
- Re: [AMBER] General question Charles Lin
- Re: [AMBER] General question Sreemol G
- Re: [AMBER] General question Charles Lin
Wednesday, 6 April 2016
- [AMBER] cpptraj: reading in previously created covariance matrix Vlad Cojocaru
- [AMBER] Amber: .rst file not created ABHIJEET CHOWDHURY
- Re: [AMBER] Run Stage 2 of the RESP fit FyD
- Re: [AMBER] Convergence problem with the SCC-DFTB example. Gustavo Seabra
- [AMBER] Amber14/AmberTools15 compliation error Kris Feher
- Re: [AMBER] Amber14/AmberTools15 compliation error Jason Swails
- Re: [AMBER] Amber: .rst file not created Marcelo Andrade Chagas
- [AMBER] Any issues if I make PMEMD understand bonds span imaging? David Cerutti
- [AMBER] General Type Improper Dihedrals vs. Specifics Robert Molt
- Re: [AMBER] General Type Improper Dihedrals vs. Specifics David Cerutti
- [AMBER] running charmm force field in amber Neha Gandhi
- Re: [AMBER] General Type Improper Dihedrals vs. Specifics David A Case
- Re: [AMBER] running charmm force field in amber Hai Nguyen
- Re: [AMBER] running charmm force field in amber Ross Walker
- Re: [AMBER] running charmm force field in amber Jason Swails
- Re: [AMBER] General Type Improper Dihedrals vs. Specifics David Cerutti
- Re: [AMBER] running charmm force field in amber Neha Gandhi
Thursday, 7 April 2016
- [AMBER] test: not getting emails from the list Vlad Cojocaru
- Re: [AMBER] Amber: .rst file not created ABHIJEET CHOWDHURY
- [AMBER] Hbond command use with non-hydrogen bonds Krantzman, Kristin D
- Re: [AMBER] Hbond command use with non-hydrogen bonds Daniel Roe
- Re: [AMBER] Amber: .rst file not created Jason Swails
- Re: [AMBER] test: not getting emails from the list Jason Swails
- [AMBER] PCA Sofia Vasilakaki
- [AMBER] MMPBSA : Calculation when keeping explicit water molecules 楊承翰
- [AMBER] on the MD of protein-ligand Brett
- Re: [AMBER] on the MD of protein-ligand David Cerutti
Friday, 8 April 2016
- [AMBER] RMSD graph for protein-RNA complex Sreemol G
- [AMBER] CpHMD 赵聪
- Re: [AMBER] QM calculation mohammad r
- Re: [AMBER] RMSD graph for protein-RNA complex Dr. Anselm Horn
- [AMBER] Regarding MM-PBSA calculation Sivanandam M
- [AMBER] Regarding MM-PBSA free energy calculation Sivanandam M
- Re: [AMBER] RMSD graph for protein-RNA complex Sreemol G
- Re: [AMBER] RMSD graph for protein-RNA complex David A Case
- Re: [AMBER] CpHMD Jason Swails
- Re: [AMBER] MMPBSA : Calculation when keeping explicit water molecules Jason Swails
- Re: [AMBER] Regarding MM-PBSA calculation Jason Swails
- Re: [AMBER] Regarding MM-PBSA free energy calculation Jason Swails
- Re: [AMBER] MMPBSA : Calculation when keeping explicit water molecules Alessandro Contini
- [AMBER] Metal geometry Vasantha Kumar
- Re: [AMBER] Metal geometry Carlos Simmerling
- Re: [AMBER] Metal geometry David Cerutti
- Re: [AMBER] RMSD graph for protein-RNA complex Daniel Roe
- Re: [AMBER] PCA Daniel Roe
- [AMBER] Problem with MCPB.py Surya Prakash Tiwari
- [AMBER] Error -per residue Energy Decomposition Arati Paudyal
- Re: [AMBER] Metal geometry Vasantha Kumar
- Re: [AMBER] Metal geometry Vasantha Kumar
- Re: [AMBER] Error -per residue Energy Decomposition Jason Swails
- [AMBER] How to prepare files cyclodextrin to use witch glycam04 CRISTIAN ROSSI PERARO
- Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04 Lachele Foley
- Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04 CRISTIAN ROSSI PERARO
- Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04 Lachele Foley
Saturday, 9 April 2016
- Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04 FyD
- Re: [AMBER] Metal geometry FyD
- Re: [AMBER] Problem with MCPB.py FyD
- Re: [AMBER] Metal geometry Vasantha Kumar
- Re: [AMBER] Metal geometry Pengfei Li
- [AMBER] query regarding dssp plot cpptraj. Saman Yousuf ali
- Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04 CRISTIAN ROSSI PERARO
- Re: [AMBER] Error -per residue Energy Decomposition Arati Paudyal
- Re: [AMBER] Metal geometry Pengfei Li
Sunday, 10 April 2016
- [AMBER] Amber script to delete all hydrogen atoms from protein? Michael Shokhen
- Re: [AMBER] Amber script to delete all hydrogen atoms from protein? Marcelo Andrade Chagas
- Re: [AMBER] Amber script to delete all hydrogen atoms from protein? Arati Paudyal
- [AMBER] PMF calculation via tunnel (SMD) wjli
- Re: [AMBER] Amber script to delete all hydrogen atoms from protein? Michael Shokhen
- Re: [AMBER] Metal geometry Vasantha Kumar
- Re: [AMBER] query regarding dssp plot cpptraj. Daniel Roe
- [AMBER] mm_pbsa.pl, that I'm doing this right? CRISTIAN ROSSI PERARO
- [AMBER] Is it possible to run TI with pmemd using the AMOEBA force field? Sumsamber Lee
- Re: [AMBER] Is it possible to run TI with pmemd using the AMOEBA force field? Jason Swails
- Re: [AMBER] Is it possible to run TI with pmemd using the AMOEBA force field? David Cerutti
- [AMBER] query regarding -refc ABHIJEET CHOWDHURY
- Re: [AMBER] query regarding -refc David Cerutti
- Re: [AMBER] query regarding -refc ABHIJEET CHOWDHURY
Monday, 11 April 2016
- [AMBER] Refinement in explicit solvent Vasantha Kumar
- [AMBER] MD tutorial workflows James Starlight
- [AMBER] Could not find angle parameter Jesmita Dhar
- [AMBER] geometric center with cpptraj Batuhan Kav
- [AMBER] Box dimensions 達南杰
- Re: [AMBER] Refinement in explicit solvent David A Case
- Re: [AMBER] query regarding -refc David Cerutti
- [AMBER] ff12SB force field wjli
- Re: [AMBER] ff12SB force field Carlos Simmerling
- Re: [AMBER] geometric center with cpptraj Hai Nguyen
- Re: [AMBER] ff12SB force field wjli
- Re: [AMBER] mm_pbsa.pl, that I'm doing this right? Ray Luo
- [AMBER] Multiple restraints for minimization Stevens, David Ryan
- Re: [AMBER] Could not find angle parameter Daniel Roe
- Re: [AMBER] Box dimensions Daniel Roe
- Re: [AMBER] Multiple restraints for minimization Daniel Roe
- [AMBER] CHAMBER and CMAP error using new c36 FF Jun Feng
- [AMBER] Implicit Solvent simulation - membrane proteins Balaji Selvam
- Re: [AMBER] Implicit Solvent simulation - membrane proteins Hai Nguyen
- Re: [AMBER] Implicit Solvent simulation - membrane proteins Ray Luo
- Re: [AMBER] Multiple restraints for minimization Bill Ross
- Re: [AMBER] Multiple restraints for minimization Stevens, David Ryan
- Re: [AMBER] mm_pbsa.pl, that I'm doing this right? CRISTIAN ROSSI PERARO
- Re: [AMBER] Multiple restraints for minimization Daniel Roe
- Re: [AMBER] ff12SB force field David Cerutti
- Re: [AMBER] Multiple restraints for minimization Stevens, David Ryan
- Re: [AMBER] Refinement in explicit solvent Vasantha Kumar
- [AMBER] Alanine Scanning ERROR!!! Jag Silwal
- Re: [AMBER] Box dimensions 達南杰
- Re: [AMBER] Box dimensions Daniel Roe
- Re: [AMBER] Metal geometry Pengfei Li
- Re: [AMBER] Box dimensions 達南杰
- [AMBER] error while running MMPBSA script Harmeet Kaur
- Re: [AMBER] RMSD graph for protein-RNA complex Sreemol G
- Re: [AMBER] Could not find angle parameter Jesmita Dhar
Tuesday, 12 April 2016
- Re: [AMBER] Amber14/AmberTools15 compliation error Kris Feher
- Re: [AMBER] RMSD graph for protein-RNA complex David A Case
- Re: [AMBER] RMSD graph for protein-RNA complex Sreemol G
- Re: [AMBER] error while running MMPBSA script Jason Swails
- [AMBER] CHAMBER and CMAP error using new c36 FF Jun Feng
- Re: [AMBER] CHAMBER and CMAP error using new c36 FF Jason Swails
- Re: [AMBER] CHAMBER and CMAP error using new c36 FF Hai Nguyen
- [AMBER] CHAMBER error for the updated CHARMM36 force fields Chitrak Gupta
- Re: [AMBER] CHAMBER error for the updated CHARMM36 force fields Hai Nguyen
- Re: [AMBER] CHAMBER and CMAP error using new c36 FF Jun Feng
- Re: [AMBER] RMSD graph for protein-RNA complex Daniel Roe
- [AMBER] Protein-DNA docking Lara rajam
- Re: [AMBER] Protein-DNA docking Hai Nguyen
- Re: [AMBER] Protein-DNA docking Carlos Simmerling
- Re: [AMBER] Protein-DNA docking Lara rajam
- Re: [AMBER] RMSD graph for protein-RNA complex Sreemol G
- Re: [AMBER] RMSD graph for protein-RNA complex Andy Watkins
- Re: [AMBER] RMSD graph for protein-RNA complex Sreemol G
Wednesday, 13 April 2016
- [AMBER] Antechamber Problem Beale, John
- Re: [AMBER] Antechamber Problem Bill Ross
- Re: [AMBER] Antechamber Problem Beale, John
- Re: [AMBER] Antechamber Problem Bill Ross
- Re: [AMBER] CHAMBER and CMAP error using new c36 FF Jason Swails
- Re: [AMBER] RMSD graph for protein-RNA complex Daniel Roe
- Re: [AMBER] RMSD graph for protein-RNA complex David A Case
- Re: [AMBER] Could not find angle parameter David A Case
- [AMBER] Quasi-harmonic calculation Amika Sood
- [AMBER] Both positional and distance restraints Damiano Spadoni
- [AMBER] Natural bond orbital analysis Kenneth McGuinness
- [AMBER] MMGBSA and dielectric constants Cortopassi, Wilian
- Re: [AMBER] MMGBSA and dielectric constants Jason Swails
- Re: [AMBER] Alanine Scanning ERROR!!! Jason Swails
- Re: [AMBER] Alanine Scanning ERROR!!! Jag Silwal
- [AMBER] Amber custom hardware setup Leonardo Lazzaro
- Re: [AMBER] Natural bond orbital analysis David A Case
- Re: [AMBER] Alanine Scanning ERROR!!! Jason Swails
- Re: [AMBER] Amber custom hardware setup Jason Swails
Thursday, 14 April 2016
- [AMBER] Regarding Input file preparation in AMBER Sivanandam M
- Re: [AMBER] Regarding Input file preparation in AMBER Bill Ross
- [AMBER] mm_pbsa.pl ERROR yhzahsc
- Re: [AMBER] mm_pbsa.pl ERROR Bill Ross
- [AMBER] LEAP RUN FAILED Neal Broomhead
- [AMBER] how to embed amber14 Ayesha Kanwal
- Re: [AMBER] LEAP RUN FAILED Bill Ross
- Re: [AMBER] mm_pbsa.pl ERROR David A Case
- Re: [AMBER] Alanine Scanning ERROR!!! Jag Silwal
- Re: [AMBER] Natural bond orbital analysis Kenneth McGuinness
- [AMBER] Modelling of proteins Aishani Prem
- Re: [AMBER] Modelling of proteins David Cerutti
- [AMBER] How can I extract PDB files from a molecular dynamics simulation Luis Esteban
- Re: [AMBER] How can I extract PDB files from a molecular dynamics simulation Kenneth McGuinness
- Re: [AMBER] mm_pbsa.pl ERROR yhzahsc
- Re: [AMBER] mm_pbsa.pl ERROR yhzahsc
- Re: [AMBER] How can I extract PDB files from a molecular dynamics simulation Luis Esteban
- [AMBER] hbond analysis of phosphotyrosine Wu Xu
- Re: [AMBER] hbond analysis of phosphotyrosine Hai Nguyen
Friday, 15 April 2016
- [AMBER] Fortran Modernisation Workshop - Numerical Algorithms Group NAG CHAMI F.
- [AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file Shreeramesh
- Re: [AMBER] hbond analysis of phosphotyrosine David A Case
- [AMBER] Conversion of CHARMM-GUI generated file into Lipid14 readable file Shreeramesh
- Re: [AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file David A Case
- Re: [AMBER] hbond analysis of phosphotyrosine Wu Xu
- Re: [AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file Shreeramesh
- Re: [AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file Batuhan Kav
- Re: [AMBER] hbond analysis of phosphotyrosine Daniel Roe
- Re: [AMBER] How can I extract PDB files from a molecular dynamics simulation Daniel Roe
- Re: [AMBER] hbond analysis of phosphotyrosine Wu Xu
- Re: [AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file Jason Swails
- [AMBER] TI Calculation doubt Mary Varughese
Saturday, 16 April 2016
- Re: [AMBER] TI Calculation doubt Hannes Loeffler
- Re: [AMBER] hbond analysis of phosphotyrosine Daniel Roe
- Re: [AMBER] hbond analysis of phosphotyrosine Wu Xu
- [AMBER] facing problems simulating in implicit solvent Avik Bhattacharjee
- Re: [AMBER] facing problems simulating in implicit solvent Daniel Roe
- Re: [AMBER] facing problems simulating in implicit solvent Avik Bhattacharjee
- Re: [AMBER] facing problems simulating in implicit solvent Carlos Simmerling
- Re: [AMBER] How can I extract PDB files from a molecular dynamics simulation Luis Esteban
- [AMBER] Change PBRadii after simulation Jag Silwal
- Re: [AMBER] Change PBRadii after simulation Carlos Simmerling
- Re: [AMBER] Change PBRadii after simulation Jag Silwal
- [AMBER] cpptraj SolventAcc and ligand distance plotting Saman Yousuf ali
Sunday, 17 April 2016
- Re: [AMBER] Change PBRadii after simulation Carlos Simmerling
- Re: [AMBER] Change PBRadii after simulation Jason Swails
- Re: [AMBER] how to embed amber14 Jason Swails
- [AMBER] error in MCPB.py 3b jixiaofeng
- [AMBER] was the MCPB.py compiled correctly？ jixiaofeng
- [AMBER] Error in 3DRISM calculation ATUL KUMAR
- Re: [AMBER] Error in 3DRISM calculation Tyler Luchko (Lists)
- [AMBER] on antechamber Brett
- Re: [AMBER] on antechamber hannes.loeffler.stfc.ac.uk
Monday, 18 April 2016
- [AMBER] on antechamber Brett
- Re: [AMBER] how to embed amber14 Ayesha Kanwal
- Re: [AMBER] how to embed amber14 Jason Swails
- Re: [AMBER] on antechamber David A Case
- Re: [AMBER] how to embed amber14 David A Case
- Re: [AMBER] Both positional and distance restraints David A Case
- Re: [AMBER] Quasi-harmonic calculation David A Case
- Re: [AMBER] Change PBRadii after simulation Jag Silwal
- Re: [AMBER] Change PBRadii after simulation Carlos Simmerling
- Re: [AMBER] Change PBRadii after simulation Arati Paudyal
- Re: [AMBER] on antechamber Daniel Roe
- Re: [AMBER] cpptraj SolventAcc and ligand distance plotting Daniel Roe
- [AMBER] clustering waleed zalloum
- [AMBER] mpi problems Gard Nelson
- Re: [AMBER] Both positional and distance restraints Damiano Spadoni
- Re: [AMBER] mpi problems Marcelo Andrade Chagas
- [AMBER] Early bird extended! ISQBP2016 meeting - Bergen Norway Vlad Cojocaru
- [AMBER] amber v16 Arjun Sharma
- Re: [AMBER] amber v16 Hai Nguyen
- [AMBER] glycam O-glycosylation at Ser Neha Gandhi
- Re: [AMBER] glycam O-glycosylation at Ser Lachele Foley
Tuesday, 19 April 2016
- Re: [AMBER] glycam O-glycosylation at Ser Neha Gandhi
- [AMBER] want to ask you about MMPBSA.py .mdcrd file Ayesha Kanwal
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Dr. M. Shahid
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Ayesha Kanwal
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Dr. M. Shahid
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Ayesha Kanwal
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Ayesha Kanwal
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Dr. M. Shahid
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Ayesha Kanwal
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Ayesha Kanwal
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Ayesha Kanwal
- [AMBER] HEME group in a protein Anna Cebrian Prats
- [AMBER] query about .mdcrd file Ayesha Kanwal
- Re: [AMBER] HEME group in a protein David A Case
- [AMBER] [cpptraj] Automating pcmin/pcmax selection of modes command Eiros Zamora, Juan
- [AMBER] Approach for transmembrane protein Elisa Pieri
- [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj peter.schmidtke.discngine.servier.com
- Re: [AMBER] query about .mdcrd file Dr. M. Shahid
- Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj David A Case
- Re: [AMBER] Approach for transmembrane protein anu chandra
- Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj peter.schmidtke.discngine.servier.com
- Re: [AMBER] [cpptraj] Automating pcmin/pcmax selection of modes command Daniel Roe
- Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj Daniel Roe
- Re: [AMBER] cpptraj SolventAcc and ligand distance plotting Daniel Roe
- Re: [AMBER] query about .mdcrd file Ayesha Kanwal
- [AMBER] building DNA with extruded base giulia palermo
- Re: [AMBER] query about .mdcrd file Christina Bergonzo
- Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj David A Case
- Re: [AMBER] building DNA with extruded base David A Case
- Re: [AMBER] building DNA with extruded base Christina Bergonzo
- [AMBER] interactive MD applied to AI Bill Ross
- Re: [AMBER] building DNA with extruded base giulia palermo
- [AMBER] Electrostatic Energies - MMPBSA Cortopassi, Wilian
- Re: [AMBER] Electrostatic Energies - MMPBSA Jason Swails
- [AMBER] Regarding atom types Elvis Martis
- Re: [AMBER] query about .mdcrd file Ayesha Kanwal
Wednesday, 20 April 2016
- [AMBER] error while putting the whole path into python script Ayesha Kanwal
- Re: [AMBER] error while putting the whole path into python script Marc van der Kamp
- Re: [AMBER] error while putting the whole path into python script Bill Ross
- [AMBER] XLeap didn't save the parameter file Nikolay N. Kuzmich
- Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj peter.schmidtke.discngine.servier.com
- Re: [AMBER] XLeap didn't save the parameter file Bill Ross
- [AMBER] problem in 3DRISM convergence ATUL KUMAR
- Re: [AMBER] Electrostatic Energies - MMPBSA Cortopassi, Wilian
- Re: [AMBER] XLeap didn't save the parameter file David A Case
- Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj David A Case
- Re: [AMBER] problem in 3DRISM convergence David A Case
- Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj peter.schmidtke.discngine.servier.com
- [AMBER] questions about energy terms of amber MD yuandandan
- [AMBER] warning message for antechamber by acpype Brett
- Re: [AMBER] Electrostatic Energies - MMPBSA Jason Swails
- Re: [AMBER] cpptraj SolventAcc and ligand distance plotting Daniel Roe
- [AMBER] Force field parameters for glycerophophate anu chandra
Thursday, 21 April 2016
- [AMBER] Error in the conversion of CHARMM-GUI generated file into lipid14 readable format Shreeramesh
- [AMBER] How to read mdinfo file without crashing the simulation? Karolina Markowska
- Re: [AMBER] How to read mdinfo file without crashing the simulation? Dr. M. Shahid
- Re: [AMBER] How to read mdinfo file without crashing the simulation? Karolina Markowska
- Re: [AMBER] How to read mdinfo file without crashing the simulation? Hannes Loeffler
- Re: [AMBER] How to read mdinfo file without crashing the simulation? Karolina Markowska
- Re: [AMBER] questions about energy terms of amber MD David A Case
- Re: [AMBER] How to read mdinfo file without crashing the simulation? David A Case
- Re: [AMBER] How to read mdinfo file without crashing the simulation? Hannes Loeffler
- [AMBER] qmmm mmpbsa spin multiplicity problem Ayesha Fatima
- [AMBER] GeForce GTX 960 ? Marek Maly
- Re: [AMBER] qmmm mmpbsa spin multiplicity problem Jason Swails
- Re: [AMBER] Regarding atom types Daniel Roe
- Re: [AMBER] GeForce GTX 960 ? Ross Walker
- Re: [AMBER] How to read mdinfo file without crashing the simulation? Bill Ross
- Re: [AMBER] How to read mdinfo file without crashing the simulation? Bill Ross
- Re: [AMBER] warning message for antechamber by acpype David A Case
- [AMBER] mmpbsa complex McElheny, Dan
- [AMBER] Building Cyclic Peptide in xleap Maral Aminpour
- Re: [AMBER] cpptraj SolventAcc and ligand distance plotting Saman Yousuf ali
- Re: [AMBER] GeForce GTX 960 ? Marek Maly
- Re: [AMBER] Building Cyclic Peptide in xleap David A Case
- Re: [AMBER] Building Cyclic Peptide in xleap Bill Ross
- Re: [AMBER] interactive MD applied to AI Bill Ross
- Re: [AMBER] interactive MD applied to AI Hai Nguyen
- [AMBER] How to deal with monoatomic ion, such as ILs cation Takuya Uto
- Re: [AMBER] interactive MD applied to AI Bill Ross
- Re: [AMBER] How to deal with monoatomic ion, such as ILs cation Bill Ross
- [AMBER] How to deal with monoatomic ion, such as ILs anion Takuya Uto
- Re: [AMBER] How to deal with monoatomic ion, such as ILs anion kurisaki
- Re: [AMBER] mmpbsa complex Jason Swails
- Re: [AMBER] qmmm mmpbsa spin multiplicity problem Ayesha Fatima
- [AMBER] atom does not have a type jixiaofeng
- Re: [AMBER] atom does not have a type jixiaofeng
- Re: [AMBER] interactive MD applied to AI Hai Nguyen
- Re: [AMBER] interactive MD applied to AI Bill Ross
Friday, 22 April 2016
- [AMBER] CUDA and restraint Domenico Marson
- Re: [AMBER] How to read mdinfo file without crashing the simulation? Karolina Markowska
- Re: [AMBER] XLeap didn't save the parameter file Nikolay N. Kuzmich
- [AMBER] System size limitations for Amber 14 pmemd.cuda? Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] Regarding atom types Elvis Martis
- Re: [AMBER] XLeap didn't save the parameter file Bill Ross
- Re: [AMBER] Building Cyclic Peptide in xleap Kenneth McGuinness
- [AMBER] Decomposition energy after mutation! Jag Silwal
- Re: [AMBER] Building Cyclic Peptide in xleap David Cerutti
- Re: [AMBER] XLeap didn't save the parameter file David A Case
- Re: [AMBER] Modelling of proteins Aishani Prem
- Re: [AMBER] Modelling of proteins Bill Ross
Saturday, 23 April 2016
- Re: [AMBER] How to deal with monoatomic ion, such as ILs anion Takuya Uto
- [AMBER] Hydroxyproline Mijiddorj Batsaikhan
- Re: [AMBER] Hydroxyproline Carlos Simmerling
- Re: [AMBER] Hydroxyproline David A Case
- Re: [AMBER] How to deal with monoatomic ion, such as ILs anion Bill Ross
- Re: [AMBER] How to deal with monoatomic ion, such as ILs anion Andrew Schaub
- Re: [AMBER] How to deal with monoatomic ion, such as ILs anion Bill Ross
- Re: [AMBER] How to read mdinfo file without crashing the simulation? Bill Ross
- Re: [AMBER] How to read mdinfo file without crashing the simulation? Bill Ross
- Re: [AMBER] Decomposition energy after mutation! Jason Swails
Sunday, 24 April 2016
- [AMBER] No torsion terms for CB-N*-CR-H5 Prayagraj Fandilolu
- Re: [AMBER] How to read mdinfo file without crashing the simulation? Karolina Markowska
- Re: [AMBER] How to read mdinfo file without crashing the simulation? Bill Ross
- Re: [AMBER] No torsion terms for CB-N*-CR-H5 David A Case
Monday, 25 April 2016
- [AMBER] Read/visualize volmap output (opendx) Jean-Patrick Francoia
- [AMBER] Energies in QM/MM MD 王美婷
- [AMBER] How to rebuild pH-based trajectory files from CpHMD restarted simulations Elisa Pieri
- Re: [AMBER] Read/visualize volmap output (opendx) Jason Swails
- Re: [AMBER] How to rebuild pH-based trajectory files from CpHMD restarted simulations Jason Swails
- Re: [AMBER] How to deal with monoatomic ion, such as ILs anion Takuya Uto
- Re: [AMBER] Read/visualize volmap output (opendx) Jean-Patrick Francoia
- Re: [AMBER] How to read mdinfo file without crashing the simulation? Karolina Markowska
- [AMBER] Error while converting CHARMM-GUI generated file Shreeramesh
- Re: [AMBER] How to read mdinfo file without crashing the simulation? Dr. M. Shahid
- Re: [AMBER] Read/visualize volmap output (opendx) Jason Swails
- Re: [AMBER] Read/visualize volmap output (opendx) Jean-Patrick Francoia
- Re: [AMBER] Error while converting CHARMM-GUI generated file Batuhan Kav
- [AMBER] protein complex dissociation during md Brett
- Re: [AMBER] Read/visualize volmap output (opendx) Daniel Roe
- Re: [AMBER] GeForce GTX 960 ? Ross Walker
- [AMBER] rotation angle around an axes giulia palermo
- Re: [AMBER] rotation angle around an axes Daniel Roe
- Re: [AMBER] Read/visualize volmap output (opendx) Jean-Patrick Francoia
- Re: [AMBER] Read/visualize volmap output (opendx) Daniel Roe
- Re: [AMBER] Read/visualize volmap output (opendx) Jean-Patrick Francoia
- [AMBER] Problem Running MMPBSA.py Martin Floor
- [AMBER] Using PBSA to Calculate Solvation Free Energy Jiaqi Jin
- Re: [AMBER] Using PBSA to Calculate Solvation Free Energy Ray Luo
- Re: [AMBER] Energies in QM/MM MD Brian Radak
- Re: [AMBER] Problem Running MMPBSA.py Dwight McGee
Tuesday, 26 April 2016
- Re: [AMBER] Problem Running MMPBSA.py Jason Swails
- [AMBER] parmed.py Sanjib Paul
- Re: [AMBER] parmed.py Daniel Roe
- Re: [AMBER] AMBER Project Niharikav Veeresh
- Re: [AMBER] AMBER Project Daniel Roe
- Re: [AMBER] Energies in QM/MM MD Dr. Andreas W. Goetz
- [AMBER] MD of 1:1 mixture compound Saman Yousuf ali
- [AMBER] debug issue Zhenyu Meng
Wednesday, 27 April 2016
- [AMBER] tleap parametrization of metalo-binding proteins James Starlight
- [AMBER] Question about RESP with iodine Lorenzo Gontrani
- Re: [AMBER] tleap parametrization of metalo-binding proteins Yigal Lahav
- Re: [AMBER] debug issue David A Case
- Re: [AMBER] Question about RESP with iodine David A Case
- Re: [AMBER] tleap parametrization of metalo-binding proteins James Starlight
- Re: [AMBER] Question about RESP with iodine Pengfei Li
- Re: [AMBER] Question about RESP with iodine Lorenzo Gontrani
- Re: [AMBER] tleap parametrization of metalo-binding proteins Pengfei Li
- Re: [AMBER] tleap parametrization of metalo-binding proteins James Starlight
- [AMBER] Problem in calculating auto time correlation function with ptraj Saheb Dutta
- Re: [AMBER] Problem in calculating auto time correlation function with ptraj Daniel Roe
- Re: [AMBER] Problem in calculating auto time correlation function with ptraj David A Case
- Re: [AMBER] debug issue Zhenyu Meng
- Re: [AMBER] No torsion terms for CB-N*-CR-H5 Prayagraj Fandilolu
Thursday, 28 April 2016
- Re: [AMBER] No torsion terms for CB-N*-CR-H5 Bill Ross
- Re: [AMBER] debug issue Zhenyu Meng
- [AMBER] How can I use FF14SB in DOCK6 calculation? Mijiddorj Batsaikhan
- [AMBER] CUDA and restraint Domenico Marson
- Re: [AMBER] How can I use FF14SB in DOCK6 calculation? Dwight McGee
- Re: [AMBER] tleap parametrization of metalo-binding proteins Pengfei Li
- Re: [AMBER] Building Cyclic Peptide in xleap Maral Aminpour
- [AMBER] tleap - protein + ligand + heme group Anna Cebrian Prats
- Re: [AMBER] CUDA and restraint Charles Lin
- [AMBER] Targeted MD error Shukla, Saurabh
- Re: [AMBER] Targeted MD error Charles Lin
- Re: [AMBER] Targeted MD error Carlos Simmerling
- Re: [AMBER] tleap - protein + ligand + heme group David A Case
- Re: [AMBER] tleap - protein + ligand + heme group Scott Brozell
- [AMBER] Cpptraj LipidOrder error: mask groups are not the same length Amy Rice
- Re: [AMBER] Cpptraj LipidOrder error: mask groups are not the same length Chris Moth
- Re: [AMBER] Cpptraj LipidOrder error: mask groups are not the same length hannes.loeffler.stfc.ac.uk
- Re: [AMBER] Cpptraj LipidOrder error: mask groups are not the same length hannes.loeffler.stfc.ac.uk
- Re: [AMBER] Cpptraj LipidOrder error: mask groups are not the same length Amy Rice
- Re: [AMBER] How can I use FF14SB in DOCK6 calculation? Mijiddorj Batsaikhan
- [AMBER] fortran i/o on system shared memory Bill Ross
- Re: [AMBER] fortran i/o on system shared memory Bill Ross
Friday, 29 April 2016
- Re: [AMBER] How can I use FF14SB in DOCK6 calculation? Marc van der Kamp
- Re: [AMBER] CUDA and restraint Domenico Marson
- Re: [AMBER] CUDA and restraint Bill Ross
- Re: [AMBER] CUDA and restraint Bill Ross
- Re: [AMBER] protein complex dissociation during md Dr. Anselm Horn
- Re: [AMBER] CUDA and restraint Domenico Marson
- Re: [AMBER] CUDA and restraint Charles Lin
- [AMBER] Calculate Percentage of Hydrogen Occurrence Jag Silwal
- Re: [AMBER] CUDA and restraint Domenico Marson
- [AMBER] ambpdb error Arati Paudyal
- Re: [AMBER] ambpdb error Daniel Roe
- Re: [AMBER] tleap - protein + ligand + heme group Anna Cebrian Prats
- Re: [AMBER] Calculate Percentage of Hydrogen Occurrence Daniel Roe
- Re: [AMBER] ambpdb error Arati Paudyal
- Re: [AMBER] ambpdb error Daniel Roe
- Re: [AMBER] CUDA and restraint Ross Walker
- Re: [AMBER] ambpdb error Jason Swails
- Re: [AMBER] ambpdb error Daniel Roe
- Re: [AMBER] ambpdb error Daniel Roe
- Re: [AMBER] tleap - protein + ligand + heme group David A Case
- [AMBER] accelerated MD on set of dihedrals Giuseppina La Sala
- Re: [AMBER] ambpdb error Arati Paudyal
- Re: [AMBER] ambpdb error Daniel Roe
- Re: [AMBER] accelerated MD on set of dihedrals Daniel Roe
- Re: [AMBER] ambpdb error Jason Swails
- Re: [AMBER] accelerated MD on set of dihedrals giulia palermo
- Re: [AMBER] mmpbsa complex McElheny, Dan
- Re: [AMBER] accelerated MD on set of dihedrals Giuseppina La Sala
- Re: [AMBER] accelerated MD on set of dihedrals Giuseppina La Sala
- Re: [AMBER] mmpbsa complex Jason Swails
Saturday, 30 April 2016
- [AMBER] on antechamber Brett
- Re: [AMBER] on antechamber David A Case
- [AMBER] Release of Amber16 and AmberTools16 David A Case
- Re: [AMBER] help identifying dihedral parameters for paracetemol using Antechamber Andrew Schaub

Last message date: Sat Apr 30 2016 - 22:30:03 PDT
Archived on: Wed Apr 24 2024 - 05:55:19 PDT

Amber Archive Apr 2016 by date