Amber Archive Sep 2019: by date

Sunday, 1 September 2019
- [AMBER] running NAMD with AMBER inputs Rui Chen
- Re: [AMBER] running NAMD with AMBER inputs David Case
- Re: [AMBER] running NAMD with AMBER inputs David Case
- [AMBER] MMGBSA.py lignad maryam azimzadehirani
- Re: [AMBER] MMGBSA.py lignad Elvis Martis
- Re: [AMBER] MMGBSA.py lignad maryam azimzadehirani
- Re: [AMBER] MMGBSA.py lignad Elvis Martis
Monday, 2 September 2019
- Re: [AMBER] MMGBSA.py lignad Elvis Martis
- Re: [AMBER] MMGBSA.py lignad maryam azimzadehirani
- [AMBER] Cpptraj watershell CUDA Max Knicker
- [AMBER] Error creating topology and coordinates file charalamm.cheng.auth.gr
- Re: [AMBER] Error creating topology and coordinates file charalamm.cheng.auth.gr
- Re: [AMBER] Cpptraj watershell CUDA Elvis Martis
- Re: [AMBER] H - bond calculations shivangi agarwal
- [AMBER] Installing on Mac - Back at it Gustaf Olsson
- Re: [AMBER] H - bond calculations Gustaf Olsson
- [AMBER] issue during TI minimisation Núbia Prates
- Re: [AMBER] issue during TI minimisation David Case
- [AMBER] restraintmask (Cannot match namelist object name :1-294) Parviz Seifpanahi Shabane
- Re: [AMBER] restraintmask (Cannot match namelist object name :1-294) Adrian Roitberg
- [AMBER] Generating parameters for iron-sulfur protein 崔佳文
- [AMBER] Problem with CPPTRAJ (RMSD) Rui Chen
Tuesday, 3 September 2019
- [AMBER] AMBER18 installation error xmgign.126.com
- Re: [AMBER] issue during TI minimisation Núbia Prates
- [AMBER] Ligand parameterization Hira Jabeen
- Re: [AMBER] AMBER18 installation error Daniel Roe
- Re: [AMBER] Problem with CPPTRAJ (RMSD) Daniel Roe
- Re: [AMBER] Ligand parameterization Gerald Monard
- Re: [AMBER] AMBER18 installation error David A Case
- Re: [AMBER] Cpptraj watershell CUDA Daniel Roe
- Re: [AMBER] Problem with CPPTRAJ (RMSD) Rui Chen
- Re: [AMBER] AMBER18 installation error aa
- Re: [AMBER] Ligand parameterization Hira Jabeen
- Re: [AMBER] Ligand parameterization David A Case
- Re: [AMBER] Problem with CPPTRAJ (RMSD) Daniel Roe
- Re: [AMBER] Problem with CPPTRAJ (RMSD) Rui Chen
- [AMBER-Developers] Job opening for AMBER developer. Christian Schafmeister
- Re: [AMBER] Preparation of trajectory for stfc diffusion calculations Daniel Roe
- Re: [AMBER] Lateral diffusion of lipid head groups Daniel Roe
- [AMBER] lipid order per leaflet Violeta Burns Casamayor
- [AMBER] ff14SB overestimation of helical comformation Lod King
- Re: [AMBER] ff14SB overestimation of helical comformation Carlos Simmerling
- Re: [AMBER] ff14SB overestimation of helical comformation Lod King
- Re: [AMBER] Print non bonded pair list Song, Lin
- Re: [AMBER] Constant PH simulations for non-proteins and nonstandard residues Kolattukudy P. Santo
- [AMBER] GBSA Kolattukudy P. Santo
- Re: [AMBER] Print non bonded pair list David Cerutti
- Re: [AMBER] Print non bonded pair list Song, Lin
- Re: [AMBER] Print non bonded pair list David Cerutti
- Re: [AMBER] GBSA David Case
- Re: [AMBER] GBSA Kolattukudy P. Santo
Wednesday, 4 September 2019
- [AMBER] Amber 18 installation Sunita Patel
- [AMBER] how to load amber rst file in vmd for observing box size Sadaf Rani
- Re: [AMBER] how to load amber rst file in vmd for observing box size Elvis Martis
- Re: [AMBER] how to load amber rst file in vmd for observing box size Sadaf Rani
- Re: [AMBER] how to load amber rst file in vmd for observing box size Fabian Glaser
- Re: [AMBER] how to load amber rst file in vmd for observing box size Elvis Martis
- Re: [AMBER] how to load amber rst file in vmd for observing box size Sadaf Rani
- Re: [AMBER] how to load amber rst file in vmd for observing box size Elvis Martis
- Re: [AMBER] how to load amber rst file in vmd for observing box size Sadaf Rani
- Re: [AMBER] how to load amber rst file in vmd for observing box size Sadaf Rani
- Re: [AMBER] how to load amber rst file in vmd for observing box size Gustaf Olsson
Thursday, 5 September 2019
- [AMBER] cloud vs purchase Fabian Glaser
- Re: [AMBER] cloud vs purchase Gustaf Olsson
- [AMBER] how to read the outup file of QMMM MD simulation with Amber combined with Gaussian (Geng Dong) 东庚
- Re: [AMBER] how to read the outup file of QMMM MD simulation with Amber combined with Gaussian (Geng Dong) David A Case
- Re: [AMBER] cloud vs purchase Ross Walker
- [AMBER] Recent updates to how Amber carries out softcore free energy calculations David A Case
- Re: [AMBER] cloud vs purchase Fabian Glaser
- [AMBER] Calculating RMSF Martín Pettinati
- Re: [AMBER] Calculating RMSF Daniel Roe
- [AMBER] How to generate parameter files of modified terminal amino acid residue using Antechamber Shankha Banerjee
- [AMBER] Explicit understanding the force computed from U(CMAP) term Lod King
Friday, 6 September 2019
- Re: [AMBER] Explicit understanding the force computed from U(CMAP) term David Cerutti
- Re: [AMBER] Explicit understanding the force computed from U(CMAP) term Lod King
- Re: [AMBER] Regarding setting up FEP calculations in AMBER18 Sadaf Rani
- Re: [AMBER] How to generate parameter files of modified terminal amino acid residue using Antechamber David Case
- [AMBER] Recent Enhancements to secstruct/dssp in Cpptraj Daniel Roe
- Re: [AMBER] how to load amber rst file in vmd for observing box size Sadaf Rani
- Re: [AMBER] Explicit understanding the force computed from U(CMAP) term Lod King
- Re: [AMBER] How to generate parameter files of modified terminal amino acid residue using Antechamber Shankha Banerjee
Saturday, 7 September 2019
- [AMBER] Generating the parameters for non-standard amino-acid residue RITUPARNA ROY
- Re: [AMBER] how to load amber rst file in vmd for observing box size Gustaf Olsson
- [AMBER] Error in calculation of per residue decomposition shivangi agarwal
- Re: [AMBER] Generating parameters for iron-sulfur protein Pengfei Li
Sunday, 8 September 2019
- [AMBER] bad atom type i Johnny Guevara
- Re: [AMBER] bad atom type i Elvis Martis
Monday, 9 September 2019
- [AMBER] Energy minimization in Implicit solvent for Langevin dynamics simulation Vishal Singh
- [AMBER] tMD and free energy calculation Elena Gomez
- Re: [AMBER] tMD and free energy calculation Bill Ross
- Re: [AMBER] Generating the parameters for non-standard amino-acid residue David A Case
- Re: [AMBER] Force conversion David A Case
- Re: [AMBER] Energy minimization in Implicit solvent for Langevin dynamics simulation David A Case
- Re: [AMBER] how to load amber rst file in vmd for observing box size Gustaf Olsson
- Re: [AMBER] Generating the parameters for non-standard amino-acid residue RITUPARNA ROY
- Re: [AMBER] Generating the parameters for non-standard amino-acid residue Carlos Simmerling
- Re: [AMBER] Error in calculation of per residue decomposition shivangi agarwal
- Re: [AMBER] Error in calculation of per residue decomposition koushik kasavajhala
- Re: [AMBER] Difference in velocity values between parmed and pytraj Jason Swails
- Re: [AMBER] GROMACS to AMBER .top and .pdb conversion using gromber Jason Swails
- Re: [AMBER] Generating the parameters for non-standard amino-acid residue RITUPARNA ROY
- Re: [AMBER] Explicit understanding the force computed from U(CMAP) term David Cerutti
- Re: [AMBER] Generating the parameters for non-standard amino-acid residue Carlos Simmerling
- Re: [AMBER] Explicit understanding the force computed from U(CMAP) term Lod King
- [AMBER] Implicit solvent simulation. Parviz Seifpanahi Shabane
Tuesday, 10 September 2019
- [AMBER] Query regarding plot Airy Sanjeev
- Re: [AMBER] Implicit solvent simulation. David A Case
- [AMBER] Small Molecules parameters Alaa Abdelrahman
- [AMBER] Amber_Cpptraj Avirup Ghosh
- [AMBER] Force field for aMD cpimenta
- Re: [AMBER] Force field for aMD Carlos Simmerling
- Re: [AMBER] Implicit solvent simulation. Saeed Izadi
Wednesday, 11 September 2019
- [AMBER] titratable residues cuda M. Pyrka
- [AMBER] PCA calculation projection Aashish Bhatt
- [AMBER] Helix Structures Lost during Heating and Equilibrium Steps Bharat Manna
- Re: [AMBER] Helix Structures Lost during Heating and Equilibrium Steps Carlos Simmerling
- Re: [AMBER] PCA calculation projection Pratul Agarwal
- [AMBER] problem with random seed Jinfeng Huang
- Re: [AMBER] problem with random seed Carlos Simmerling
- [AMBER] PNEB--"vlimit exceeded" error Anthony Bogetti
- Re: [AMBER] problem with random seed diane lynch
- [AMBER] error regarding MCPB.py Hemant Kisan
- [AMBER] optimizing GAFF2 torsional parameters Christos Deligkaris
- [AMBER] Protein-ligand simulation and help w.r.t files for carrying out simulation Renato Araujo
- Re: [AMBER] error regarding MCPB.py Aashish Bhatt
- Re: [AMBER] PCA calculation projection Aashish Bhatt
- Re: [AMBER] Protein-ligand simulation and help w.r.t files for carrying out simulation Gustaf Olsson
- [AMBER] Fwd: AmberTools19 installation error 174026008.iitb.ac.in
- Re: [AMBER] Recent updates to how Amber carries out softcore free energy calculations Ruxi Qi
Thursday, 12 September 2019
- Re: [AMBER] optimizing GAFF2 torsional parameters Karl Kirschner
- [AMBER] How to generate parameter files of N-terminal modified amino acid residue? Shankha Banerjee
- [AMBER] ASMD iat define Nisha Amarnath Jonniya
- Re: [AMBER] PCA calculation projection Pratul Agarwal
- Re: [AMBER] Fwd: AmberTools19 installation error David Case
- Re: [AMBER] Error creating topology and coordinates file Matias Machado
- Re: [AMBER] Error creating topology and coordinates file Matias Machado
- Re: [AMBER] GBSA Matias Machado
- [AMBER] the structure of cellulose II in Glycam-06h force field 冷灿
- [AMBER] AmberTools19 installation error 174026008.iitb.ac.in
Friday, 13 September 2019
- [AMBER] Amber not working after installation - Help from github charalamm.cheng.auth.gr
- [AMBER] Bug in Amber-Orca communication ? Åsmund Røhr Kjendseth
- Re: [AMBER] Amber not working after installation - Help from github Elvis Martis
- Re: [AMBER] Amber not working after installation - Help from github charalamm.cheng.auth.gr
- Re: [AMBER] GBSA Carlos Simmerling
- Re: [AMBER] Amber not working after installation - Help from github Elvis Martis
- Re: [AMBER] GBSA Kolattukudy P. Santo
- [AMBER] Fwd: tutorial for finding binding free energies Sadaf Rani
- Re: [AMBER] lipid order per leaflet Daniel Roe
- Re: [AMBER] Amber_Cpptraj Daniel Roe
- Re: [AMBER] AmberTools19 installation error Tyler Luchko (Lists)
- Re: [AMBER] Amber not working after installation - Help from github charalamm.cheng.auth.gr
- Re: [AMBER] Amber not working after installation - Help from github Elvis Martis
- Re: [AMBER] Amber not working after installation - Help from github Hai Nguyen
- Re: [AMBER] Amber not working after installation - Help from github Hai Nguyen
- Re: [AMBER] Fwd: tutorial for finding binding free energies David Case
Saturday, 14 September 2019
- Re: [AMBER] Amber not working after installation - Help from github charalamm.cheng.auth.gr
- [AMBER] sqm error 174026008.iitb.ac.in
- Re: [AMBER] sqm error David Case
- Re: [AMBER] Amber not working after installation - Help from github Hai Nguyen
Sunday, 15 September 2019
- Re: [AMBER] Amber not working after installation - Help from github charalamm.cheng.auth.gr
- Re: [AMBER] Amber not working after installation - Help from github Elvis Martis
- [AMBER] sander.MPI gives segfault if compiled with Intel compilers viktor drobot
- Re: [AMBER] Amber not working after installation - Help from github Hai Nguyen
- [AMBER] How can I make the initial configuration and topology with polarizable force field? 조준범
Monday, 16 September 2019
- [AMBER] AMBER: error in reading namelist cntrl 조준범
- Re: [AMBER] AMBER: error in reading namelist cntrl Elvis Martis
- Re: [AMBER] AMBER: error in reading namelist cntrl 조준범
- Re: [AMBER] AMBER: error in reading namelist cntrl Elvis Martis
- [AMBER] AMBER: Segmentation fault 조준범
- Re: [AMBER] AMBER: Segmentation fault Bill Ross
- Re: [AMBER] sander.MPI gives segfault if compiled with Intel compilers David A Case
- Re: [AMBER] How can I make the initial configuration and topology with polarizable force field? David A Case
- Re: [AMBER] AMBER: error in reading namelist cntrl David A Case
- Re: [AMBER] AMBER: Segmentation fault David A Case
- Re: [AMBER] sander.MPI gives segfault if compiled with Intel compilers viktor drobot
- [AMBER] Modified variables in cphstats cpimenta
- [AMBER] Question about unusual RMSD behaviour Amit Kumar
- Re: [AMBER] Question about unusual RMSD behaviour Carlos Simmerling
- Re: [AMBER] Modified variables in cphstats Daniel Roe
- Re: [AMBER] Amber 18 installation Daniel Roe
- [AMBER] Hybrid topology for mutating residue Aashish Bhatt
- Re: [AMBER] lipid order per leaflet Violeta Burns Casamayor
- Re: [AMBER] lipid order per leaflet Daniel Roe
- [AMBER] Coordinate resetting (SHAKE) can not be accomplished Sunita Patel
Tuesday, 17 September 2019
- Re: [AMBER] Coordinate resetting (SHAKE) can not be accomplished Ahmed Elrashedy
- Re: [AMBER] Question about unusual RMSD behaviour Amit Kumar
- Re: [AMBER] Question about unusual RMSD behaviour Carlos Simmerling
- [AMBER] Small ligand activators molecule shivangi agarwal
- [AMBER] Error installing Amber on Centos 7 Juan Etchart
- [AMBER] seek for how to calculate the binding free energy of a covalent inhibitor 石娜
- Re: [AMBER] Amber 18 installation David A Case
- Re: [AMBER] Hybrid topology for mutating residue David A Case
- Re: [AMBER] seek for how to calculate the binding free energy of a covalent inhibitor Ahmed Elrashedy
- Re: [AMBER] Question about unusual RMSD behaviour Amit Kumar
- [AMBER] problem with random seed Jinfeng Huang
- Re: [AMBER] Question about unusual RMSD behaviour Carlos Simmerling
- Re: [AMBER] seek for how to calculate the binding free energy of a covalent inhibitor Carlos Simmerling
- Re: [AMBER] problem with random seed Carlos Simmerling
- Re: [AMBER] Error installing Amber on Centos 7 David A Case
- Re: [AMBER] seek for how to calculate the binding free energy of a covalent inhibitor David A Case
- [AMBER] Amber17 to Amber18 considerations and archive? Shayna Hilburg
Wednesday, 18 September 2019
- [AMBER] unit conversion during umbrella sampling and then PMF calculation SATYAJIT KHATUA
- [AMBER] Cpptraj RDF onlyframes Nikolay N. Kuzmich
- Re: [AMBER] Cpptraj RDF onlyframes Gustaf Olsson
- Re: [AMBER] Cpptraj RDF onlyframes Elvis Martis
- Re: [AMBER] Small ligand activators molecule David A Case
- [AMBER] Trouble installing Amber 18 Groner, Rob
- Re: [AMBER] Trouble installing Amber 18 Daniel Roe
- Re: [AMBER] unit conversion during umbrella sampling and then PMF calculation Song, Lin
- Re: [AMBER] Trouble installing Amber 18 Scott Brozell
- Re: [AMBER] sander.MPI gives segfault if compiled with Intel compilers Scott Brozell
- Re: [AMBER] cloud vs purchase Thomas Cheatham
- Re: [AMBER] sander.MPI gives segfault if compiled with Intel compilers viktor drobot
- Re: [AMBER] sander.MPI gives segfault if compiled with Intel compilers David Case
- Re: [AMBER] Amber17 to Amber18 considerations and archive? David Case
- [AMBER] How big a molecule can antechamber (sqm) put charges on? Liao
- [AMBER] Cpptraj extracting coordinate data of a projectile Hadi Rahmaninejad
Thursday, 19 September 2019
- Re: [AMBER] Cpptraj extracting coordinate data of a projectile Daniel Roe
- [AMBER] ambpdb error while conversion Sunita Patel
- Re: [AMBER] ambpdb error while conversion Elvis Martis
- [AMBER] ANTECHAMBER_AC 2018808152.njau.edu.cn
- [AMBER] Force field problem : Acyl tail fragments parameters Pierre Leprovost
- Re: [AMBER] ANTECHAMBER_AC Matias Machado
- Re: [AMBER] How big a molecule can antechamber (sqm) put charges on? David A Case
- Re: [AMBER] ANTECHAMBER_AC David A Case
- Re: [AMBER] Cpptraj extracting coordinate data of a projectile Hadi Rahmaninejad
- Re: [AMBER] ANTECHAMBER_AC Matias Machado
- Re: [AMBER] Cpptraj RDF onlyframes Nikolay N. Kuzmich
- [AMBER] trajectory coordinate out of box Hadi Rahmaninejad
- Re: [AMBER] trajectory coordinate out of box Daniel Roe
- Re: [AMBER] Cpptraj extracting coordinate data of a projectile Daniel Roe
- Re: [AMBER] trajectory coordinate out of box Hadi Rahmaninejad
- Re: [AMBER] trajectory coordinate out of box David A Case
Friday, 20 September 2019
- [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered 石娜
- [AMBER] EstJ6_DBP_bound_sus 2018808152.njau.edu.cn
- Re: [AMBER] EstJ6_DBP_bound_sus Bill Ross
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered Bill Ross
- [AMBER] Replica Exchange pH simulations with explicit solvent Jon Uranga
- [AMBER] TI residue mutation with pmemd on GPU Hosein Geraili Daronkola
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered David Case
- Re: [AMBER] EstJ6_DBP_bound_sus David Case
- Re: [AMBER] TI residue mutation with pmemd on GPU David Case
- Re: [AMBER] ambpdb error while conversion David Case
- Re: [AMBER] TI residue mutation with pmemd on GPU Premila Samuel Mohan Dass
- [AMBER] cpptraj rms with different pdb Lenka
- Re: [AMBER] cpptraj rms with different pdb Elvis Martis
Saturday, 21 September 2019
- Re: [AMBER] cpptraj rms with different pdb Lenka
- Re: [AMBER] cpptraj rms with different pdb Elvis Martis
Sunday, 22 September 2019
- [AMBER] angles analysis Fabian Glaser
- Re: [AMBER] cpptraj rms with different pdb Lenka
Monday, 23 September 2019
- [AMBER] MD distorted MYRIAN TORRES RICO
- Re: [AMBER] MD distorted Bill Ross
- [AMBER] md distorted MYRIAN TORRES RICO
- Re: [AMBER] md distorted Bill Ross
- [AMBER] DNA methylation parameters 李振东
- Re: [AMBER] cpptraj rms with different pdb Daniel Roe
- Re: [AMBER] ambpdb error while conversion Daniel Roe
- [AMBER] Unable to generate parameters of modified amino acids using LEAP Shankha Banerjee
- Re: [AMBER] cpptraj rms with different pdb Lenka
- [AMBER] PARAMFIT David Ricardo Figueroa Blanco
- Re: [AMBER] Unable to generate parameters of modified amino acids using LEAP David Case
- [AMBER] many failures on "make test" David Mathog
- Re: [AMBER] many failures on "make test" Hai Nguyen
- Re: [AMBER] many failures on "make test" David Mathog
- Re: [AMBER] many failures on "make test" Hai Nguyen
- Re: [AMBER] PARAMFIT Robin Betz
- Re: [AMBER] many failures on "make test" David Mathog
- [AMBER] About Thermodynamic Integration tutorial (A9) with pmemd.cuda (GPU) HOCHEOL LIM
- Re: [AMBER] About Thermodynamic Integration tutorial (A9) with pmemd.cuda (GPU) Hosein Geraili Daronkola
Tuesday, 24 September 2019
- [AMBER] EstJ6_DBP_bound_sus 2018808152.njau.edu.cn
- [AMBER] restraints error MYRIAN TORRES RICO
- Re: [AMBER] EstJ6_DBP_bound_sus Elvis Martis
- Re: [AMBER] ambpdb error while conversion Sunita Patel
- Re: [AMBER] ambpdb error while conversion Bill Ross
- Re: [AMBER] ambpdb error while conversion Carlos Simmerling
- Re: [AMBER] ambpdb error while conversion Sunita Patel
- Re: [AMBER] ambpdb error while conversion Elvis Martis
- Re: [AMBER] ambpdb error while conversion Sunita Patel
- Re: [AMBER] EstJ6_DBP_bound_sus David Case
- Re: [AMBER] ambpdb error while conversion Elvis Martis
- Re: [AMBER] restraints error David Case
- Re: [AMBER] restraints error MYRIAN TORRES RICO
- [AMBER] Packmol and Amber emanuele falbo
- [AMBER] installation error ilhan.yavuz
- Re: [AMBER] installation error David Mathog
- [AMBER] MMPBSA.py -> FATAL: NATOM mismatch in coord and topology files charalamm.cheng.auth.gr
- [AMBER] up to date CUDA versions? Shayna Hilburg
- [AMBER] On AWS instance, MD stops running after sometime without producing any error neha rana
- [AMBER] Problem in calculating MMPBSA-GBSA Airy Sanjeev
Wednesday, 25 September 2019
- Re: [AMBER] ambpdb error while conversion Sunita Patel
- Re: [AMBER] ambpdb error while conversion Bill Ross
- Re: [AMBER] ambpdb error while conversion Sunita Patel
- [AMBER] aMD on a protein-protein complex maryam azimzadehirani
- [AMBER] which force field should be used for proteins when phosaa10 is used for phosphorylated serine? Ming Tang
- Re: [AMBER] ambpdb error while conversion Elvis Martis
- [AMBER] Question regarding ntx and irest Gustaf Olsson
- Re: [AMBER] ambpdb error while conversion Bill Ross
- Re: [AMBER] up to date CUDA versions? Ross Walker
- [AMBER] MMGBSA energy calculation problem for RNA Liao
- Re: [AMBER] ambpdb error while conversion Sunita Patel
- Re: [AMBER] ambpdb error while conversion Bill Ross
- Re: [AMBER] ambpdb error while conversion David Case
- Re: [AMBER] Packmol and Amber David Case
- Re: [AMBER] installation error David Case
- Re: [AMBER] Installaiton of pmemd for Amber16 Ryoichi Utsumi
- Re: [AMBER] Question regarding ntx and irest David Case
- Re: [AMBER] MMGBSA energy calculation problem for RNA David Case
- Re: [AMBER] Packmol and Amber Matias Machado
- [AMBER] Self-update: MMGBSA energy calculation problem for RNA Liao
- Re: [AMBER] MMGBSA energy calculation problem for RNA Liao
- Re: [AMBER] Problem in calculating MMPBSA-GBSA Ray Luo
- Re: [AMBER] MMGBSA energy calculation problem for RNA Carlos Simmerling
- Re: [AMBER] MMGBSA energy calculation problem for RNA Hai Nguyen
- [AMBER] Please how to solve the unfilled valence problem in antechamber Renato Araujo
- Re: [AMBER] Question regarding ntx and irest Gustaf Olsson
- Re: [AMBER] Please how to solve the unfilled valence problem in antechamber Liao
- Re: [AMBER] MMGBSA energy calculation problem for RNA Liao
- [AMBER] How can I change the default unit of density? 조준범
- [AMBER] -Antechamber error for modified residues Patil Pranita Uttamrao
- [AMBER] Rotational/torsion energy Gustaf Olsson
Thursday, 26 September 2019
- Re: [AMBER] Rotational/torsion energy Karl Kirschner
- Re: [AMBER] How can I change the default unit of density? Adrian Roitberg
- [AMBER] Compilation of Amber on Cray Suman Chakrabarty
- [AMBER] BORON parameters Monika Choudhary
- Re: [AMBER] Rotational/torsion energy Gustaf Olsson
- Re: [AMBER] Compilation of Amber on Cray David Case
- Re: [AMBER] BORON parameters David Case
- Re: [AMBER] not able to install python...using cygwin David Case
- Re: [AMBER] not able to install python...using cygwin David Case
- [AMBER] free energy calculation Sadaf Rani
- Re: [AMBER] TI residue mutation with pmemd on GPU Hosein Geraili Daronkola
- Re: [AMBER] Compilation of Amber on Cray Hai Nguyen
- Re: [AMBER] problem installing miniconda ABEL Stephane
- Re: [AMBER] imin=5 fails to produce output Casalini Tommaso
- Re: [AMBER] Compilation of Amber on Cray Suman Chakrabarty
- Re: [AMBER] cpptraj rms with different pdb Daniel Roe
- Re: [AMBER] imin=5 fails to produce output Casalini Tommaso
- Re: [AMBER] Compilation of Amber on Cray David Case
- Re: [AMBER] free energy calculation David Case
- [AMBER] PCA reweighting Aswin Hanagal
Friday, 27 September 2019
- [AMBER] problem with heavy atom (Cl atom) of ligand in tleap Seketoulie Keretsu
- Re: [AMBER] problem with heavy atom (Cl atom) of ligand in tleap Elvis Martis
- Re: [AMBER] problem with heavy atom (Cl atom) of ligand in tleap Seketoulie Keretsu
- Re: [AMBER] problem with heavy atom (Cl atom) of ligand in tleap Elvis Martis
- [AMBER] avoiding protein residue renumbering during tleap processing Seketoulie Keretsu
- [AMBER] How to incorporate new lipid molecules through packmol-memgen Chetna Tyagi
- [AMBER] Restart file format. Parviz Seifpanahi Shabane
- Re: [AMBER] Restart file format. Elvis Martis
- Re: [AMBER] Restart file format. Daniel Roe
- Re: [AMBER] imin=5 fails to produce output Daniel Roe
- Re: [AMBER] avoiding protein residue renumbering during tleap processing David A Case
- [AMBER] Query regarding mmgbsa Saikat Pal
Saturday, 28 September 2019
- Re: [AMBER] Query regarding mmgbsa David Case
- Re: [AMBER] -Antechamber error for modified residues David Case
- Re: [AMBER] imin=5 fails to produce output Daniel Roe
- Re: [AMBER] Please how to solve the unfilled valence problem in antechamber David Case
- Re: [AMBER] DNA methylation parameters David Case
- Re: [AMBER] Small Molecules parameters David Case
Sunday, 29 September 2019
- Re: [AMBER] Compilation of Amber on Cray Suman Chakrabarty
- Re: [AMBER] Compilation of Amber on Cray David Case
- Re: [AMBER] Compilation of Amber on Cray Jason Swails
Monday, 30 September 2019
- Re: [AMBER] How to incorporate new lipid molecules through packmol-memgen Stephan Schott
- [AMBER] Free energy calculation Sadaf Rani
- Re: [AMBER] Compilation of Amber on Cray Suman Chakrabarty
- Re: [AMBER] Amber18 installation Sunita Patel
- Re: [AMBER] Compilation of Amber on Cray Daniel Roe
- Re: [AMBER] How to incorporate new lipid molecules through packmol-memgen Chetna Tyagi
- Re: [AMBER] Free energy calculation David Case
- Re: [AMBER] Amber18 installation David Case
- Re: [AMBER] How to incorporate new lipid molecules through packmol-memgen Stephan Schott
- Re: [AMBER] Compilation of Amber on Cray Suman Chakrabarty

Last message date: Mon Sep 30 2019 - 11:00:02 PDT
Archived on: Fri Nov 15 2024 - 05:55:56 PST

Amber Archive Sep 2019 by date