Amber Archive Dec 2020: by date

Tuesday, 1 December 2020
- Re: [AMBER] TI electrostatic free energy Franz Waibl
- [AMBER] pmemd.cuda: error while loading shared libraries: libgfortran.so.4: cannot open shared object file: No such file or directory Sruthi Sudhakar
- Re: [AMBER] TI electrostatic free energy] David A Case
- Re: [AMBER] pmemd.cuda: error while loading shared libraries: libgfortran.so.4: cannot open shared object file: No such file or directory David A Case
- Re: [AMBER] TI electrostatic free energy] Franz Waibl
- [AMBER] MMBSA.py.MPI installation Jose Manuel Granadino Roldán
- [AMBER] C++ Programmer Position Lachele Foley
- [AMBER] amber 20 compilation problem Jordi Bujons
- Re: [AMBER] TI electrostatic free energy] David A Case
- [AMBER] question about dihedral angles Gordon Richard Chalmers
- Re: [AMBER] question about dihedral angles Gordon Richard Chalmers
- Re: [AMBER] amber 20 compilation problem David A Case
- Re: [AMBER] question about dihedral angles David A Case
- Re: [AMBER] question about dihedral angles Gordon Richard Chalmers
- [AMBER] Imaging issue in DNA - cpptraj Satyaseelan C
- Re: [AMBER] question about dihedral angles Karl Kirschner
Wednesday, 2 December 2020
- Re: [AMBER] Imaging issue in DNA - cpptraj Gustaf Olsson
- Re: [AMBER] Imaging issue in DNA - cpptraj Dr. Anselm Horn
- Re: [AMBER] Imaging issue in DNA - cpptraj lomzov
- Re: [AMBER] NOE analysis with cpptraj Pavlína Pokorná
- Re: [AMBER] question about dihedral angles David A Case
- Re: [AMBER] Imaging issue in DNA - cpptraj David A Case
- Re: [AMBER] question about dihedral angles Gordon Richard Chalmers
- Re: [AMBER] question about dihedral angles Gordon Richard Chalmers
- Re: [AMBER] question about dihedral angles Gordon Richard Chalmers
- Re: [AMBER] question about dihedral angles Daniel Roe
- [AMBER] Terminal O5'/O3' for nucleosides in ff86? Kenneth Huang
- Re: [AMBER] question about dihedral angles Gordon Richard Chalmers
- Re: [AMBER] question about dihedral angles Carlos Simmerling
- Re: [AMBER] question about dihedral angles Gordon Richard Chalmers
- Re: [AMBER] question about dihedral angles Gordon Richard Chalmers
- Re: [AMBER] question about dihedral angles Gordon Richard Chalmers
- [AMBER] How to use GAFF2? Alexander Izvorski
- Re: [AMBER] question about dihedral angles Bill Ross
- Re: [AMBER] question about dihedral angles Bill Ross
- Re: [AMBER] question about dihedral angles Bill Ross
- [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA 贺俊宏
- Re: [AMBER] question about dihedral angles Gordon Richard Chalmers
- [AMBER] Mixing Force Constants In DISANG Files Sharif Nada
- Re: [AMBER] question about dihedral angles Gordon Richard Chalmers
- [AMBER] app.run_mmpbsa() and mdout files were not created divyabharathi korlepara
Thursday, 3 December 2020
- Re: [AMBER] How to use GAFF2? Gustaf Olsson
- Re: [AMBER] Mixing Force Constants In DISANG Files Carlos Simmerling
- Re: [AMBER] How to use GAFF2? David A Case
- Re: [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA David A Case
- Re: [AMBER] app.run_mmpbsa() and mdout files were not created David A Case
- Re: [AMBER] Terminal O5'/O3' for nucleosides in ff86? David A Case
- Re: [AMBER] app.run_mmpbsa() and mdout files were not created divyabharathi korlepara
- Re: [AMBER] MMPBSA.py bad atom type: M1 error Vaibhav Dixit
- Re: [AMBER] Terminal O5'/O3' for nucleosides in ff86? Kenneth Huang
- Re: [AMBER] MMPBSA.py bad atom type: M1 error Ray Luo
- Re: [AMBER] Mixing Force Constants In DISANG Files Sharif Nada
- [AMBER] MMPBSA.py.MPI parallel installation using run_cmake divyabharathi korlepara
- [AMBER] Calculation halted while running simulation angad sharma
- Re: [AMBER] Calculation halted while running simulation Carlos Simmerling
- [AMBER] Missing Iron (Fe) DFTB3 parameters for QM/MM simulation of Enzyme Hafiz Saqib Ali
- [AMBER] G quadruplex ions minimization Jisha B
- Re: [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA 贺俊宏
- Re: [AMBER] MMPBSA.py bad atom type: M1 error Vaibhav Dixit
- Re: [AMBER] MMPBSA.py bad atom type: M1 error Ray Luo
- Re: [AMBER] MMPBSA.py bad atom type: M1 error Vaibhav Dixit
- Re: [AMBER] How to use GAFF2? Alexander Izvorski
- Re: [AMBER] How to use GAFF2? Alexander Izvorski
Friday, 4 December 2020
- Re: [AMBER] G quadruplex ions minimization Juraj Dobias
- Re: [AMBER] Calculation halted while running simulation David A Case
- Re: [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA David A Case
- Re: [AMBER] How to use GAFF2? David A Case
- Re: [AMBER] MMPBSA.py.MPI parallel installation using run_cmake David A Case
- Re: [AMBER] An error during NPT/production (GPU run) David A Case
- Re: [AMBER] MMBSA.py.MPI installation David A Case
- Re: [AMBER] amber 20 compilation problem (David A Case) Jordi Bujons
- Re: [AMBER] Imaging issue in DNA - cpptraj Satyaseelan C
- Re: [AMBER] G quadruplex ions minimization Bill Ross
- [AMBER] Question about atomic charges Pinky Mazumder
- Re: [AMBER] Question about atomic charges Bill Ross
- Re: [AMBER] G quadruplex ions minimization Jiri Sponer
- Re: [AMBER] How to use GAFF2? Alexander Izvorski
- Re: [AMBER] Question about atomic charges Carlos Simmerling
- Re: [AMBER] Imaging issue in DNA - cpptraj Daniel Roe
- Re: [AMBER] ABMD NFE queries Feng Pan
- Re: [AMBER] Regarding to the parameters setup in SMD simulation Feng Pan
- Re: [AMBER] MMBSA.py.MPI installation Jose Manuel Granadino Roldán
- [AMBER] Identifying the equilibrated production region of a MD simulation trajectory Leena Aggarwal
Saturday, 5 December 2020
- Re: [AMBER] MMBSA.py.MPI installation David A Case
- Re: [AMBER] Identifying the equilibrated production region of a MD simulation trajectory Carlos Simmerling
- Re: [AMBER] Identifying the equilibrated production region of a MD simulation trajectory Thomas Cheatham
Sunday, 6 December 2020
- [AMBER] Effects of scalpha in softcore runs Sharif Nada
- Re: [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA 贺俊宏
Monday, 7 December 2020
- Re: [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA David A Case
- [AMBER] error after simulation angad sharma
- Re: [AMBER] Tri-coordination environment in zinc Pengfei Li
- Re: [AMBER] Tri-coordination environment in zinc Pengfei Li
- Re: [AMBER] error after simulation Thomas Cheatham
- Re: [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA 贺俊宏
Tuesday, 8 December 2020
- Re: [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA David A Case
- [AMBER] lj1264 in vacuum Brian Radak
- Re: [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA 贺俊宏
Wednesday, 9 December 2020
- Re: [AMBER] An error during NPT/production (GPU run) David Cerutti
- Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? David Cerutti
- [AMBER] Regarding Ions renumbering. DHEERAJ CHITARA
- Re: [AMBER] Regarding Ions renumbering. Gustaf Olsson
- [AMBER] Regarding Gaussian Accelerated MD Sruthi Sudhakar
- [AMBER] Negative values in RDF analyses? Gustaf Olsson
- Re: [AMBER] Regarding Ions renumbering. Christina Bergonzo
- Re: [AMBER] Tri-coordination environment in zinc SATYAJIT KHATUA
Thursday, 10 December 2020
- [AMBER] B-ob-si-c3 dihedral parametization RESP/Scan problem Erdem Yeler
Wednesday, 9 December 2020
- [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Vaibhav Dixit
Thursday, 10 December 2020
- Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Raman Preet Singh
Wednesday, 9 December 2020
- Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Vaibhav Dixit
Thursday, 10 December 2020
- Re: [AMBER] Negative values in RDF analyses? Daniel Roe
- Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Raman Preet Singh
- [AMBER] Regarding Gaussian Accelerated MD Sruthi Sudhakar
- [AMBER] How to proceed if system charge is non-zero and non-integral Amit Sharma (Asstt. Prof., MCARS)
- [AMBER] Bug AmberTools20 parallel installation Arsene Marian Alain
- Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Vaibhav Dixit
- Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Raman Preet Singh
- Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Vaibhav Dixit
- Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 David A Case
- Re: [AMBER] How to proceed if system charge is non-zero and non-integral David A Case
- Re: [AMBER] Bug AmberTools20 parallel installation David A Case
- [AMBER] Charged species with antechamber Sam Walsworth (Researcher)
- Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Vaibhav Dixit
- Re: [AMBER] Tri-coordination environment in zinc SATYAJIT KHATUA
- Re: [AMBER] Charged species with antechamber Dr. Anselm Horn
- Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Vaibhav Dixit
- [AMBER] tleap building a peptide Seibold, Steve Allan
- Re: [AMBER] tleap building a peptide Carlos Simmerling
- Re: [AMBER] tleap building a peptide Bill Ross
- Re: [AMBER] Charged species with antechamber David A Case
- Re: [AMBER] tleap building a peptide Seibold, Steve Allan
- Re: [AMBER] tleap building a peptide David A Case
- Re: [AMBER] tleap building a peptide Seibold, Steve Allan
- Re: [AMBER] Charged species with antechamber Sam Walsworth (Researcher)
- [AMBER] how to convert (psf) to (prmtop) and (incprd) Pinky Mazumder
- Re: [AMBER] cellulose crystal structure ( cellulose bundles) Pinky Mazumder
Friday, 11 December 2020
- Re: [AMBER] Charged species with antechamber Gustaf Olsson
- [AMBER] Box info not found in prmtop file Amit Sharma (Asstt. Prof., MCARS)
- Re: [AMBER] Box info not found in prmtop file Carlos Simmerling
- Re: [AMBER] An error during NPT/production (GPU run) Женя Елизарова
- [AMBER] S2 order parameter not being calculated in IRED analysis. Chetna Tyagi
- Re: [AMBER] how to convert (psf) to (prmtop) and (incprd) David A Case
- Re: [AMBER] Box info not found in prmtop file Amit Sharma (Asstt. Prof., MCARS)
- Re: [AMBER] An error during NPT/production (GPU run) David Cerutti
- Re: [AMBER] Box info not found in prmtop file Carlos Simmerling
- Re: [AMBER] Box info not found in prmtop file Amit Sharma (Asstt. Prof., MCARS)
- Re: [AMBER] Box info not found in prmtop file Carlos Simmerling
- Re: [AMBER] Box info not found in prmtop file Amit Sharma (Asstt. Prof., MCARS)
- Re: [AMBER] Box info not found in prmtop file Carlos Simmerling
- Re: [AMBER] Box info not found in prmtop file Amit Sharma (Asstt. Prof., MCARS)
- Re: [AMBER] Box info not found in prmtop file Carlos Simmerling
- Re: [AMBER] Box info not found in prmtop file Amit Sharma (Asstt. Prof., MCARS)
- Re: [AMBER] lj1264 in vacuum Brian Radak
- [AMBER] tleap seems Si atom as S ... I don't know why Erdem Yeler
Saturday, 12 December 2020
- [AMBER] MMPBSA.py.MPI not build in Amber20 Setyanto Md
- Re: [AMBER] MMPBSA.py.MPI not build in Amber20 Elvis Martis
- [AMBER] Hydrogen bond and Dissociation constant Kehinde Idowu
- [AMBER] How to specify SHAKE on all bonds including hydrogen in the input file Amit Sharma (Asstt. Prof., MCARS)
- Re: [AMBER] How to specify SHAKE on all bonds including hydrogen in the input file Carlos Simmerling
- Re: [AMBER] How to specify SHAKE on all bonds including hydrogen in the input file Bill Ross
- Re: [AMBER] how to convert (psf) to (prmtop) and (incprd) Pinky Mazumder
- Re: [AMBER] how to convert (psf) to (prmtop) and (incprd) Carlos Simmerling
- Re: [AMBER] how to convert (psf) to (prmtop) and (incprd) Pinky Mazumder
- [AMBER] refene2.solvent_energies refene2.dielc2_energies and refene2.dielc2.solvent_energies Luis Simon
- [AMBER] parameters for benzene, pyerene, anthracene, and coronene Boutheïna KERKENI
- Re: [AMBER] MMPBSA.py.MPI not build in Amber20 Setyanto Md
- Re: [AMBER] Charged species with antechamber David A Case
- Re: [AMBER] tleap seems Si atom as S ... I don't know why David A Case
- Re: [AMBER] Hydrogen bond and Dissociation constant David A Case
- Re: [AMBER] how to convert (psf) to (prmtop) and (incprd) David A Case
- [AMBER] Error in Quasi-Harmonic Entropy Setyanto Md
Sunday, 13 December 2020
- [AMBER] Stacking distance in CPPTRAJ Athena N
- Re: [AMBER] Stacking distance in CPPTRAJ Carlos Simmerling
- Re: [AMBER] parameters for benzene, pyerene, anthracene, and coronene Boutheïna KERKENI
Monday, 14 December 2020
- [AMBER] Disulphide bonds Gustaf Olsson
- [AMBER] RMSD Protein-DNA complex Plot Manisha
Sunday, 13 December 2020
- [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit
Monday, 14 December 2020
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Elvis Martis
- [AMBER] parameters for benzene, pyerene, anthracene, and coronene Boutheïna KERKENI
Sunday, 13 December 2020
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit
Monday, 14 December 2020
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Elvis Martis
Sunday, 13 December 2020
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit
Monday, 14 December 2020
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Elvis Martis
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Elvis Martis
- Re: [AMBER] RMSD Protein-DNA complex Plot Bill Ross
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit
- Re: [AMBER] Disulphide bonds Bill Ross
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Elvis Martis
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit
- Re: [AMBER] Disulphide bonds Gustaf Olsson
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Elvis Martis
- Re: [AMBER] Disulphide bonds Carlos Simmerling
- Re: [AMBER] parameters for benzene, pyerene, anthracene, and coronene David A Case
- Re: [AMBER] Error in Quasi-Harmonic Entropy David A Case
- Re: [AMBER] Disulphide bonds David A Case
- Re: [AMBER] parameters for benzene, pyerene, anthracene, and coronene Carlos Simmerling
- Re: [AMBER] parameters for benzene, pyerene, anthracene, and coronene Boutheïna KERKENI
- Re: [AMBER] parameters for benzene, pyerene, anthracene, and coronene Carlos Simmerling
- [AMBER] box_dims question Carlos
- Re: [AMBER] An error during NPT/production (GPU run) David Cerutti
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Elvis Martis
- Re: [AMBER] Disulphide bonds Gustaf Olsson
Tuesday, 15 December 2020
- Re: [AMBER] RMSD Protein-DNA complex Plot Dr. Anselm Horn
Monday, 14 December 2020
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit
Tuesday, 15 December 2020
- Re: [AMBER] S2 order parameter not being calculated in IRED analysis. Gupta, Arun
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit
- Re: [AMBER] S2 order parameter not being calculated in IRED analysis. Daniel Roe
- Re: [AMBER] Stacking distance in CPPTRAJ Daniel Roe
- [AMBER] error finding MMPBSA.py.MPI redirected to amber18 instead of amber20 Vaibhav Dixit
- Re: [AMBER] error finding MMPBSA.py.MPI redirected to amber18 instead of amber20 Ray Luo
- [AMBER] VDWAALS energy shoots up suddenly during transition from Minimization to Heating Chris Lee
- Re: [AMBER] error finding MMPBSA.py.MPI redirected to amber18 instead of amber20 Vaibhav Dixit
- Re: [AMBER] VDWAALS energy shoots up suddenly during transition from Minimization to Heating Bill Ross
- Re: [AMBER] Amber 4/pre Amber 7 binaries? Bill Ross
- [AMBER] Getting error while compile AMBER20 with cuda support Raman Jangra
- Re: [AMBER] Getting error while compile AMBER20 with cuda support Bill Ross
- Re: [AMBER] Amber 4/pre Amber 7 binaries? Kenneth Huang
- [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi
- [AMBER] ambpdb or other scipt? Jisha B
- Re: [AMBER] ambpdb or other scipt? Bill Ross
- Re: [AMBER] ambpdb or other scipt? Jisha B
- Re: [AMBER] ambpdb or other scipt? Bill Ross
Wednesday, 16 December 2020
- [AMBER] Top Mode Contribution in PCA Analysis. DHEERAJ CHITARA
- Re: [AMBER] VDWAALS energy shoots up suddenly during transition from Minimization to Heating David A Case
- Re: [AMBER] Getting error while compile AMBER20 with cuda support David A Case
- Re: [AMBER] PROTEIN-DNA rmsd plot David A Case
- Re: [AMBER] Amber 4/pre Amber 7 binaries? David A Case
- Re: [AMBER] VDWAALS energy shoots up suddenly during transition from Minimization to Heating Matias Machado
- Re: [AMBER] VDWAALS energy shoots up suddenly during transition from Minimization to Heating Matias Machado
- [AMBER] positive Amber FF energies? Vaibhav Dixit
- Re: [AMBER] Amber 4/pre Amber 7 binaries? Kenneth Huang
- Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? Liao
- Re: [AMBER] Amber 4/pre Amber 7 binaries? Ryan Novosielski
- [AMBER] MMPBSA.py.MPI installation divyabharathi korlepara
- [AMBER] Antechamber vs R.E.D. Server Sam Walsworth (Researcher)
- Re: [AMBER] Amber 4/pre Amber 7 binaries? Kenneth Huang
- Re: [AMBER] Amber 4/pre Amber 7 binaries? Ryan Novosielski
- Re: [AMBER] Amber 4/pre Amber 7 binaries? Kenneth Huang
- Re: [AMBER] Amber 4/pre Amber 7 binaries? Ryan Novosielski
- Re: [AMBER] Amber 4/pre Amber 7 binaries? Bill Ross
- Re: [AMBER] Amber 4/pre Amber 7 binaries? Bill Ross
- Re: [AMBER] MMPBSA.py.MPI installation Elvis Martis
- Re: [AMBER] positive Amber FF energies? Jason Swails
- Re: [AMBER] positive Amber FF energies? Thomas Cheatham
- [AMBER] nc files contain lesser number of atoms compared to prmtop Sruthi Sudhakar
- Re: [AMBER] positive Amber FF energies? Vaibhav Dixit
Thursday, 17 December 2020
- Re: [AMBER] MMPBSA.py.MPI installation Jaime Rubio Martinez
- [AMBER] Renumbering Gustaf Olsson
- Re: [AMBER] Renumbering Gustaf Olsson
- Re: [AMBER] Renumbering Carlos Simmerling
- Re: [AMBER] Renumbering Gustaf Olsson
- Re: [AMBER] tleap seems Si atom as S ... I don't know why Erdem Yeler
- [AMBER] Using sander.MPI in Docker Erdem Yeler
- Re: [AMBER] AMBER Digest, Vol 3215, Issue 1 David A Case
- [AMBER] cpptraj warnings topology flags being ignored Vaibhav Dixit
- Re: [AMBER] Antechamber vs R.E.D. Server Dr. Anselm Horn
- [AMBER] Conversion .rst to .inpcrd Eduardo R. Almeida
- Re: [AMBER] cpptraj warnings topology flags being ignored David A Case
- Re: [AMBER] Renumbering Daniel Roe
- Re: [AMBER] nc files contain lesser number of atoms compared to prmtop Daniel Roe
- Re: [AMBER] Conversion .rst to .inpcrd Daniel Roe
- Re: [AMBER] Top Mode Contribution in PCA Analysis. Daniel Roe
- Re: [AMBER] box_dims question Daniel Roe
- Re: [AMBER] cpptraj warnings topology flags being ignored Daniel Roe
- Re: [AMBER] Renumbering Gustaf Olsson
- Re: [AMBER] Antechamber vs R.E.D. Server Sam Walsworth (Researcher)
- [AMBER] pbsa calcerror Neha Gandhi
- Re: [AMBER] pbsa calcerror Ray Luo
- Re: [AMBER] pbsa calcerror Neha Gandhi
Friday, 18 December 2020
- Re: [AMBER] Top Mode Contribution in PCA Analysis. DHEERAJ CHITARA
- Re: [AMBER] error finding MMPBSA.py.MPI redirected to amber18 instead of amber20 Vaibhav Dixit
- Re: [AMBER] Antechamber vs R.E.D. Server Dr. Anselm Horn
Thursday, 17 December 2020
- [AMBER] strange jump in the rmsd protein complex Vaibhav Dixit
Friday, 18 December 2020
- Re: [AMBER] strange jump in the rmsd protein complex Vaibhav Dixit
- Re: [AMBER] MMPBSA.py.MPI installation divyabharathi korlepara
- Re: [AMBER] MMPBSA.py.MPI installation divyabharathi korlepara
- Re: [AMBER] MMPBSA.py.MPI installation Elvis Martis
- Re: [AMBER] Conversion .rst to .inpcrd Eduardo R. Almeida
- Re: [AMBER] strange jump in the rmsd protein complex Daniel Roe
- Re: [AMBER] error finding MMPBSA.py.MPI redirected to amber18 instead of amber20 Ray Luo
- Re: [AMBER] strange jump in the rmsd protein complex Vaibhav Dixit
- Re: [AMBER] error finding MMPBSA.py.MPI redirected to amber18 instead of amber20 Vaibhav Dixit
- [AMBER] Cannot minimize structure with sander George Yacu
- Re: [AMBER] Cannot minimize structure with sander David A Case
- [AMBER] Molecular Dynamics Tutorial for Membrane-Bound Proteins in Amber ANDRES IBACACHE
- [AMBER] Minimization Time Limit Error with Sander Aanshi Gandhi
- Re: [AMBER] Minimization Time Limit Error with Sander Carlos Simmerling
- Re: [AMBER] Minimization Time Limit Error with Sander Aanshi Gandhi
- Re: [AMBER] Minimization Time Limit Error with Sander Carlos Simmerling
- Re: [AMBER] Minimization Time Limit Error with Sander Aanshi Gandhi
- Re: [AMBER] Minimization Time Limit Error with Sander Carlos Simmerling
- Re: [AMBER] Minimization Time Limit Error with Sander David A Case
- Re: [AMBER] Minimization Time Limit Error with Sander Bill Ross
- [AMBER] AMBER20 on Ubuntu 20.04 and CUDA 11.2? Rudy Richardson
- Re: [AMBER] pbsa calcerror Ray Luo
Saturday, 19 December 2020
- Re: [AMBER] AMBER20 on Ubuntu 20.04 and CUDA 11.2? David A Case
- Re: [AMBER] AMBER20 on Ubuntu 20.04 and CUDA 11.2? Rudy Richardson
Sunday, 20 December 2020
- Re: [AMBER] Error in Quasi-Harmonic Entropy Setyanto Md
- Re: [AMBER] Getting error while compile AMBER20 with cuda support Raman Jangra
- Re: [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi
Monday, 21 December 2020
- [AMBER] Cpptraj (post-processing rotation) Женя Елизарова
- [AMBER] question pmemd.cuda MYRIAN TORRES RICO
- Re: [AMBER] question pmemd.cuda Elvis Martis
- Re: [AMBER] PROTEIN-DNA rmsd plot David A Case
- [AMBER] Query on some old sander inputs (dele, idiel, dielc) Kenneth Huang
- Re: [AMBER] Cpptraj (post-processing rotation) Kenneth Huang
- [AMBER] ff15ipq-m force field for protein mimetics Lillian Chong
- [AMBER] crystallographic plane Pinky Mazumder
- Re: [AMBER] crystallographic plane Bill Ross
Tuesday, 22 December 2020
- [AMBER] How to graph CPPTRAJ in (ns) instead of timesteps Maghsoud, Yazdan
- Re: [AMBER] How to graph CPPTRAJ in (ns) instead of timesteps Maria Nagan
- [AMBER] Cation-pi interaction characterization Ramanathan Rajesh
- Re: [AMBER] MD run on GPU machine Carlos Simmerling
- [AMBER] Electrostatic distance plot Sruthi Sudhakar
Wednesday, 23 December 2020
- Re: [AMBER] Electrostatic distance plot David A Case
- Re: [AMBER] Electrostatic distance plot Sruthi Sudhakar
- Re: [AMBER] How to graph CPPTRAJ in (ns) instead of timesteps Daniel Roe
- Re: [AMBER] Cpptraj (post-processing rotation) Daniel Roe
- Re: [AMBER] Electrostatic distance plot Carlos Simmerling
- [AMBER] how to know degrees of system angad sharma
- Re: [AMBER] how to know degrees of system Carlos Simmerling
- Re: [AMBER] Electrostatic distance plot Sruthi Sudhakar
- Re: [AMBER] Electrostatic distance plot Adrian Roitberg
- Re: [AMBER] Electrostatic distance plot Maria Nagan
- [AMBER] Parmed error Jisha B
- Re: [AMBER] Parmed error Elvis Martis
- Re: [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi
Thursday, 24 December 2020
- [AMBER] CPU versus GPU Divergent Minimizations Matthew Guberman-Pfeffer
- [AMBER] Position of the solute (center of mass) in the simulation box Eduardo R. Almeida
- Re: [AMBER] CPU versus GPU Divergent Minimizations David A Case
- Re: [AMBER] Parmed error Hai Nguyen
- Re: [AMBER] Position of the solute (center of mass) in the simulation box Matias Machado
- Re: [AMBER] Position of the solute (center of mass) in the simulation box Matias Machado
Friday, 25 December 2020
- [AMBER] Has anyone tried and succeeded at compiling Amber 18 with CUDA 11? Homeo Morphism
Saturday, 26 December 2020
- Re: [AMBER] Query on some old sander inputs (dele, idiel, dielc) David A Case
- [AMBER] Reweighting error in Gaussian accelerated MD- PyReweighting-1D.py Athena N
Sunday, 27 December 2020
- [AMBER] Problem forming circular DNA Sebastian S
- [AMBER] SHAKE problem Jonathan Church
Monday, 28 December 2020
- Re: [AMBER] SHAKE problem Bill Ross
- Re: [AMBER] Problem forming circular DNA David A Case
- Re: [AMBER] Problem forming circular DNA Sebastian S
- [AMBER] Amber20 Installation Error Li,Haoxi
Tuesday, 29 December 2020
- Re: [AMBER] Amber20 Installation Error David A Case
- Re: [AMBER] SHAKE problem Jonathan Church
- [AMBER] CMP-GMP Holly Freedman
- Re: [AMBER] CMP-GMP David A Case
Wednesday, 30 December 2020
- [AMBER] cremer MYRIAN TORRES RICO
- Re: [AMBER] cremer David A Case
- Re: [AMBER] crystallographic plane Daniel Roe
- Re: [AMBER] Position of the solute (center of mass) in the simulation box Daniel Roe
- Re: [AMBER] PROTEIN-DNA rmsd plot Daniel Roe
- Re: [AMBER] Electrostatic distance plot Daniel Roe
- Re: [AMBER] Cation-pi interaction characterization Daniel Roe
- Re: [AMBER] CMP-GMP Holly Freedman
- Re: [AMBER] Query on some old sander inputs (dele, idiel, dielc) Kenneth Huang
- Re: [AMBER] Query on some old sander inputs (dele, idiel, dielc) David Cerutti
- Re: [AMBER] Amber20 Installation Error David A Case
- Re: [AMBER] CMP-GMP David A Case
- Re: [AMBER] CMP-GMP Holly Freedman
- Re: [AMBER] Query on some old sander inputs (dele, idiel, dielc) Kenneth Huang
- Re: [AMBER] Amber20 Installation Error Li,Haoxi
Thursday, 31 December 2020
- Re: [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi
- Re: [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi
- Re: [AMBER] PROTEIN-DNA rmsd plot Dr. Anselm Horn
- Re: [AMBER] cremer MYRIAN TORRES RICO
- [AMBER] doubt frames simulation MYRIAN TORRES RICO
- [AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card liu kai
- Re: [AMBER] Amber20 Installation Error David A Case
- Re: [AMBER] cremer Daniel Roe
- Re: [AMBER] doubt frames simulation Daniel Roe
- Re: [AMBER] cremer MYRIAN TORRES RICO
- Re: [AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card Ross Walker
- Re: [AMBER] cremer David A Case
- Re: [AMBER] cremer MYRIAN TORRES RICO
- Re: [AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card David A Case
- Re: [AMBER] PROTEIN-DNA rmsd plot David A Case

Last message date: Thu Dec 31 2020 - 19:00:02 PST
Archived on: Wed Apr 24 2024 - 05:56:01 PDT

Amber Archive Dec 2020 by date