Amber Archive Jul 2016: by date

Thursday, 30 June 2016
- [AMBER] cpptraj.hbond: water in the complex chemjxn
- Re: [AMBER] bad atom type decomp Bruno Falcone
- [AMBER] Help: make test fails during parallel amber installation Dr. M. K. Yadav
- Re: [AMBER] Umbrella Sampling bharat gupta
- Re: [AMBER] Slow performance of Amber12 on cluster bharat gupta
- Re: [AMBER] Help: make test fails during parallel amber installation Hai Nguyen
- Re: [AMBER] Slow performance of Amber12 on cluster Hai Nguyen
- [AMBER] Regarding GIST calculation ATUL KUMAR
Friday, 1 July 2016
- Re: [AMBER] Structural refinement of the protein complexed with metalo-ions James Starlight
- [AMBER] can MCPB build non amino-acid containing complex? Zhenyu Meng
- Re: [AMBER] Regarding GIST calculation Steven Ramsey
- Re: [AMBER] Slow performance of Amber12 on cluster Ross Walker
- Re: [AMBER] can MCPB build non amino-acid containing complex? zoran matovic
- Re: [AMBER] Structural refinement of the protein complexed with metalo-ions Pengfei Li
- Re: [AMBER] can MCPB build non amino-acid containing complex? Pengfei Li
- Re: [AMBER] cpptraj.hbond: water in the complex Daniel Roe
- [AMBER] MMPBSA -O: command not found Thakur, Abhishek
- Re: [AMBER] MMPBSA -O: command not found Hai Nguyen
- Re: [AMBER] MMPBSA -O: command not found Thakur, Abhishek
- Re: [AMBER] MCPB Fabrício Bracht
Saturday, 2 July 2016
- Re: [AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt Jose Manuel
- Re: [AMBER] can MCPB build non amino-acid containing complex? Zhenyu Meng
- Re: [AMBER] MMPBSA -O: command not found David A Case
- Re: [AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt David A Case
- Re: [AMBER] Regarding ho parameter in gaff David A Case
- Re: [AMBER] addAtomType problem David A Case
- Re: [AMBER] Umbrella Sampling bharat gupta
- Re: [AMBER] can MCPB build non amino-acid containing complex? Zhenyu Meng
Sunday, 3 July 2016
- [AMBER] convert amber topology and coordinates files into gromacs topology Ming Tang
- Re: [AMBER] convert amber topology and coordinates files into gromacs topology Jason Swails
Monday, 4 July 2016
- [AMBER] Lipid14 with ntr=1 Himanshu Joshi
- [AMBER] ParmEd Neha Gandhi
- [AMBER] Ambertool16 - MCPB.py angle cut off and Error with Pdbsearcher.py Bilal Nizami
- Re: [AMBER] Structural refinement of the protein complexed with metalo-ions James Starlight
- [AMBER] Question about Charge derivation for GLYCAM force field Casalini Tommaso
- [AMBER] Potential on each atom Elisa Pieri
- Re: [AMBER] ParmEd Hai Nguyen
- Re: [AMBER] Potential on each atom Adrian Roitberg
- Re: [AMBER] MCPB Fabrício Bracht
- Re: [AMBER] MCPB Marcelo Andrade Chagas
- Re: [AMBER] MCPB Pengfei Li
- Re: [AMBER] ParmEd Neha Gandhi
- Re: [AMBER] ParmEd Jason Swails
- [AMBER] SMD at constant force Ming Tang
- Re: [AMBER] ParmEd Neha Gandhi
- Re: [AMBER] ParmEd Daniel Roe
- Re: [AMBER] ParmEd Jason Swails
- Re: [AMBER] SMD at constant force Jason Swails
- [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng
- Re: [AMBER] MCPB Pengfei Li
- Re: [AMBER] MCPB.py cannot recognize Cl Pengfei Li
- Re: [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng
- Re: [AMBER] MCPB.py cannot recognize Cl Pengfei Li
- Re: [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng
- Re: [AMBER] ParmEd Neha Gandhi
- Re: [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng
- Re: [AMBER] Question about Charge derivation for GLYCAM force field Lachele Foley
- Re: [AMBER] MCPB.py cannot recognize Cl zoran matovic
- Re: [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng
- Re: [AMBER] MCPB.py cannot recognize Cl zoran matovic
- Re: [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng
Tuesday, 5 July 2016
- [AMBER] iwrap=0 Ming Tang
- Re: [AMBER] iwrap=0 Daniel Roe
- Re: [AMBER] Error during amber 12 installation bharat gupta
- Re: [AMBER] Error during amber 12 installation Daniel Roe
- Re: [AMBER] bad atom type decomp Bruno Falcone
- Re: [AMBER] Potential on each atom Elisa Pieri
- Re: [AMBER] MCPB Fabrício Bracht
- Re: [AMBER] MCPB Fabrício Bracht
- Re: [AMBER] Potential on each atom Jason Swails
- Re: [AMBER] Potential on each atom Adrian Roitberg
- Re: [AMBER] bad atom type decomp Jason Swails
- Re: [AMBER] MCPB Pengfei Li
- Re: [AMBER] MCPB.py cannot recognize Cl Pengfei Li
- Re: [AMBER] Ambertool16 - MCPB.py angle cut off and Error with Pdbsearcher.py Pengfei Li
- Re: [AMBER] Help with Umbrella Sampling bharat gupta
Wednesday, 6 July 2016
- Re: [AMBER] Potential on each atom Elisa Pieri
- [AMBER] Amber12 or lated on POWER8 platform Sanman Sabane
- [AMBER] Problem to extending Simulation ATUL KUMAR
- Re: [AMBER] Ambertool16 - MCPB.py angle cut off and Error with Pdbsearcher.py Bilal Nizami
- Re: [AMBER] Amber12 or lated on POWER8 platform Jason Swails
- Re: [AMBER] Problem to extending Simulation Jason Swails
- Re: [AMBER] Problem to extending Simulation ATUL KUMAR
- Re: [AMBER] Potential on each atom Elisa Pieri
- Re: [AMBER] Potential on each atom Jason Swails
- Re: [AMBER] Problem to extending Simulation Daniel Roe
- Re: [AMBER] MCPB Fabrício Bracht
- [AMBER] Multiplicity in antechamber Fabrício Bracht
- Re: [AMBER] MCPB Fabrício Bracht
- Re: [AMBER] Multiplicity in antechamber Jason Swails
- [AMBER] Amber16 tutorials Corum, Katharine W
- Re: [AMBER] Amber16 tutorials Corum, Katharine W
- Re: [AMBER] Amber16 tutorials Hai Nguyen
- [AMBER] DPPC simulation temperature gsottile.unq.edu.ar
- Re: [AMBER] Amber16 tutorials Corum, Katharine W
- [AMBER] Question on SMD Ming Tang
- [AMBER] Query on SMD Ming Tang
- [AMBER] A question on SMD simulations Ming Tang
- Re: [AMBER] A question on SMD simulations Hai Nguyen
- [AMBER] Stuck somewhere using antechamber Xiaoyu Wang
- Re: [AMBER] Stuck somewhere using antechamber Hai Nguyen
- Re: [AMBER] Problem to extending Simulation ATUL KUMAR
Thursday, 7 July 2016
- Re: [AMBER] Problem to extending Simulation Bill Ross
- Re: [AMBER] Defining reaction coordinate for US bharat gupta
- [AMBER] Gunning GIST in parallel ATUL KUMAR
- Re: [AMBER] Stuck somewhere using antechamber David A Case
- Re: [AMBER] Problem to extending Simulation David A Case
- [AMBER] An attempt for TI with QM/MM Hamiltonian Xiangyu Jia
- Re: [AMBER] re-imaging bilayer Sally Pias
- Re: [AMBER] re-imaging bilayer Daniel Roe
- Re: [AMBER] Amber16 tutorials Corum, Katharine W
- Re: [AMBER] Amber16 tutorials Hirdesh Kumar
- Re: [AMBER] Amber16 tutorials Corum, Katharine W
- Re: [AMBER] Amber16 tutorials Daniel Roe
- Re: [AMBER] Gunning GIST in parallel Daniel Roe
- Re: [AMBER] Amber16 tutorials Corum, Katharine W
- Re: [AMBER] Amber16 tutorials Hai Nguyen
- Re: [AMBER] Amber16 tutorials Daniel Roe
- Re: [AMBER] Amber16 tutorials Corum, Katharine W
- Re: [AMBER] re-imaging bilayer Dickson, Callum J
- Re: [AMBER] re-imaging bilayer Amy Rice
- [AMBER] VMD Thakur, Abhishek
- Re: [AMBER] VMD Daniel Roe
- Re: [AMBER] VMD Nhai
- [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice
- [AMBER] GLYCAM naming Fabrício Bracht
- Re: [AMBER] GLYCAM naming Lachele Foley
- Re: [AMBER] MCPB Pengfei Li
- Re: [AMBER] MCPB Fabrício Bracht
- [AMBER] QM/MM issue Morteza Chehel Amirani
- [AMBER] QM/MM simulations with Amber/deMon2k Morteza Chehel Amirani
- Re: [AMBER] Patching Plumed 1.3 with Amber12 bharat gupta
- Re: [AMBER] convert amber topology and coordinates files into gromacs topology Ming Tang
- Re: [AMBER] convert amber topology and coordinates files into gromacs topology Ming Tang
- Re: [AMBER] convert amber topology and coordinates files into gromacs topology David A Case
- Re: [AMBER] QM/MM simulations with Amber/deMon2k Andreas Goetz
- Re: [AMBER] QM/MM issue Dr. Andreas W. Goetz
- Re: [AMBER] QM/MM simulations with Amber/deMon2k Joan Torras
Friday, 8 July 2016
- Re: [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng
- Re: [AMBER] MCPB.py cannot recognize Cl zoran matovic
- Re: [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng
- Re: [AMBER] MCPB.py cannot recognize Cl zoran matovic
- Re: [AMBER] MCPB.py cannot recognize Cl zoran matovic
- [AMBER] rmsd plot error Saman Yousuf ali
- Re: [AMBER] rmsd plot error zoran matovic
- Re: [AMBER] rmsd plot error Saman Yousuf ali
- Re: [AMBER] rmsd plot error Vlad Cojocaru
- Re: [AMBER] rmsd plot error Saman Yousuf ali
- Re: [AMBER] rmsd plot error Vlad Cojocaru
- Re: [AMBER] rmsd plot error Saman Yousuf ali
- [AMBER] how to fix COM of a group of atoms? Ming Tang
- Re: [AMBER] rmsd plot error zoran matovic
- Re: [AMBER] Library errors while using NAB on Amber16 Slava Chushak
- Re: [AMBER] rmsd plot error Vlad Cojocaru
- Re: [AMBER] rmsd plot error Daniel Roe
- Re: [AMBER] rmsd plot error zoran matovic
- Re: [AMBER] rmsd plot error Vlad Cojocaru
- [AMBER] MMPBSA Thakur, Abhishek
- Re: [AMBER] MMPBSA Nhai
- [AMBER] ligand bond distortion during MD run. Saman Yousuf ali
- Re: [AMBER] MMPBSA Thakur, Abhishek
- Re: [AMBER] MMPBSA Hai Nguyen
- Re: [AMBER] ligand bond distortion during MD run. zoran matovic
- Re: [AMBER] MMPBSA Thakur, Abhishek
- Re: [AMBER] MMPBSA Thakur, Abhishek
- Re: [AMBER] MMPBSA Thakur, Abhishek
- Re: [AMBER] MMPBSA Daniel Roe
- Re: [AMBER] ligand bond distortion during MD run. Daniel Roe
- Re: [AMBER] Library errors while using NAB on Amber16 David A Case
- Re: [AMBER] MMPBSA Thakur, Abhishek
- Re: [AMBER] addAtomType problem Lea Natalia Toledo Carvajal
Saturday, 9 July 2016
- [AMBER] MD of an elongated active site protein. Saman Yousuf ali
- Re: [AMBER] MCPB.py cannot recognize Cl Pengfei Li
- [AMBER] adding non-standard residue to RNA strand Martina Devi
- Re: [AMBER] Lipid14 with ntr=1 Himanshu Joshi
- Re: [AMBER] Ambertool16 - MCPB.py angle cut off and Error with Pdbsearcher.py Pengfei Li
- Re: [AMBER] adding non-standard residue to RNA strand David A Case
- [AMBER] Restrain COM of a group of atoms Ming Tang
- Re: [AMBER] how to fix COM of a group of atoms? Himanshu Joshi
Sunday, 10 July 2016
- Re: [AMBER] how to fix COM of a group of atoms? Ming Tang
Monday, 11 July 2016
- Re: [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng
- [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. 朱婧涵
- [AMBER] predicting RDCs for un-restrained bonds Thomas Pochapsky
- Re: [AMBER] Library errors while using NAB on Amber16 Slava Chushak
- Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. Thakur, Abhishek
- [AMBER] Steered Molecular Dynamics Fair, Ryan
- Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. Jason Swails
- Re: [AMBER] how to fix COM of a group of atoms? Jason Swails
- Re: [AMBER] MCPB.py cannot recognize Cl Pengfei Li
- [AMBER] MMPBSA Thakur, Abhishek
- Re: [AMBER] MMPBSA Hai Nguyen
- Re: [AMBER] MMPBSA Thakur, Abhishek
- Re: [AMBER] MMPBSA Hai Nguyen
- Re: [AMBER] how to fix COM of a group of atoms? Thakur, Abhishek
- Re: [AMBER] MMPBSA Thakur, Abhishek
- Re: [AMBER] MMPBSA Hai Nguyen
- Re: [AMBER] MMPBSA Thakur, Abhishek
- [AMBER] rism1d convergence for solvent mixtures Shijie Sheng
- Re: [AMBER] predicting RDCs for un-restrained bonds David A Case
- Re: [AMBER] rism1d convergence for solvent mixtures Tyler Luchko (Lists)
- Re: [AMBER] rism1d convergence for solvent mixtures sshen004.ucr.edu
- Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. ZHU JH
- Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. Jason Swails
- Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. Thakur, Abhishek
- Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. Hai Nguyen
- Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. Hai Nguyen
Tuesday, 12 July 2016
- Re: [AMBER] Help with SMD bharat gupta
- Re: [AMBER] predicting RDCs for un-restrained bonds Thomas Pochapsky
- [AMBER] QM/MM problems with Amber/Gaussian Allen Zou
- Re: [AMBER] QM/MM problems with Amber/Gaussian Adrian Roitberg
- [AMBER] Born Mayer Potential Vivien Ramothe
- Re: [AMBER] Born Mayer Potential Hai Nguyen
- Re: [AMBER] Help with SMD Feng Pan
- Re: [AMBER] Born Mayer Potential David A Case
- Re: [AMBER] Born Mayer Potential Jason Swails
- [AMBER] Decomposition in minimization step Atila Petrosian
- Re: [AMBER] adding non-standard residue to RNA strand FyD
Wednesday, 13 July 2016
- [AMBER] strategies to speed up MM/GBSA screening Thomas Evangelidis
- Re: [AMBER] strategies to speed up MM/GBSA screening Jason Swails
- [AMBER] a question about resp restraints strength Bahaa Mostafa
- Re: [AMBER] Decomposition in minimization step Daniel Roe
- [AMBER] WHAM-2D analysis Alessandra Lacetera
- Re: [AMBER] WHAM-2D analysis Amy Rice
- Re: [AMBER] WHAM-2D analysis Christina Bergonzo
- [AMBER] Compute SASA through molsurf Francesco Gentile
- Re: [AMBER] strategies to speed up MM/GBSA screening Thomas Evangelidis
- [AMBER] carbon nanotube Neha Gandhi
- Re: [AMBER] carbon nanotube Carlos Simmerling
- Re: [AMBER] strategies to speed up MM/GBSA screening Carlos Simmerling
- Re: [AMBER] strategies to speed up MM/GBSA screening Jason Swails
- Re: [AMBER] carbon nanotube Neha Gandhi
- Re: [AMBER] carbon nanotube Jason Swails
- Re: [AMBER] carbon nanotube Neha Gandhi
- [AMBER] Generating a HETATM database to use with reduce Kucharski Jr., Amir N
- [AMBER] ff99SB*-ildn again Neha Gandhi
Thursday, 14 July 2016
- Re: [AMBER] ff99SB*-ildn again Vlad Cojocaru
- [AMBER] Is the surf or the molsurf calculate the protein surface? windy
- Re: [AMBER] WHAM-2D analysis Alessandra Lacetera
- Re: [AMBER] ff99SB*-ildn again Neha Gandhi
- [AMBER] NEW parameters with AMBER Anna Cebrian Prats
- Re: [AMBER] ff99SB*-ildn again Alessandro Contini
- Re: [AMBER] ff99SB*-ildn again Vlad Cojocaru
- Re: [AMBER] ff99SB*-ildn again Vlad Cojocaru
- [AMBER] a question about resp restraints strength Bahaa Mostafa
- [AMBER] a question about resp restraints strength Bahaa Mostafa
- Re: [AMBER] a question about resp restraints strength David A Case
- Re: [AMBER] ff99SB*-ildn again Thomas Evangelidis
- Re: [AMBER] ff99SB*-ildn again David A Case
- Re: [AMBER] NEW parameters with AMBER David A Case
- Re: [AMBER] ff99SB*-ildn again Vlad Cojocaru
- Re: [AMBER] ff99SB*-ildn again Vlad Cojocaru
- Re: [AMBER] ff99SB*-ildn again Neha Gandhi
- Re: [AMBER] ff99SB*-ildn again Vlad Cojocaru
- [AMBER] Problem with Gaussian09 with B97D/def2TZVPPD basis set from EMSL Indrajit Deb
- Re: [AMBER] a question about resp restraints strength Bahaa Mostafa
- Re: [AMBER] Problem with Gaussian09 with B97D/def2TZVPPD basis set fromEMSL zoran matovic
- Re: [AMBER] carbon nanotube Jason Swails
- Re: [AMBER] NEW parameters with AMBER Anna Cebrian Prats
- Re: [AMBER] ff99SB*-ildn again Jason Swails
- Re: [AMBER] strategies to speed up MM/GBSA screening Thomas Evangelidis
- [AMBER] RMSD plot query esther nehu
- Re: [AMBER] ff99SB*-ildn again Vlad Cojocaru
- Re: [AMBER] RMSD plot query Hai Nguyen
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice
- Re: [AMBER] strategies to speed up MM/GBSA screening Jason Swails
- Re: [AMBER] Generating a HETATM database to use with reduce David A Case
- Re: [AMBER] Generating a HETATM database to use with reduce Kucharski Jr., Amir N
- [AMBER] Is the surf or the molsurf calculate the protein surface? windy
Friday, 15 July 2016
- Re: [AMBER] how to fix COM of a group of atoms? Ming Tang
- [AMBER] REMD Reg Annie Ancy
- Re: [AMBER] Generating a HETATM database to use with reduce David A Case
- [AMBER] MMPBSA.py for complex or receptor or ligand only Bruno Falcone
- [AMBER] MMPBSA (inp=1 or inp=2)?? Thakur, Abhishek
- Re: [AMBER] MMPBSA (inp=1 or inp=2)?? Thakur, Abhishek
- Re: [AMBER] Generating a HETATM database to use with reduce Kucharski Jr., Amir N
- Re: [AMBER] carbon nanotube FyD
- Re: [AMBER] a question about resp restraints strength FyD
- Re: [AMBER] MMPBSA.py for complex or receptor or ligand only Jason Swails
- Re: [AMBER] Generating a HETATM database to use with reduce David A Case
- [AMBER] HMR 4fs failure? Gerald Monard
- Re: [AMBER] HMR 4fs failure? Hai Nguyen
- Re: [AMBER] HMR 4fs failure? David Cerutti
- Re: [AMBER] MMPBSA (inp=1 or inp=2)?? Ray Luo
- Re: [AMBER] MMPBSA (inp=1 or inp=2)?? Ray Luo
- Re: [AMBER] Generating a HETATM database to use with reduce Kucharski Jr., Amir N
- Re: [AMBER] HMR 4fs failure? Gerald Monard
- Re: [AMBER] HMR 4fs failure? Adrian Roitberg
- Re: [AMBER] HMR 4fs failure? David Cerutti
- Re: [AMBER] HMR 4fs failure? Gerald Monard
- Re: [AMBER] HMR 4fs failure? Gerald Monard
Saturday, 16 July 2016
- [AMBER] ff14SB compatible with Glycam_06j-1? yunshi11 .
- Re: [AMBER] ff14SB compatible with Glycam_06j-1? David A Case
- Re: [AMBER] a question about resp restraints strength Bahaa Mostafa
Sunday, 17 July 2016
- Re: [AMBER] Is the surf or the molsurf calculate the protein surface? David A Case
- [AMBER] Cpptraj Dd H
- Re: [AMBER] Cpptraj Hai Nguyen
- Re: [AMBER] Cpptraj Hai Nguyen
- [AMBER] Regarding Parameter file not saved Vishal Nemaysh
- Re: [AMBER] Regarding Parameter file not saved Hai Nguyen
- [AMBER] Discrepancy between mdcrd and output files for MD run jandre17
- Re: [AMBER] Discrepancy between mdcrd and output files for MD run Carlos Simmerling
- Re: [AMBER] Cpptraj Dd H
- Re: [AMBER] Cpptraj Hai Nguyen
Monday, 18 July 2016
- [AMBER] Amber 16 Installation Beale, John
- Re: [AMBER] Amber 16 Installation Bill Ross
- Re: [AMBER] Amber 16 Installation Beale, John
- Re: [AMBER] Regarding Parameter file not saved Vishal Nemaysh
- Re: [AMBER] Regarding Parameter file not saved Vishal Nemaysh
- Re: [AMBER] Regarding Parameter file not saved Bilal Nizami
- Re: [AMBER] Amber 16 Installation David A Case
- Re: [AMBER] Regarding Parameter file not saved Aleksandra Skoric
- Re: [AMBER] Amber 16 Installation Hai Nguyen
- Re: [AMBER] Regarding Parameter file not saved Vishal Nemaysh
- Re: [AMBER] Regarding Parameter file not saved Thakur, Abhishek
- Re: [AMBER] Regarding Parameter file not saved Nhai
- [AMBER] Ligand RMSD anu chandra
- [AMBER] RDF Mahmood Jasim
- Re: [AMBER] Regarding Parameter file not saved zoran matovic
- Re: [AMBER] Amber 16 Installation Corum, Katharine W
- Re: [AMBER] Ligand RMSD David A Case
- Re: [AMBER] RDF David A Case
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Dickson, Callum J
- Re: [AMBER] Regarding Parameter file not saved zoran matovic
- Re: [AMBER] Amber 16 Installation David A Case
- Re: [AMBER] REMD Reg Hai Nguyen
- [AMBER] phosphorylated residues Neha Gandhi
Tuesday, 19 July 2016
- Re: [AMBER] Regarding Parameter file not saved zoran matovic
- Re: [AMBER] phosphorylated residues Carlos Simmerling
- [AMBER] Proton wanders away from tryptophan and histadine sidechain carbon Ross Cheloha
- Re: [AMBER] Ligand RMSD anu chandra
- [AMBER] aMD with chloroform Stephan Schott
- Re: [AMBER] Proton wanders away from tryptophan and histadine sidechain carbon Carlos Simmerling
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Daniel Roe
- Re: [AMBER] how to fix COM of a group of atoms? Ming Tang
- [AMBER] Multiple Replicas on a Single GPU Bin Sun
- [AMBER] Is the surf or the molsurf calculate the protein surface? Windy CC
- Re: [AMBER] re-imaging bilayer Sally Pias
- [AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d Shijie Sheng
Wednesday, 20 July 2016
- [AMBER] sander QM/MM MD Masoud Kazemi
- [AMBER] MCPB.py - coordinate sphere FE Anna Cebrian Prats
- [AMBER] NMR restraint Ming Tang
- [AMBER] MCPB.py Anna Cebrian Prats
- Re: [AMBER] Is the surf or the molsurf calculate the protein surface? David A Case
- Re: [AMBER] MCPB.py Marcelo Andrade Chagas
- Re: [AMBER] MCPB.py - coordinate sphere FE Pengfei Li
- Re: [AMBER] MCPB.py - coordinate sphere FE Anna Cebrian Prats
- Re: [AMBER] Proton wanders away from tryptophan and histidine sidechain carbon Ross Cheloha
- [AMBER] Binding deltaG in ligand pose selction anu chandra
- Re: [AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d Tyler Luchko (Lists)
- Re: [AMBER] sander QM/MM MD Dr. Andreas W. Goetz
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice
- [AMBER] Remove rotation in postoprocess Fabrício Bracht
- [AMBER] Amber16 Parallel CUDA Tests Steven Ford
- Re: [AMBER] Remove rotation in postoprocess Jean-Marc Billod
- [AMBER] Difference of two trajectories C.D. Okafor
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Dickson, Callum J
- Re: [AMBER] NMR restraint David A Case
- Re: [AMBER] Proton wanders away from tryptophan and histidine sidechain carbon David A Case
- Re: [AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d Shijie Sheng
- Re: [AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d Tyler Luchko (Lists)
- Re: [AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d Shijie Sheng
- Re: [AMBER] NMR restraint Ming Tang
- Re: [AMBER] NMR restraint Ming Tang
Thursday, 21 July 2016
- Re: [AMBER] Amber16 Parallel CUDA Tests Ross Walker
- [AMBER] CPPTRAJ Anna Cebrian Prats
- Re: [AMBER] SMD at constant force Ming Tang
- [AMBER] MD simulation can not proceed normally 乔艳
- Re: [AMBER] MD simulation can not proceed normally Carlos Simmerling
- [AMBER] Save individual PDBs from MD trajectory Iqbal, Muhammad Sajid
- Re: [AMBER] Save individual PDBs from MD trajectory Carlos Simmerling
- Re: [AMBER] SMD and free energy value bharat gupta
- [AMBER] 回复： Re: MD simulation can not proceed normally 乔艳
- Re: [AMBER] 回复： Re: MD simulation can not proceed normally Carlos Simmerling
- [AMBER] Amber with Amoeba force field Xiaoliu Zhang
- Re: [AMBER] Binding deltaG in ligand pose selction David A Case
- [AMBER] Minimization of a small molecule in gas phase Tiffani Rovira
- [AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?) Stephan Schott
- [AMBER] Wierd line in amber-TI output Files Khabiri, Morteza
- Re: [AMBER] Minimization of a small molecule in gas phase David A Case
- Re: [AMBER] Minimization of a small molecule in gas phase David A Case
- [AMBER] selecting frames with distribution Neha Gandhi
- Re: [AMBER] selecting frames with distribution Nhai
Friday, 22 July 2016
- [AMBER] Gaussian error with MCPB ion modeling calculation Bilal Nizami
- [AMBER] MDCRD nida baig
- [AMBER] parmed chamber Neha Gandhi
- Re: [AMBER] Amber with Amoeba force field David A Case
- Re: [AMBER] MDCRD David A Case
- [AMBER] Cpptraj - Stat bug? Markus Schneider
- Re: [AMBER] parmed chamber David A Case
- Re: [AMBER] parmed chamber Neha Gandhi
- Re: [AMBER] parmed chamber Song-Ho Chong
- Re: [AMBER] parmed chamber Neha Gandhi
- Re: [AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?) David A Case
- Re: [AMBER] Wierd line in amber-TI output Files Scott Brozell
- [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Wesley Michael Botello-Smith
Saturday, 23 July 2016
- Re: [AMBER] MDCRD nida baig
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) ankita mehta
- [AMBER] NMode binding entropy Error -- Line minimizer aborted 康宁
- [AMBER] NAB ABHIJEET CHOWDHURY
- Re: [AMBER] NAB Indrajit Deb
- Re: [AMBER] NAB ABHIJEET CHOWDHURY
- [AMBER] Create x.out and x.rst from x.mdcrd Mijiddorj Batsaikhan
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) David A Case
- Re: [AMBER] MDCRD David A Case
- Re: [AMBER] NMode binding entropy Error -- Line minimizer aborted David A Case
- Re: [AMBER] Create x.out and x.rst from x.mdcrd David A Case
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Wesley Michael Botello-Smith
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) ankita mehta
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) David A Case
- Re: [AMBER] Amber16 Parallel CUDA Tests Ross Walker
Sunday, 24 July 2016
- [AMBER] SMD simulation protocols Ibrahim Said
- Re: [AMBER] SMD simulation protocols Adrian Roitberg
- Re: [AMBER] SMD simulation protocols Ibrahim Said
- Re: [AMBER] SMD simulation protocols Dwight McGee
- [AMBER] restraintmask: select residues around the coordinates of a point Thomas Evangelidis
- [AMBER] NMR restraint Ming Tang
- [AMBER] Implicit solvent with Glycam force field yunshi11 .
- Re: [AMBER] Implicit solvent with Glycam force field Lachele Foley
Monday, 25 July 2016
- Re: [AMBER] Steered Molecular Dynamics bharat gupta
- Re: [AMBER] Steered Molecular Dynamics Adrian Roitberg
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) ankita mehta
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) ankita mehta
- [AMBER] charmmlipid2amber not found Kshatresh Dutta Dubey
- Re: [AMBER] Implicit solvent with Glycam force field Carlos Simmerling
- [AMBER] ibelly to fix protein. Saman Yousuf ali
- [AMBER] Applying different restraints to different sets of atoms Dmitry Suplatov
- [AMBER] Creating topology file in MMPBSA Anwesha Sarkar
- Re: [AMBER] restraintmask: select residues around the coordinates of a point David A Case
- Re: [AMBER] Implicit solvent with Glycam force field David A Case
- Re: [AMBER] charmmlipid2amber not found David A Case
- Re: [AMBER] Creating topology file in MMPBSA Hirdesh Kumar
- Re: [AMBER] Creating topology file in MMPBSA Jason Swails
- Re: [AMBER] CPPTRAJ Jason Swails
- Re: [AMBER] charmmlipid2amber not found Kshatresh Dutta Dubey
- Re: [AMBER] charmmlipid2amber not found Adrian Roitberg
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice
- Re: [AMBER] Applying different restraints to different sets of atoms David A Case
- [AMBER] Error MCPB when send the input Tiffani Rovira
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Wesley Michael Botello-Smith
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Adrian Roitberg
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Wesley Michael Botello-Smith
- Re: [AMBER] restraintmask: select residues around the coordinates of a point Thomas Evangelidis
- Re: [AMBER] Amber16 Parallel CUDA Tests Steven Ford
- [AMBER] average pdb distorted Thakur, Abhishek
- Re: [AMBER] average pdb distorted Hai Nguyen
- Re: [AMBER] average pdb distorted Thakur, Abhishek
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Dickson, Callum J
- [AMBER] MDGX tutorial? Dickson, Callum J
- Re: [AMBER] MDGX tutorial? David Cerutti
- Re: [AMBER] restraintmask: select residues around the coordinates of a point David A Case
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Wesley Michael Botello-Smith
- Re: [AMBER] restraintmask: select residues around the coordinates of a point Thomas Evangelidis
- Re: [AMBER] MDGX tutorial? Dickson, Callum J
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Wesley Michael Botello-Smith
- Re: [AMBER] average pdb distorted David A Case
- Re: [AMBER] restraintmask: select residues around the coordinates of a point David A Case
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) David A Case
- Re: [AMBER] AMBER Digest, Vol 1646, Issue 1 bharat gupta
Tuesday, 26 July 2016
- Re: [AMBER] average pdb distorted Marc van der Kamp
- [AMBER] ntr vs ibelly. Saman Yousuf ali
- Re: [AMBER] ntr vs ibelly. Barbault Florent
- Re: [AMBER] ntr vs ibelly. Adrian Roitberg
- [AMBER] ntr vs ibelly. Saman Yousuf ali
- Re: [AMBER] ntr vs ibelly. Barbault Florent
- [AMBER] Failed to solvate the molecule during the TUTORIAL A8 Nikolay N. Kuzmich
- Re: [AMBER] Failed to solvate the molecule during the TUTORIAL A8 Kenneth Huang
- Re: [AMBER] Error MCPB when send the input Pengfei Li
- [AMBER] Error cuda Anna Cebrian Prats
- Re: [AMBER] ntr vs ibelly. David A Case
- [AMBER] cpptraj grid command multiple trajectories Sarah Graham
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Wesley Michael Botello-Smith
- Re: [AMBER] average pdb distorted Thakur, Abhishek
- Re: [AMBER] cpptraj grid command multiple trajectories Daniel Roe
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Daniel Roe
- Re: [AMBER] cpptraj grid command multiple trajectories Sarah Graham
- Re: [AMBER] cpptraj grid command multiple trajectories Daniel Roe
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) David A Case
Wednesday, 27 July 2016
- [AMBER] How to modify forcefield to use TIP4P-D water model Suguru ASAI
- Re: [AMBER] How to modify forcefield to use TIP4P-D water model David A Case
- [AMBER] paramfit Igor Marques
- Re: [AMBER] paramfit David Cerutti
- Re: [AMBER] How to modify forcefield to use TIP4P-D water model Suguru ASAI
Thursday, 28 July 2016
- [AMBER] make test.cuda failed Nikolay N. Kuzmich
- [AMBER] EEL become ****** in minimization Suguru ASAI
- Re: [AMBER] EEL become ****** in minimization David Cerutti
- [AMBER] Sander bomb: how to create a larger box Ruth Helena Tichauer
- Re: [AMBER] make test.cuda failed Marcos Serrou do Amaral
- Re: [AMBER] EEL become ****** in minimization Osman, Roman
- Re: [AMBER] EEL become ****** in minimization Suguru ASAI
- Re: [AMBER] EEL become ****** in minimization Thakur, Abhishek
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Daniel Roe
- Re: [AMBER] Cpptraj - Stat bug? Daniel Roe
- Re: [AMBER] Cpptraj - Stat bug? Daniel Roe
- Re: [AMBER] EEL become ****** in minimization David A Case
- Re: [AMBER] Cpptraj - Stat bug? Daniel Roe
- [AMBER] NMR restraint Ming Tang
- [AMBER] InVacuoWithDielc JAIME RUBIO MARTINEZ
Friday, 29 July 2016
- [AMBER] can amber14 be run with gtx1060 xjq
- Re: [AMBER] can amber14 be run with gtx1060 Ross Walker
- [AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar
- Re: [AMBER] NMR restraint David A Case
- [AMBER] Question about QM/MM Anna Cebrian Prats
- [AMBER] modified potentials Irem Altan
- Re: [AMBER] Cpptraj - Stat bug? Markus Schneider
- Re: [AMBER] Cpptraj - Stat bug? Daniel Roe
- Re: [AMBER] rmsd calculations on multiple trajectories Daniel Roe
- Re: [AMBER] modified potentials David Cerutti
- Re: [AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar
- Re: [AMBER] rmsd calculations on multiple trajectories Carlos Simmerling
- Re: [AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar
- Re: [AMBER] rmsd calculations on multiple trajectories Carlos Simmerling
- Re: [AMBER] rmsd calculations on multiple trajectories Daniel Roe
- Re: [AMBER] rmsd calculations on multiple trajectories Daniel Roe
- Re: [AMBER] modified potentials Irem Altan
- Re: [AMBER] modified potentials Carlos Simmerling
- Re: [AMBER] rmsd calculations on multiple trajectories Carlos Simmerling
- [AMBER] Problem setting AMBERHOME as environment variable Ambertools 16 Linux Elissa Fink
- Re: [AMBER] Problem setting AMBERHOME as environment variable Ambertools 16 Linux Daniel Roe
- Re: [AMBER] modified potentials David Cerutti
- Re: [AMBER] rmsd calculations on multiple trajectories Hai Nguyen
- [AMBER] MMPBSA (MD or aMD) Thakur, Abhishek
- [AMBER] figure legend problem in the tutorial? Albert
- Re: [AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar
- Re: [AMBER] MMPBSA (MD or aMD) Jason Swails
- Re: [AMBER] MMPBSA (MD or aMD) Thakur, Abhishek
- Re: [AMBER] figure legend problem in the tutorial? Robin Betz
- Re: [AMBER] paramfit Robin Betz
- Re: [AMBER] MMPBSA (MD or aMD) Thakur, Abhishek
- Re: [AMBER] rmsd calculations on multiple trajectories Daniel Roe
- Re: [AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar
- Re: [AMBER] rmsd calculations on multiple trajectories Daniel Roe
- Re: [AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar
- Re: [AMBER] rmsd calculations on multiple trajectories Daniel Roe
- Re: [AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar
- Re: [AMBER] rmsd calculations on multiple trajectories Daniel Roe
- [AMBER] Exposed hydrophobic surface area anu chandra
- Re: [AMBER] MMPBSA (MD or aMD) Jason Swails
- Re: [AMBER] Question about QM/MM Dr. Andreas W. Goetz
- Re: [AMBER] MMPBSA (MD or aMD) Daniel Roe
- Re: [AMBER] Exposed hydrophobic surface area Daniel Roe
Saturday, 30 July 2016
- [AMBER] where is amber.jupyter? Albert
- Re: [AMBER] where is amber.jupyter? Hai Nguyen
- [AMBER] Calculating Salt bridge interactions- Protein and RNA Muthukumaran R
- [AMBER] dssp xlabel conversion. Saman Yousuf ali
- Re: [AMBER] where is amber.jupyter? Albert
- Re: [AMBER] where is amber.jupyter? Hai Nguyen
- Re: [AMBER] where is amber.jupyter? Albert
- Re: [AMBER] where is amber.jupyter? Albert
- Re: [AMBER] where is amber.jupyter? Hai Nguyen
- Re: [AMBER] where is amber.jupyter? Albert
- Re: [AMBER] dssp xlabel conversion. Daniel Roe
- Re: [AMBER] InVacuoWithDielc David A Case
- Re: [AMBER] average pdb distorted kenfack cyril
- Re: [AMBER] Sander bomb: how to create a larger box Bilal Nizami
- [AMBER] hydrogen bond occupancy plot cpptraj Saman Yousuf ali
Sunday, 31 July 2016
- [AMBER] Hii ankita mehta
- Re: [AMBER] Hii Daniel Roe

Last message date: Sun Jul 31 2016 - 07:00:03 PDT
Archived on: Sun Nov 24 2024 - 05:55:36 PST

Amber Archive Jul 2016 by date