Amber Archive Oct 2018: by date

Monday, 1 October 2018
- [AMBER] Regarding calculation of RMSD DHEERAJ CHITARA
- [AMBER] Query regarding Amber installation Rakesh Srivastava
- Re: [AMBER] Query regarding Amber installation Hai Nguyen
- Re: [AMBER] Query regarding Amber installation David A Case
- Re: [AMBER] Query regarding Amber installation Rakesh Srivastava
- [AMBER] Water Density Seibold, Steve Allan
- [AMBER] Total system charge and TI simulations Veenis, Andrew Jay
- Re: [AMBER] Water Density David Case
- Re: [AMBER] Total system charge and TI simulations David Case
Tuesday, 2 October 2018
- [AMBER] ligand_preparation_general_rule Antonio Amber Carlesso
- Re: [AMBER] ligand_preparation_general_rule Bill Ross
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphälinger
- Re: [AMBER] ligand_preparation_general_rule David Case
- Re: [AMBER] Water Density Seibold, Steve Allan
- [AMBER] add12_6_4 Parmed error Nikolay N. Kuzmich
- Re: [AMBER] Reducing memory usage in lifetime analyses Daniel Roe
- Re: [AMBER] add12_6_4 Parmed error Pengfei Li
- [AMBER] NFE _Lib error Hugo Macdermott-Opeskin
Wednesday, 3 October 2018
- Re: [AMBER] ligand_preparation_general_rule Antonio Amber Carlesso
- Re: [AMBER] Reducing memory usage in lifetime analyses Gustaf Olsson
- Re: [AMBER] ligand_preparation_general_rule David Case
- Re: [AMBER] ligand_preparation_general_rule David Case
- [AMBER] Number of inter-conversions between minima on a FEL Chetna Tyagi
- [AMBER] AMBER18 compilation using intel compiler pavel.banas.upol.cz
- Re: [AMBER] AMBER18 compilation using intel compiler David A Case
- Re: [AMBER] NFE _Lib error Feng Pan
- Re: [AMBER] ligand_preparation_general_rule Antonio Amber Carlesso
- [AMBER] get energy of some residues of the molecule Johannes Kalliauer
- [AMBER] Cpptraj bond deforming Aashish Bhatt
- Re: [AMBER] Number of inter-conversions between minima on a FEL Daniel Roe
- [AMBER] Part of protein going out of the box Leena Aggarwal
- Re: [AMBER] AMBER18 compilation using intel compiler pavel.banas.upol.cz
- Re: [AMBER] Cpptraj bond deforming Daniel Roe
- Re: [AMBER] Problems with MPI compilation gb_force.F90 Ruben Ramos Horta
- Re: [AMBER] Cpptraj bond deforming Aashish Bhatt
- Re: [AMBER] Cpptraj bond deforming Daniel Roe
- Re: [AMBER] Part of protein going out of the box Daniel Roe
- Re: [AMBER] Cpptraj bond deforming Aashish Bhatt
- Re: [AMBER] Cpptraj bond deforming Daniel Roe
- Re: [AMBER] pmemd.MPI won't work in Amber 18 Hai Long
- Re: [AMBER] Cpptraj bond deforming Aashish Bhatt
Thursday, 4 October 2018
- [AMBER] Problem in saving amber prmtop file from DNA pdb file creacted using server http://structure.usc.edu/make-na/server.html) ? Subrata Paul
- [AMBER] Amber 18 installation problem MR. RABINDRANATH PAUL
- Re: [AMBER] Amber 18 installation problem Bill Ross
- Re: [AMBER] Problem in saving amber prmtop file from DNA pdb file creacted using server http://structure.usc.edu/make-na/server.html) ? Bill Ross
- Re: [AMBER] Amber 18 installation problem MR. RABINDRANATH PAUL
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphälinger
- [AMBER] How to run the test in HPC cluster and GPU Saikat Pal
- Re: [AMBER] add12_6_4 Parmed error Nikolay N. Kuzmich
- [AMBER] Amber to gromacs topology Saikat Pal
- Re: [AMBER] pmemd.MPI won't work in Amber 18 Ross Walker
- Re: [AMBER] ligand_preparation_general_rule David A Case
- Re: [AMBER] Amber 18 installation problem Daniel Roe
- Re: [AMBER] Problem in saving amber prmtop file from DNA pdb file creacted using server http://structure.usc.edu/make-na/server.html) ? David A Case
- [AMBER] FW: Problem running the adqmmm test, one mdcrd file only Dreab, Ana
- Re: [AMBER] Amber to gromacs topology Matias Machado
- Re: [AMBER] Amber to gromacs topology Saikat Pal
- Re: [AMBER] R.E.D. Server is down Stéphane Téletchéa
- Re: [AMBER] Amber to gromacs topology Matias Machado
- Re: [AMBER] Amber to gromacs topology Saikat Pal
- Re: [AMBER] FW: Problem running the adqmmm test, one mdcrd file only David A Case
- Re: [AMBER] Amber to gromacs topology David A Case
- [AMBER] Setting up parameters for a simulation at 350K Dmitry Suplatov
- Re: [AMBER] Amber 18 installation problem MR. RABINDRANATH PAUL
- Re: [AMBER] Amber 18 installation problem Hai Nguyen
- Re: [AMBER] Setting up parameters for a simulation at 350K David Cerutti
- Re: [AMBER] Setting up parameters for a simulation at 350K Dmitry Suplatov
- Re: [AMBER] Setting up parameters for a simulation at 350K Bill Ross
- Re: [AMBER] Amber 18 installation problem Bill Ross
- Re: [AMBER] Setting up parameters for a simulation at 350K David Cerutti
- Re: [AMBER] Amber 18 installation problem MR. RABINDRANATH PAUL
- Re: [AMBER] Query regarding Amber installation Rakesh Srivastava
Friday, 5 October 2018
- [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Ross Walker
- [AMBER] number of reaction coordinate in a ASMD run sangita kachhap
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Marek Maly
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Ross Walker
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers David Cerutti
- [AMBER] questions on pmemd.cuda for thermodynamic integration Song-Ho Chong
- Re: [AMBER] How to run the test in HPC cluster and GPU Charles Lin
- [AMBER] acpype_error Antonio Amber Carlesso
- Re: [AMBER] acpype_error dhaval patel
- Re: [AMBER] acpype_error Antonio Amber Carlesso
- Re: [AMBER] ligand_preparation_general_rule Antonio Amber Carlesso
- Re: [AMBER] acpype_error Alan
- Re: [AMBER] acpype_error Antonio Amber Carlesso
Saturday, 6 October 2018
- [AMBER] Warning for MMPBSA.py calculation maryam azimzadehirani
- Re: [AMBER] Problem with antechamber/acdoctor David Case
- [AMBER] Lipid Order Parameters somdev pahari
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Ross Walker
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Ross Walker
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers David Cerutti
- Re: [AMBER] FW: Problem running the adqmmm test, one mdcrd file only Dreab, Ana
- Re: [AMBER] FW: Problem running the adqmmm test, one mdcrd file only Goetz, Andreas
Sunday, 7 October 2018
- Re: [AMBER] FW: Problem running the adqmmm test, one mdcrd file only Dreab, Ana
- [AMBER] Amber Install on Mojave (ld: library not found for -lmc) Fix Andrew Schaub
Monday, 8 October 2018
- [AMBER] Testing C++11 support: Not present Gustaf Olsson
- Re: [AMBER] Testing C++11 support: Not present Bill Ross
- Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson
- [AMBER] Parameters for atom CE in lj_1264_pol.dat Nikolay N. Kuzmich
- [AMBER] Full: Parameters for atom CE in lj_1264_pol.dat Nikolay N. Kuzmich
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Marek Maly
- [AMBER] Antechamber on unknown residue Keiran Corbett
- Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers David Cerutti
- Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson
- [AMBER] GPU memory usage with center-of-mass restratints David Case
- Re: [AMBER] Amber Install on Mojave (ld: library not found for -lmc) Fix Andrew Schaub
- Re: [AMBER] Antechamber on unknown residue David Case
- [AMBER] Restrain distance for Umbrella Sampling emanuele falbo
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Charles Lin
- Re: [AMBER] Amber Install on Mojave (ld: library not found for -lmc) Fix Gustaf Olsson
- Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson
- Re: [AMBER] Restrain distance for Umbrella Sampling David A Case
- Re: [AMBER] Restrain distance for Umbrella Sampling emanuele falbo
- Re: [AMBER] Amber Install on Mojave (ld: library not found for -lmc) Fix Andrew Schaub
- Re: [AMBER] Amber Install on Mojave (ld: library not found for -lmc) Fix Andrew Schaub
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Marek Maly
- [AMBER] torsion angles of carbon allotropes Ibrahim Said
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers David Cerutti
- [AMBER] RTX 2080 Benchmarks Bisignano, Paola
- Re: [AMBER] RTX 2080 Benchmarks David Cerutti
- [AMBER] constant pH pmemd.cuda error andreas.tosstorff.cup.uni-muenchen.de
- Re: [AMBER] RTX 2080 Benchmarks Bisignano, Paola
- Re: [AMBER] constant pH pmemd.cuda error Cruzeiro,Vinicius Wilian D
- [AMBER] Errors when installing with MPI Felipe Franco Gonzalez
- Re: [AMBER] constant pH pmemd.cuda error andreas.tosstorff.cup.uni-muenchen.de
- Re: [AMBER] constant pH pmemd.cuda error Cruzeiro,Vinicius Wilian D
- Re: [AMBER] torsion angles of carbon allotropes David Case
- Re: [AMBER] Errors when installing with MPI David Case
- [AMBER] Regarding Leap Charu Sharma (JRF)
- [AMBER] Fwd: The results of your email commands Charu Sharma (JRF)
- Re: [AMBER] Regarding Leap Elvis Martis
- Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson
Tuesday, 9 October 2018
- [AMBER] Rigid body simulation of Nitrogenase's FeMo cluster Sadra Aghajani
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Marek Maly
- Re: [AMBER] torsion angles of carbon allotropes Ibrahim Said
- [AMBER] Selecting specific set of molecules for output trajectory anu chandra
- Re: [AMBER] Rigid body simulation of Nitrogenase's FeMo cluster David A Case
- Re: [AMBER] Selecting specific set of molecules for output trajectory David A Case
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Ross Walker
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Marek Maly
- Re: [AMBER] Testing C++11 support: Not present Daniel Roe
- Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson
- [AMBER] viscosity calculation Lorenzo Gontrani
- Re: [AMBER] Testing C++11 support: Not present Daniel Roe
- [AMBER] hydrogen bond analysis Qinghua Liao
- Re: [AMBER] Full: Parameters for atom CE in lj_1264_pol.dat Pengfei Li
- Re: [AMBER] hydrogen bond analysis Zuo, Zhicheng
- Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson
- [AMBER] Regarding calculation of RMSD using AMBER-18 CPPTRAJ V-18.01 DHEERAJ CHITARA
Wednesday, 10 October 2018
- [AMBER] Unkown residue to AMBER Keiran Corbett
- Re: [AMBER] hydrogen bond analysis Qinghua Liao
- [AMBER] Striping distance based water residues Kshatresh Dutta Dubey
- Re: [AMBER] Regarding Leap Charu Sharma (JRF)
- Re: [AMBER] Unkown residue to AMBER David A Case
- Re: [AMBER] Striping distance based water residues Daniel Roe
- Re: [AMBER] Regarding calculation of RMSD using AMBER-18 CPPTRAJ V-18.01 Daniel Roe
- Re: [AMBER] hydrogen bond analysis Daniel Roe
- [AMBER] Cationic dummy Zinc atom in accelerated molecular dynamics M RCC
- Re: [AMBER] Testing C++11 support: Not present Daniel Roe
- [AMBER] FW: Fatal error in RESP calculation fateme haghighi
- Re: [AMBER] FW: Fatal error in RESP calculation David A Case
- Re: [AMBER] Regarding Leap Elvis Martis
- [AMBER] Fwd: Lipid Order Parameters somdev pahari
- Re: [AMBER] hydrogen bond analysis Qinghua Liao
- Re: [AMBER] Striping distance based water residues Kshatresh Dutta Dubey
- Re: [AMBER] Lipid Order Parameters Daniel Roe
- [AMBER] Water do not see the system.... Vito GENNA
- [AMBER] .gesp file is not generated for Antechamber M RCC
- [AMBER] AMBER and plumed Pierre GIRARD
- Re: [AMBER] AMBER and plumed Qinghua Liao
- Re: [AMBER] Water do not see the system.... David A Case
- Re: [AMBER] AMBER and plumed Pierre GIRARD
- Re: [AMBER] AMBER and plumed Qinghua Liao
- Re: [AMBER] Water do not see the system.... Vito GENNA
- Re: [AMBER] AMBER and plumed Pierre GIRARD
- [AMBER] RTX2080 Performance Update for AMBER 18 Ross Walker
- [AMBER] AMBER 18 INSTALLATION ON CLUSTER - ERROR Midhun K Madhu
Thursday, 11 October 2018
- [AMBER] error in RESP calculation fateme haghighi
- Re: [AMBER] Regarding calculation of RMSD using AMBER-18 CPPTRAJ V-18.01 DHEERAJ CHITARA
- Re: [AMBER] Water do not see the system.... Vito GENNA
- [AMBER] RTX2080TI Performance Ross Walker
- [AMBER] calculation of free binding energy when a residue is mutated to residues other than alanine? ali akbar
- Re: [AMBER] Regarding calculation of RMSD using AMBER-18 CPPTRAJ V-18.01 Daniel Roe
- Re: [AMBER] AMBER 18 INSTALLATION ON CLUSTER - ERROR David A Case
- Re: [AMBER] error in RESP calculation David A Case
- Re: [AMBER] RTX2080TI Performance David Cerutti
- [AMBER] SIRAH 2.0: a finer taste in coarse-grained protiens Matias Machado
- Re: [AMBER] Water do not see the system.... Matias Machado
- Re: [AMBER] Water do not see the system.... Vito GENNA
- Re: [AMBER] Water do not see the system.... Daniel Roe
- Re: [AMBER] Water do not see the system.... Daniel Roe
- Re: [AMBER] RTX2080TI Performance Marek Maly
- [AMBER] Installation issues on Mac OSX 10.14 Matthew Fisher
- [AMBER] Commented AmberTools functions Ruben Ramos Horta
- Re: [AMBER] Water do not see the system.... Vito GENNA
- Re: [AMBER] Testing C++11 support: Not present Andrew Schaub
- Re: [AMBER] Installation issues on Mac OSX 10.14 David Case
- Re: [AMBER] Installation issues on Mac OSX 10.14 Gustaf Olsson
- Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson
Friday, 12 October 2018
- Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson
- Re: [AMBER] AMBER Digest, Vol 2436, Issue 1 Midhun K Madhu
- Re: [AMBER] viscosity calculation David A Case
- Re: [AMBER] Amber Install on Mojave David A Case
- Re: [AMBER] Testing C++11 support: Not present Daniel Roe
- Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson
- Re: [AMBER] RTX2080TI Performance Ross Walker
- Re: [AMBER] Full: Parameters for atom CE in lj_1264_pol.dat Nikolay N. Kuzmich
- Re: [AMBER] viscosity calculation Arun Srikanth
- [AMBER] How to use ff99SB-ILDN in Amber16 Yang, Tianyi
- Re: [AMBER] How to use ff99SB-ILDN in Amber16 Qinghua Liao
- Re: [AMBER] How to use ff99SB-ILDN in Amber16 Vito GENNA
- Re: [AMBER] Regarding Leap Charu Sharma (JRF)
Saturday, 13 October 2018
- Re: [AMBER] Regarding Leap Elvis Martis
- Re: [AMBER] Regarding Leap Charu Sharma (JRF)
Sunday, 14 October 2018
- Re: [AMBER] Regarding Leap Elvis Martis
- [AMBER] Fondaparinux Amber Force Field Marcelo Andrade Chagas
Monday, 15 October 2018
- [AMBER] GAMD not running in CPU cluster Midhun K Madhu
- [AMBER] more on building Amber18 on Mojave David A Case
- Re: [AMBER] Installation issues on Mac OSX 10.14 Matthew Fisher
- [AMBER] GLYCAM Amber Force Field to Fondaparinux...? Marcelo Andrade Chagas
- Re: [AMBER] Using custom non-bonding potential, drude oscillator in Amber18 Kyeong-jun Jeong
Tuesday, 16 October 2018
- Re: [AMBER] more on building Amber18 on Mojave Gustaf Olsson
- Re: [AMBER] Using custom non-bonding potential, drude oscillator in Amber18 David A Case
- Re: [AMBER] GLYCAM Amber Force Field to Fondaparinux...? Lachele Foley
- [AMBER] Using custom non-bonding potential, drude oscillator in Amber18 Kyeong-jun Jeong
- [AMBER] using parmed (python api) to merge two parm7 files for TI Wesley Michael Botello-Smith
- Re: [AMBER] using parmed (python api) to merge two parm7 files for TI Wesley Michael Botello-Smith
Wednesday, 17 October 2018
- [AMBER] does surf command use for stripped trajectory? g.bakrani.sci.ui.ac.ir
- Re: [AMBER] Regarding Leap Charu Sharma (JRF)
- Re: [AMBER] Regarding Leap Chetna Tyagi
- Re: [AMBER] Regarding Leap Charu Sharma (JRF)
- Re: [AMBER] Regarding Leap Charu Sharma (JRF)
- Re: [AMBER] Regarding Leap Chetna Tyagi
- Re: [AMBER] Regarding Leap Charu Sharma (JRF)
- [AMBER] error in Resp fateme haghighi
- Re: [AMBER] Regarding Leap Chetna Tyagi
- Re: [AMBER] does surf command use for stripped trajectory? Daniel Roe
- Re: [AMBER] more on building Amber18 on Mojave David A Case
- [AMBER] Problem with tleap Ali Khodayari
- Re: [AMBER] Problem with tleap Bill Ross
- [AMBER] sugar derivatives parametrization Bisignano, Paola
- [AMBER] Parametarization error senal dinuka
- Re: [AMBER] Parametarization error Bill Ross
- [AMBER] Amber workshop in Europe? Albert
Thursday, 18 October 2018
- Re: [AMBER] more on building Amber18 on Mojave Gustaf Olsson
- Re: [AMBER] Parametarization error senal dinuka
- Re: [AMBER] Parametarization error Bill Ross
- [AMBER] FW: fatal error in Resp fateme haghighi
- Re: [AMBER] Parametarization error senal dinuka
- Re: [AMBER] Parametarization error Bill Ross
- [AMBER] Question about stripping waters Maria Clelia Milletti
- Re: [AMBER] sugar derivatives parametrization David Case
- Re: [AMBER] Parametarization error David Case
- [AMBER] Alternative way to do targeted MD Xiaoling Leng
- [AMBER] FW: fatal error in Resp fateme haghighi
- Re: [AMBER] Alternative way to do targeted MD Feng Pan
- Re: [AMBER] Question about stripping waters Daniel Roe
- Re: [AMBER] more on building Amber18 on Mojave Daniel Roe
- [AMBER] pi-pi And Aromatic Interactions Meng Wu
- Re: [AMBER] sugar derivatives parametrization Lachele Foley
- Re: [AMBER] sugar derivatives parametrization Lachele Foley
- Re: [AMBER] pi-pi And Aromatic Interactions Chris Neale
- Re: [AMBER] Parametarization error senal dinuka
- Re: [AMBER] more on building Amber18 on Mojave Gustaf Olsson
Friday, 19 October 2018
- Re: [AMBER] FW: fatal error in Resp David Case
- Re: [AMBER] pi-pi And Aromatic Interactions Christina Bergonzo
- [AMBER] Constrained QM.MM minimization Vito GENNA
- Re: [AMBER] Constrained QM.MM minimization Zuo, Zhicheng
- Re: [AMBER] Constrained QM.MM minimization Vito GENNA
- Re: [AMBER] Constrained QM.MM minimization Timothy Schutt
- Re: [AMBER] Constrained QM.MM minimization Timothy Schutt
- Re: [AMBER] Constrained QM.MM minimization Vito GENNA
- Re: [AMBER] sugar derivatives parametrization Bisignano, Paola
- Re: [AMBER] Constrained QM.MM minimization Vito GENNA
- Re: [AMBER] using parmed (python api) to merge two parm7 files for TI Jason Swails
- Re: [AMBER] Constrained QM.MM minimization David Case
- Re: [AMBER] Constrained QM.MM minimization Vito GENNA
- Re: [AMBER] pi-pi And Aromatic Interactions Chris Neale
- Re: [AMBER] Question about stripping waters Maria Clelia Milletti
- Re: [AMBER] pi-pi And Aromatic Interactions Carlos Simmerling
- Re: [AMBER] pi-pi And Aromatic Interactions Chris Neale
- Re: [AMBER] pi-pi And Aromatic Interactions Carlos Simmerling
- Re: [AMBER] pi-pi And Aromatic Interactions Jiri Sponer
- Re: [AMBER] pi-pi And Aromatic Interactions Jiri Sponer
- [AMBER] Amber force field for non-natural amino acids Mijiddorj B
Saturday, 20 October 2018
- Re: [AMBER] Amber force field for non-natural amino acids Carlos Simmerling
- Re: [AMBER] Question about stripping waters David Case
Sunday, 21 October 2018
- [AMBER] tleap gamma-carboxyglutamic acid linkage error Rajbinder Kaur Virk
Monday, 22 October 2018
- [AMBER] The make_na web service, and corresponding code David A Case
- Re: [AMBER] Amber force field for non-natural amino acids Mijiddorj B
- [AMBER] Error in Running tLEaP for Protein File Amartya Pradhan
- Re: [AMBER] Error in Running tLEaP for Protein File David A Case
- [AMBER] Simulating a covalently bound ligand senal dinuka
Tuesday, 23 October 2018
- Re: [AMBER] Simulating a covalently bound ligand David A Case
- Re: [AMBER] Question about stripping waters Maria Clelia Milletti
- [AMBER] Effective born radii calculations - No correct statistics returned at the end of the mdout file Eric Lang
- Re: [AMBER] Effective born radii calculations - No correct statistics returned at the end of the mdout file David A Case
- [AMBER] Struggling to convert AMBER .frcmod and .mol2 to GROMACS for HEME Matthew Fisher
- Re: [AMBER] Amber force field for non-natural amino acids Thomas Fox
- Re: [AMBER] Amber force field for non-natural amino acids Carlos Simmerling
- [AMBER] Material simulation using Amber and Interface FF Sundar
- Re: [AMBER] Struggling to convert AMBER .frcmod and .mol2 to GROMACS for HEME Bill Ross
- Re: [AMBER] Amber force field for non-natural amino acids Thomas Fox
- Re: [AMBER] Amber force field for non-natural amino acids Carlos Simmerling
- Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Matias Machado
- Re: [AMBER] Struggling to convert AMBER .frcmod and .mol2 to GROMACS for HEME David Case
Wednesday, 24 October 2018
- Re: [AMBER] Struggling to convert AMBER .frcmod and .mol2 to GROMACS for HEME ABEL Stephane
- [AMBER] TR : Struggling to convert AMBER .frcmod and .mol2 to GROMACS for HEME ABEL Stephane
- Re: [AMBER] Effective born radii calculations - No correct statistics returned at the end of the mdout file Eric Lang
- [AMBER] Topological error for Mg in .prepin file. Anuja Ware
- Re: [AMBER] Topological error for Mg in .prepin file. ABEL Stephane
- Re: [AMBER] Topological error for Mg in .prepin file. Anuja Ware
- Re: [AMBER] Topological error for Mg in .prepin file. ABEL Stephane
- [AMBER] Temperature-Replica Exchange MD Gilberto Pereira
- Re: [AMBER] Temperature-Replica Exchange MD Alessandro Contini
- Re: [AMBER] Alternative way to do targeted MD Xiaoling Leng
- Re: [AMBER] Temperature-Replica Exchange MD Cruzeiro,Vinicius Wilian D
- Re: [AMBER] Alternative way to do targeted MD Feng Pan
- Re: [AMBER] Topological error for Mg in .prepin file. David Case
- Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Rajbinder Kaur Virk
Thursday, 25 October 2018
- [AMBER] MD_Box_size_and_counterions_counting_general_rule Antonio Amber Carlesso
- [AMBER] Ca ion bond distances restraints with chelator ? Michael Shokhen
- Re: [AMBER] MD_Box_size_and_counterions_counting_general_rule David A Case
- Re: [AMBER] Ca ion bond distances restraints with chelator ? David A Case
- Re: [AMBER] sugar derivatives parametrization Lachele Foley
- [AMBER] Measuring Membrane Curvature somdev pahari
- [AMBER] Sander and Thermodynamic integration and softcore Khabiri, Morteza
- Re: [AMBER] Alternative way to do targeted MD Xiaoling Leng
- Re: [AMBER] Alternative way to do targeted MD Feng Pan
- [AMBER] Na+ ion got stuck at one C-terminal end Rakesh Srivastava
Friday, 26 October 2018
- [AMBER] error in distance restraint input file Michael Shokhen
- [AMBER] parmchk2 frcmod file Jon Uranga
- Re: [AMBER] Simulating a covalently bound ligand senal dinuka
- Re: [AMBER] Sander and Thermodynamic integration and softcore David A Case
- Re: [AMBER] error in distance restraint input file David A Case
- Re: [AMBER] parmchk2 frcmod file David A Case
- Re: [AMBER] error in distance restraint input file Michael Shokhen
- Re: [AMBER] parmchk2 frcmod file Jon Uranga
- [AMBER] Question Regarding GRID Saikat Pal
- [AMBER] non-bonded params hosein geraili
- Re: [AMBER] non-bonded params Matias Machado
- Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Matias Machado
- Re: [AMBER] Alternative way to do targeted MD Xiaoling Leng
- Re: [AMBER] Material simulation using Amber and Interface FF Pengfei Li
- Re: [AMBER] Topological error for Mg in .prepin file. Pengfei Li
- Re: [AMBER] Na+ ion got stuck at one C-terminal end Pengfei Li
- [AMBER] Post-process calculation of atomic forces SARAH JEANNE LEFAVE
- Re: [AMBER] Na+ ion got stuck at one C-terminal end Rakesh Srivastava
Saturday, 27 October 2018
- [AMBER] the unperturbed charge of the unit is not zero soukaina louerdi
- Re: [AMBER] the unperturbed charge of the unit is not zero David Case
Sunday, 28 October 2018
- Re: [AMBER] the unperturbed charge of the unit is not zero soukaina louerdi
- Re: [AMBER] Alternative way to do targeted MD Feng Pan
Monday, 29 October 2018
- Re: [AMBER] the unperturbed charge of the unit is not zero David A Case
- [AMBER] Interplane angles using vector and vectormath in cpptraj Matthew Turner
- Re: [AMBER] Interplane angles using vector and vectormath in cpptraj Wesley Michael Botello-Smith
Tuesday, 30 October 2018
- Re: [AMBER] the unperturbed charge of the unit is not zero soukaina louerdi
- Re: [AMBER] the unperturbed charge of the unit is not zero David A Case
- Re: [AMBER] the unperturbed charge of the unit is not zero soukaina louerdi
- Re: [AMBER] Interplane angles using vector and vectormath in cpptraj Daniel Roe
- [AMBER] AMBER18: user-defined reaction coordinate in umbrella sampling 李耀
- Re: [AMBER] Post-process calculation of atomic forces Daniel Roe
- Re: [AMBER] Regarding Leap Charu Sharma (JRF)
- Re: [AMBER] the unperturbed charge of the unit is not zero David A Case
- Re: [AMBER] Regarding Leap David A Case
- Re: [AMBER] the unperturbed charge of the unit is not zero Charu Sharma (JRF)
- Re: [AMBER] Regarding Leap Charu Sharma (JRF)
- Re: [AMBER] Regarding Leap Charu Sharma (JRF)
- Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Rajbinder Kaur Virk
- [AMBER] Fortran runtime error: Bad value during integer read Thomas Evangelidis
- Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error David Case
- Re: [AMBER] Fortran runtime error: Bad value during integer read David Case
- [AMBER] Amber Error (an illegal memory access) Avirup Ghosh
Wednesday, 31 October 2018
- Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Rajbinder Kaur Virk
- Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Bill Ross
- Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Bill Ross
- [AMBER] amber18 installation problem Mary Dutta
- Re: [AMBER] Fortran runtime error: Bad value during integer read Thomas Evangelidis
- Re: [AMBER] Fortran runtime error: Bad value during integer read Carlos Simmerling
- Re: [AMBER] Fortran runtime error: Bad value during integer read Thomas Evangelidis
- Re: [AMBER] Fortran runtime error: Bad value during integer read Carlos Simmerling
- [AMBER] Problem regarding radial command Saikat Pal
- Re: [AMBER] amber18 installation problem David A Case
- Re: [AMBER] amber18 installation problem David A Case
- Re: [AMBER] MD_Box_size_and_counterions_counting_general_rule Matias Machado
- [AMBER] CUDA 10.0 vs CUDA 9.2 for Amber18&1080Ti GTX - any gain in performance? Nikolay N. Kuzmich
- Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Matias Machado
- Re: [AMBER] Post-process calculation of atomic forces SARAH JEANNE LEFAVE
- Re: [AMBER] CUDA 10.0 vs CUDA 9.2 for Amber18&1080Ti GTX - any gain in performance? Ross Walker

Last message date: Wed Oct 31 2018 - 13:30:03 PDT
Archived on: Fri Apr 26 2024 - 05:55:49 PDT

Amber Archive Oct 2018 by date