Amber Archive May 2019: by date

Wednesday, 1 May 2019
- [AMBER] Vina Zinc Beale, John
- Re: [AMBER] Library for Phosphate ion David A Case
- Re: [AMBER] Library for Phosphate ion Sowmya Indrakumar
- [AMBER] SMD using contact number Chem Jubilant
- Re: [AMBER] mol2 files for FEW David A Case
- Re: [AMBER] Simulation with Protein, cofactor and Ligand David A Case
- [AMBER] CPPTRAJ average residue-wise contact map anu chandra
- [AMBER] Error using mm_pbsa.pl binding energy calculations Jaimes, Luis
Thursday, 2 May 2019
- [AMBER] Random segfaults (invalid memory reference) in sander Charo del Genio
- [AMBER] FEW not producing *.lib file for ligand ali akbar
- Re: [AMBER] CPPTRAJ average residue-wise contact map Daniel Roe
- Re: [AMBER] CPPTRAJ gnu extension not working Daniel Roe
- Re: [AMBER] CPPTRAJ average residue-wise contact map anu chandra
- Re: [AMBER] SMD using contact number Feng Pan
- [AMBER] Distance calculation and distance matrix giving discrepant results Jonathan Huihui
- Re: [AMBER] Novel Force Field Parameters for Aromatic Dihedrals Carlos Simmerling
- Re: [AMBER] Random segfaults (invalid memory reference) in sander James Kress
- Re: [AMBER] Random segfaults (invalid memory reference) in sander Charo del Genio
- [AMBER] Force field for nucleobases, nucleosides and nucleotides Elisa Pieri
- Re: [AMBER] Force field for nucleobases, nucleosides and nucleotides Elisa Pieri
Friday, 3 May 2019
- [AMBER] Random segfaults (invalid memory reference) in sander Margarita I. Bernal-Uruchurtu
- Re: [AMBER] Novel Force Field Parameters for Aromatic Dihedrals Erdem Yeler
- [AMBER] Files for Tutorial 32 (Deriving bonded parameters with mdgx) Michiel de Hoon
- [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Erdem Yeler
- Re: [AMBER] Random segfaults (invalid memory reference) in sander Daniel Roe
- Re: [AMBER] Random segfaults (invalid memory reference) in sander Daniel Roe
- Re: [AMBER] Force field for nucleobases, nucleosides and nucleotides David A Case
- Re: [AMBER] Random segfaults (invalid memory reference) in sander Charo del Genio
- Re: [AMBER] Random segfaults (invalid memory reference) in sander scanya.interia.eu
- Re: [AMBER] Guidance on WHAM Ruth Helena Tichauer
- [AMBER] FLAG_POINTERS in prmtop file Feng, Zimin
- Re: [AMBER] Guidance on WHAM Carlos Simmerling
- Re: [AMBER] Guidance on WHAM Ruth Helena Tichauer
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Kellon Belfon
- Re: [AMBER] [mjldehoon.yahoo.com: Files for Tutorial 32 (Deriving bonded parameters with mdgx)] David Cerutti
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Kellon Belfon
- Re: [AMBER] FLAG_POINTERS in prmtop file Feng, Zimin
- Re: [AMBER] Distance calculation and distance matrix giving discrepant results Daniel Roe
- Re: [AMBER] Distance calculation and distance matrix giving discrepant results Jonathan Huihui
- [AMBER] Are R.E.D. tools still a thing? Luca Codutti
- Re: [AMBER] Are R.E.D. tools still a thing? Feng, Zimin
- [AMBER] Question regarding compatibility of Temperature replica exchange MD (TREMD) with constant pH MD Pacheco, Sayuri
- Re: [AMBER] Question regarding compatibility of Temperature replica exchange MD (TREMD) with constant pH MD Cruzeiro,Vinicius Wilian D
- Re: [AMBER] issues with pmemd.cuda Veenis, Andrew Jay
- Re: [AMBER] Question regarding compatibility of Temperature replica exchange MD (TREMD) with constant pH MD Pacheco, Sayuri
- [AMBER] SIRAH force field goes quantum in AMBER Matias Machado
Saturday, 4 May 2019
- [AMBER] FEW- an issue generating *.lib for ligand ali akbar
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Erdem Yeler
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Erdem Yeler
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Carlos Simmerling
- [AMBER] AmberTools hardcodes library names into binaries viktor drobot
- Re: [AMBER] AmberTools hardcodes library names into binaries David Case
Sunday, 5 May 2019
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Erdem Yeler
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Carlos Simmerling
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Erdem Yeler
- [AMBER] check version Akshay Prabhakant
- Re: [AMBER] check version Pratul Agarwal
- [AMBER] umbrella sampling using pmemd in amber/2016 Akshay Prabhakant
- Re: [AMBER] check version David Case
Monday, 6 May 2019
- [AMBER] Ambertools2018/SQM installation Sina
- Re: [AMBER] Random segfaults (invalid memory reference) in sander Charo del Genio
- [AMBER] matching energies betwen amber-md and gromacs using amber parameters in both Akshay Prabhakant
- Re: [AMBER] matching energies betwen amber-md and gromacs using amber parameters in both Karl Kirschner
- Re: [AMBER] Ambertools2018/SQM installation Gustaf Olsson
- Re: [AMBER] matching energies betwen amber-md and gromacs using amber parameters in both Akshay Prabhakant
- Re: [AMBER] Ambertools2018/SQM installation David A Case
- Re: [AMBER] Random segfaults (invalid memory reference) in sander David A Case
- Re: [AMBER] Ambertools2018/SQM installation Sina
- Re: [AMBER] Any help on how to implement it in cpptraj? Debarati DasGupta
Tuesday, 7 May 2019
- Re: [AMBER] matching energies betwen amber-md and gromacs using amber parameters in both Karl Kirschner
- [AMBER] three letter code for unprotonated carboxyglutamates Tanusree S
- Re: [AMBER] three letter code for unprotonated carboxyglutamates Pietro Aronica
- [AMBER] running qsub files in a single standalone workstation ali akbar
- Re: [AMBER] running qsub files in a single standalone workstation David A Case
- [AMBER] different energy values from mdout and cpptraj Batuhan Kav
- Re: [AMBER] different energy values from mdout and cpptraj David A Case
- [AMBER] SPAM bulk solvent free energy parameters Debarati DasGupta
- Re: [AMBER] umbrella sampling using pmemd in amber/2016 Feng Pan
- Re: [AMBER] cuda test failing after installation Ravi Abrol
- Re: [AMBER] cuda test failing after installation David Cerutti
- Re: [AMBER] Guidance on WHAM Daniel Fernández Remacha
- [AMBER] NVidia backwards compatibility James Kress
- Re: [AMBER] cuda test failing after installation Ravi Abrol
- [AMBER] Unequal distribution of water Piotr Fajer
- Re: [AMBER] Unequal distribution of water Carlos Simmerling
- [AMBER] distance restraint failed in minimization and MD wujue
- Re: [AMBER] AMBER Digest, Vol 2638, Issue 1 ali akbar
- [AMBER] running qsub files in a single standalone workstation ali akbar
- Re: [AMBER] running qsub files in a single standalone workstation Nadine Homeyer
- [AMBER] Thermostat question Markowska
Wednesday, 8 May 2019
- Re: [AMBER] Thermostat question David Cerutti
- [AMBER] CPPTRAJ OPENMP - MPI Lorenzo Gontrani
- [AMBER] Capping a dipeptide with Boc Saikat Pal
- Re: [AMBER] Capping a dipeptide with Boc Alessandro Contini
- Re: [AMBER] CPPTRAJ OPENMP - MPI Daniel Roe
- Re: [AMBER] distance restraint failed in minimization and MD David A Case
- Re: [AMBER] NVidia backwards compatibility David A Case
- Re: [AMBER] Capping a dipeptide with Boc Saikat Pal
- Re: [AMBER] Thermostat question Daniel Roe
- Re: [AMBER] NVidia backwards compatibility James Kress
- Re: [AMBER] Capping a dipeptide with Boc Alessandro Contini
- [AMBER] pmemd.cuda "cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered" Akshay Prabhakant
- Re: [AMBER] pmemd.cuda "cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered" Pratul Agarwal
- Re: [AMBER] Capping a dipeptide with Boc Saikat Pal
- Re: [AMBER] Capping a dipeptide with Boc Alessandro Contini
- Re: [AMBER] Capping a dipeptide with Boc Saikat Pal
- [AMBER] AMBER 16 vs 18 on different cuda Xiaoyu Wang
- Re: [AMBER] AMBER 16 vs 18 on different cuda David Cerutti
- Re: [AMBER] Thermostat question Markowska
Thursday, 9 May 2019
- [AMBER] continuous DNA Qinghua Liao
- [AMBER] GPU versions: pmemd.cuda* Yin, Guowei
- Re: [AMBER] GPU versions: pmemd.cuda* Pratul Agarwal
- Re: [AMBER] continuous DNA David A Case
- Re: [AMBER] Thermostat question Daniel Roe
- Re: [AMBER] SPAM bulk solvent free energy parameters Daniel Roe
- Re: [AMBER] Any help on how to implement it in cpptraj? Daniel Roe
- Re: [AMBER] continuous DNA Thomas C. Bishop
- [AMBER] Energy shifted energy term Debarati DasGupta
Friday, 10 May 2019
- [AMBER] Fwd: August 5-8.SBU: 2019 Summer School Parallel Computing in Molecular Sciences Carlos Simmerling
- Re: [AMBER] Energy shifted energy term Jason Swails
- Re: [AMBER] Are R.E.D. tools still a thing? Jason Swails
- Re: [AMBER] FLAG_POINTERS in prmtop file Jason Swails
- Re: [AMBER] Energy shifted energy term Debarati DasGupta
- [AMBER] Regarding GTX 1050 Ti Rajarshi Roy
Saturday, 11 May 2019
- [AMBER] Fwd: The unperturbed charge of the unit: 4.003000 is not zero Sadaf Rani
- [AMBER] Failed to generate parameters Sadaf Rani
- Re: [AMBER] Regarding GTX 1050 Ti Ross Walker
- Re: [AMBER] Regarding GTX 1050 Ti Rajarshi Roy
- Re: [AMBER] Fwd: The unperturbed charge of the unit: 4.003000 is not zero Bill Ross
- [AMBER] MC barostat cause the system to stuck indefinitely Zhiyi Wu
- [AMBER] Problem with preparing parameters with antechamber for modified amino acid Saikat Dutta chowdhury
Sunday, 12 May 2019
- Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid Bill Ross
- [AMBER] Residence time around ions Reber, David
- [AMBER] Center of mass velocity autocorrelation function Reber, David
Monday, 13 May 2019
- Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid Saikat Dutta chowdhury
- Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid Bill Ross
- Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid Bill Ross
- Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid Saikat Dutta chowdhury
- [AMBER] tleap split lipid when it shouldn't Maximilien BERNE
- Re: [AMBER] MC barostat cause the system to stuck indefinitely David A Case
- Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid David A Case
- Re: [AMBER] tleap split lipid when it shouldn't David A Case
- [AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016 Akshay Prabhakant
- Re: [AMBER] tleap split lipid when it shouldn't Dickson, Callum
- Re: [AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016 Akshay Prabhakant
- Re: [AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016 Pratul Agarwal
- Re: [AMBER] tleap split lipid when it shouldn't Maximilien BERNE
- Re: [AMBER] tleap split lipid when it shouldn't Maximilien BERNE
- Re: [AMBER] tleap split lipid when it shouldn't Dickson, Callum
- Re: [AMBER] tleap split lipid when it shouldn't Maximilien BERNE
- [AMBER] Atom type (C.2) is not in PARMCHK.DAT Segmentation fault (core dumped) Sadaf Rani
- Re: [AMBER] tleap split lipid when it shouldn't Dickson, Callum
- [AMBER] MMPBSA radiopt effect on EDISPER Thomas Gaillard
- [AMBER] amber18 parallel cpu make test hanging at first test Ravi Abrol
- Re: [AMBER] cuda test failing after installation Ravi Abrol
- [AMBER] Average structure vs Individual frames Yin, Guowei
- Re: [AMBER] Average structure vs Individual frames Bill Ross
- Re: [AMBER] Average structure vs Individual frames Yin, Guowei
- Re: [AMBER] Average structure vs Individual frames Bill Ross
- Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid Saikat Dutta chowdhury
Tuesday, 14 May 2019
- Re: [AMBER] Building inpcrd and prmtop for a non-standard residue containing cyclic peptide Pietro Aronica
- Re: [AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016 Akshay Prabhakant
- Re: [AMBER] Atom type (C.2) is not in PARMCHK.DAT Segmentation fault (core dumped) David A Case
- Re: [AMBER] amber18 parallel cpu make test hanging at first test David A Case
- Re: [AMBER] Average structure vs Individual frames David A Case
- Re: [AMBER] Building inpcrd and prmtop for a non-standard residue containing cyclic peptide David A Case
- Re: [AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016 Pratul Agarwal
- Re: [AMBER] Building inpcrd and prmtop for a non-standard residue containing cyclic peptide Schröder, David Christopher
- [AMBER] Solute free non-water solvent razie yousefi
- Re: [AMBER] Solute free non-water solvent David A Case
- [AMBER] 3D-RISM options Ryan Pavlovicz
- Re: [AMBER] 3D-RISM options Tyler Luchko (Lists)
- Re: [AMBER] 3D-RISM options Ryan Pavlovicz
- Re: [AMBER] 3D-RISM options Tyler Luchko (Lists)
- Re: [AMBER] amber18 parallel cpu make test hanging at first test Ravi Abrol
- Re: [AMBER] 3D-RISM options Ryan Pavlovicz
Wednesday, 15 May 2019
- [AMBER] Entropy calculation for a protein homodimerization Rakesh Srivastava
- [AMBER] hbond lifetime filesize issues Reber, David
- Re: [AMBER] tleap split lipid when it shouldn't Maximilien BERNE
- [AMBER] set RA, RT and n_partition in adQM/MM run Ruth Helena Tichauer
- Re: [AMBER] Entropy calculation for a protein homodimerization Pratul Agarwal
- Re: [AMBER] Entropy calculation for a protein homodimerization Rakesh Srivastava
- [AMBER] Crashed dynamics : connectivity emanuele falbo
- Re: [AMBER] 3D-RISM options David A Case
- Re: [AMBER] tleap split lipid when it shouldn't David A Case
- Re: [AMBER] hbond lifetime filesize issues Daniel Roe
- Re: [AMBER] tleap split lipid when it shouldn't Maximilien BERNE
- Re: [AMBER] 3D-RISM options Ryan Pavlovicz
- Re: [AMBER] Crashed dynamics : connectivity David A Case
- Re: [AMBER] Random segfaults (invalid memory reference) in sander Charo del Genio
- [AMBER] nvidia tesla-t4 and amber Luca Codutti
- Re: [AMBER] nvidia tesla-t4 and amber Shenglong Wang
- Re: [AMBER] Random segfaults (invalid memory reference) in sander Daniel Roe
- Re: [AMBER] nvidia tesla-t4 and amber David Cerutti
- Re: [AMBER] nvidia tesla-t4 and amber Luca Codutti
- Re: [AMBER] tleap split lipid when it shouldn't Matias Machado
- Re: [AMBER] 3D-RISM options Tyler Luchko (Lists)
- Re: [AMBER] tleap split lipid when it shouldn't Stephan Schott
- Re: [AMBER] tleap split lipid when it shouldn't Stephan Schott
- Re: [AMBER] Atom type (C.2) is not in PARMCHK.DAT Segmentation fault (core dumped) Sadaf Rani
- [AMBER] Missing file amber tutorial Sadaf Rani
- Re: [AMBER] Missing file amber tutorial Pratul Agarwal
- [AMBER] NetCDF trajectory file does not contain information about time/timestep Markowska
- [AMBER] Releasing SIRAH lipids! A complete coarse-grained force field running on AMBER Matias Machado
- Re: [AMBER] Missing file amber tutorial Pratul Agarwal
- Re: [AMBER] tleap split lipid when it shouldn't Sally Pias
- Re: [AMBER] hbond lifetime filesize issues Reber, David
- Re: [AMBER] hbond lifetime filesize issues Reber, David
Thursday, 16 May 2019
- [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file Gargi Borgohain
- [AMBER] Bubbles during NPT and NVT simulations Stefano Motta
- Re: [AMBER] Bubbles during NPT and NVT simulations Carlos Simmerling
- Re: [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file Bill Ross
- Re: [AMBER] Bubbles during NPT and NVT simulations Bill Ross
- [AMBER] RMSF of combined trajectory Rinsha Chk
- Re: [AMBER] RMSF of combined trajectory Bill Ross
- Re: [AMBER] Bubbles during NPT and NVT simulations David A Case
- [AMBER] Simulating Water Exchange to Buried Binding Sites Debarati DasGupta
- Re: [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file Charles Lin
- Re: [AMBER] RMSF of combined trajectory Rinsha Chk
- Re: [AMBER] RMSF of combined trajectory Bill Ross
- Re: [AMBER] RMSF of combined trajectory Bill Ross
Friday, 17 May 2019
- Re: [AMBER] RMSF of combined trajectory Rinsha Chk
- [AMBER] Error in step 3 of MCPB.py Shahila Muhammed
- [AMBER] Selecting number of waters in tleap Elena Gomez
- [AMBER] Open position for doctoral candidate in biomolecular simulations Jan Brezovsky
- Re: [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file Gargi Borgohain
- Re: [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file Joan Torras
- [AMBER] Suggestion about proper ANTECHAMBER usage Saikat Dutta chowdhury
- Re: [AMBER] RMSF of combined trajectory Daniel Roe
- Re: [AMBER] Suggestion about proper ANTECHAMBER usage David A Case
- Re: [AMBER] Suggestion about proper ANTECHAMBER usage Saikat Dutta chowdhury
- Re: [AMBER] Simulating Water Exchange to Buried Binding Sites Matias Machado
- Re: [AMBER] Selecting number of waters in tleap Matias Machado
- Re: [AMBER] NetCDF trajectory file does not contain information about time/timestep Daniel Roe
- Re: [AMBER] Simulating Water Exchange to Buried Binding Sites Charles Lin
- Re: [AMBER] Selecting number of waters in tleap Kellon Belfon
- Re: [AMBER] Simulating Water Exchange to Buried Binding Sites Debarati DasGupta
- Re: [AMBER] Simulating Water Exchange to Buried Binding Sites Matias Machado
- [AMBER] Velocity rescaling between different temperatures? Kenneth Huang
- [AMBER] DRMSD utility in cpptraj Debarati DasGupta
Saturday, 18 May 2019
- [AMBER] Force field for intrinsically disordered proteins Markowska
- Re: [AMBER] NetCDF trajectory file does not contain information about time/timestep Markowska
Sunday, 19 May 2019
- [AMBER] Catalysis mechanism of ATPase sunyeping
- Re: [AMBER] Force field for intrinsically disordered proteins David Case
- Re: [AMBER] RMSF of combined trajectory Rinsha Chk
Monday, 20 May 2019
- Re: [AMBER] Velocity rescaling between different temperatures? Daniel Roe
- Re: [AMBER] tleap split lipid when it shouldn't Maximilien BERNE
- Re: [AMBER] Velocity rescaling between different temperatures? Kenneth Huang
- Re: [AMBER] Velocity rescaling between different temperatures? Daniel Roe
- Re: [AMBER] Simulating Water Exchange to Buried Binding Sites Charles Lin
- Re: [AMBER] Simulating Water Exchange to Buried Binding Sites Charles Lin
- Re: [AMBER] NetCDF trajectory file does not contain information about time/timestep Daniel Roe
- Re: [AMBER] mol2 files for FEW Nadine Homeyer
- Re: [AMBER] DRMSD utility in cpptraj Daniel Roe
- Re: [AMBER] Catalysis mechanism of ATPase Pratul Agarwal
Tuesday, 21 May 2019
- Re: [AMBER] DRMSD utility in cpptraj Debarati DasGupta
- Re: [AMBER] Error in step 3 of MCPB.py Pengfei Li
- Re: [AMBER] hbond lifetime filesize issues Daniel Roe
- Re: [AMBER] hbond lifetime filesize issues Reber, David
- [AMBER] Regarding building of parallel version of AMBER18 in centos 7 Rajarshi Roy
Wednesday, 22 May 2019
- Re: [AMBER] Regarding building of parallel version of AMBER18 in centos 7 David A Case
- Re: [AMBER] Error in step 3 of MCPB.py Shahila Muhammed
- [AMBER] Temperature variation in QM/MM simulation with AMBER18/G09 Abhilash J
Thursday, 23 May 2019
- Re: [AMBER] Temperature variation in QM/MM simulation with AMBER18/G09 David A Case
- Re: [AMBER] Regarding building of parallel version of AMBER18 in centos 7 Rajarshi Roy
- [AMBER] amber inputs Sina
- [AMBER] Volmap command in cpptraj followed by SPAM Debarati DasGupta
- [AMBER] Lennard Jones parameters in frcmod Stefano Motta
- Re: [AMBER] amber inputs David A Case
- Re: [AMBER] Lennard Jones parameters in frcmod Matias Machado
Friday, 24 May 2019
- [AMBER] Different potential energies between recomputed and original simulations from PMEMD? 杨明俊
- [AMBER] Qm minimization, Sina
- Re: [AMBER] Qm minimization, David Case
- Re: [AMBER] Different potential energies between recomputed and original simulations from PMEMD? 杨明俊
- [AMBER] Some basic question Sina
- Re: [AMBER] Temperature variation in QM/MM simulation with AMBER18/G09 Abhilash J
- [AMBER] jobs getting cancelled on cuda7 gpus maryam azimzadehirani
Saturday, 25 May 2019
- [AMBER] PCA with a really giant trajectory David Cerutti
Sunday, 26 May 2019
- [AMBER] Print Hessian matrix in (3,3) dimension Bouibes Amine
- [AMBER] How to generate the correct force field parameter for a large molecule? xmgign.126.com
Monday, 27 May 2019
- Re: [AMBER] PCA with a really giant trajectory Chris Neale
- Re: [AMBER] How to generate the correct force field parameter for a large molecule? Bill Ross
- [AMBER] graph Charu Sharma (JRF)
- [AMBER] compiling Amber Tools 19 Vlad Cojocaru
- Re: [AMBER] compiling Amber Tools 19 Vlad Cojocaru
- [AMBER] Protein-Lipid Bilayer PDB preparation Issue(s) Abhishek Sirohiwal
- Re: [AMBER] Protein-Lipid Bilayer PDB preparation Issue(s) Stephan Schott
- Re: [AMBER] Protein-Lipid Bilayer PDB preparation Issue(s) Abhishek Sirohiwal
- [AMBER] rmsd Hirdesh Kumar
- Re: [AMBER] Protein-Lipid Bilayer PDB preparation Issue(s) Stephan Schott
- Re: [AMBER] rmsd Kenneth Huang
- Re: [AMBER] Print Hessian matrix in (3,3) dimension David Case
- Re: [AMBER] compiling Amber Tools 19 David Case
- Re: [AMBER] rmsd David Case
- [AMBER] GCC 2019, November 3-5 in Mainz, Deadline extendend to June 23, 2019 Stefan.Guessregen.sanofi.com
Tuesday, 28 May 2019
- Re: [AMBER] compiling Amber Tools 19 Vlad Cojocaru
- Re: [AMBER] Missing file amber tutorial Sadaf Rani
- [AMBER] Problem in simulating peptide with modified amino acid - vlimit exceeded Saikat Dutta chowdhury
- [AMBER] reduce info.log Sadaf Rani
- Re: [AMBER] compiling Amber Tools 19 David A Case
- Re: [AMBER] Problem in simulating peptide with modified amino acid - vlimit exceeded David A Case
- Re: [AMBER] compiling Amber Tools 19 Vlad Cojocaru
- Re: [AMBER] reduce info.log David A Case
- Re: [AMBER] Installation of AMBER 18 regarding David A Case
- Re: [AMBER] PCA with a really giant trajectory David Cerutti
- Re: [AMBER] Some basic question David A Case
- [AMBER] Changes to AmberTools antechamber Makefile Jocelyn Sunseri
- Re: [AMBER] PCA with a really giant trajectory Daniel Roe
- Re: [AMBER] PCA with a really giant trajectory David Cerutti
- [AMBER] amber 16 installation on Ubuntu 18 Ming Tang
Wednesday, 29 May 2019
- Re: [AMBER] reduce info.log Sadaf Rani
- [AMBER] Minimization input Sadaf Rani
- Re: [AMBER] Minimization input Carlos Simmerling
- Re: [AMBER] Changes to AmberTools antechamber Makefile David A Case
- Re: [AMBER] amber 16 installation on Ubuntu 18 David A Case
- [AMBER] problem of srun Albert
- Re: [AMBER] problem of srun David A Case
- Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5 Bill Ross
- [AMBER] phosphor tyrosine bound to C5' terminal DA5 Fabian Glaser
- [AMBER] error with loading HEM parameters for constph redox calcuations Vaibhav Dixit
- Re: [AMBER] error with loading HEM parameters for constph redox calcuations David A Case
- [AMBER] deselect residues for step1 model in MCPB.py SARAH JEANNE LEFAVE
- Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5 Fabian Glaser
- Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5 Bill Ross
- Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5 Fabian Glaser
- Re: [AMBER] error with loading HEM parameters for constph redox calcuations Vaibhav Dixit
- [AMBER] Help compiling AMBER18 GPU Code- Cannot find compiler cl.exe in PATH Jay Spencer
- [AMBER] Radgyr or distance averages Reber, David
- [AMBER] Optimization of geometry in xleap Shilpa Gupta
- Re: [AMBER] Optimization of geometry in xleap Bill Ross
Thursday, 30 May 2019
- [AMBER] anybody has any idea? Albert
- Re: [AMBER] error with loading HEM parameters for constph redox calcuations Vaibhav Dixit
- [AMBER] How to generate boron atom force field parameters Meng Wu
- Re: [AMBER] Help compiling AMBER18 GPU Code- Cannot find compiler cl.exe in PATH David A Case
- Re: [AMBER] anybody has any idea? David A Case
- Re: [AMBER] anybody has any idea? Albert
- [AMBER] empty cein file redox potential calculations Vaibhav Dixit
- Re: [AMBER] empty cein file redox potential calculations Marcos Serrou do Amaral
- Re: [AMBER] empty cein file redox potential calculations Vaibhav Dixit
- Re: [AMBER] empty cein file redox potential calculations Marcos Serrou do Amaral
- [AMBER] parameter file for dUTP sunyeping
- Re: [AMBER] compiling Amber Tools 19 Hashemi, Mohtadin
- Re: [AMBER] empty cein file redox potential calculations Vaibhav Dixit
- Re: [AMBER] Radgyr or distance averages Daniel Roe
- Re: [AMBER] graph Daniel Roe
- Re: [AMBER] parameter file for dUTP Zachary Fallon
- Re: [AMBER] compiling Amber Tools 19 Hai Nguyen
- Re: [AMBER] compiling Amber Tools 19 Hashemi, Mohtadin
- Re: [AMBER] empty cein file redox potential calculations Cruzeiro,Vinicius Wilian D
- Re: [AMBER] parameter file for dUTP sunyeping
- Re: [AMBER] parameter file for dUTP Zachary Fallon
- Re: [AMBER] Radgyr or distance averages Reber, David
- Re: [AMBER] Radgyr or distance averages Daniel Roe
- Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5 David Case
- Re: [AMBER] Radgyr or distance averages Reber, David
- Re: [AMBER] How to generate boron atom force field parameters David Case
- Re: [AMBER] Radgyr or distance averages Daniel Roe
- Re: [AMBER] Radgyr or distance averages Reber, David
- Re: [AMBER] Radgyr or distance averages Daniel Roe
- Re: [AMBER] parameter file for dUTP David Case
- Re: [AMBER] Radgyr or distance averages Reber, David
- Re: [AMBER] Radgyr or distance averages Thomas Cheatham
- Re: [AMBER] Radgyr or distance averages Reber, David
- Re: [AMBER] Radgyr or distance averages Thomas Cheatham
- Re: [AMBER] Radgyr or distance averages Reber, David
- Re: [AMBER] Radgyr or distance averages Thomas Cheatham
- Re: [AMBER] Radgyr or distance averages Reber, David
- Re: [AMBER] Radgyr or distance averages Thomas Cheatham
- Re: [AMBER] Radgyr or distance averages Reber, David
Friday, 31 May 2019
- [AMBER] Using a box of organic solvent Alessandro LANDI
- [AMBER] Boron QM/MM Pär Håkansson
- Re: [AMBER] Using a box of organic solvent David A Case
- Re: [AMBER] Boron QM/MM Pär Håkansson
- Re: [AMBER] Radgyr or distance averages Daniel Roe
- [AMBER] make test fail Sadaf Rani
- [AMBER] Question about sander running parallel Sadaf Rani
- Re: [AMBER] make test fail David A Case
- Re: [AMBER] Question about sander running parallel David A Case
- Re: [AMBER] error with loading HEM parameters for constph redox calcuations Vaibhav Dixit
- Re: [AMBER] Question about sander running parallel Charo del Genio
- Re: [AMBER] error with loading HEM parameters for constph redox calcuations Vaibhav Dixit

Last message date: Fri May 31 2019 - 13:00:02 PDT
Archived on: Wed Dec 25 2024 - 05:55:49 PST

Amber Archive May 2019 by date