Amber Archive Apr 2022 by date

117 messages: Starting Fri Apr 01 2022 - 02:30:02 PDT, Ending Sat Apr 30 2022 - 02:00:02 PDT
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Friday, 1 April 2022
- [AMBER] Pd (palladium not "pd" for p) lost bonds after minimization and seem as "P" atom Erdem Yeler
- Re: [AMBER] Pd (palladium not "pd" for p) lost bonds after minimization and seem as "P" atom Erdem Yeler
- [AMBER] Announcing new Fast AF MD in Amber Jason Swails
- Re: [AMBER] Pd (palladium not "pd" for p) lost bonds after minimization and seem as "P" atom David A Case
- Re: [AMBER] Pd (palladium not "pd" for p) lost bonds after minimization and seem as "P" atom Erdem Yeler
- Re: [AMBER] Announcing new Fast AF MD in Amber Matias Machado
- Re: [AMBER] Announcing new Fast AF MD in Amber ABEL Stephane
- Re: [AMBER] Announcing new Fast AF MD in Amber Scott Brozell
- Re: [AMBER] Announcing new Fast AF MD in Amber Matias Machado
- [AMBER] MDGX Error Problem with Recognizing Torsion Type Eken, Yigitcan
- Re: [AMBER] PySander availability in PyTraj Jason Swails
- Re: [AMBER] MDGX Error Problem with Recognizing Torsion Type Erdem Yeler
Saturday, 2 April 2022
- Re: [AMBER] mmpbsa divalent ion bug Jason Swails
- Re: [AMBER] MMPBSA.py.MPI and pytraj bugs David A Case
- [AMBER] PySander availability in PyTraj David Poole
- Re: [AMBER] PySander availability in PyTraj Hai Nguyen
- Re: [AMBER] MMPBSA.py.MPI and pytraj bugs Hai Nguyen
- Re: [AMBER] PySander availability in PyTraj Hai Nguyen
Monday, 4 April 2022
- [AMBER] MMPBSA.py PB calculation not working Richard Kullmann
- [AMBER] Water bridge formed between protein and ligand Shakuntala Dhurua
- Re: [AMBER] Water bridge formed between protein and ligand Daniel Roe
- Re: [AMBER] MMPBSA.py PB calculation not working Ray Luo
- [AMBER] FEW FILES DISTRIBUTION Aki
- Re: [AMBER] Water bridge formed between protein and ligand Shakuntala Dhurua
- Re: [AMBER] CUDART lib not found during install Charlotta Lebedenko
Tuesday, 5 April 2022
- Re: [AMBER] WSL2 failing at netcdf configure step David A Case
- [AMBER] A5000 vs 2080 Ti Fabian Glaser
- Re: [AMBER] PySander availability in PyTraj David A Case
- Re: [AMBER] A5000 vs 2080 Ti Stephan Schott
- Re: [AMBER] MMPBSA.py PB calculation not working Richard Kullmann
- Re: [AMBER] FEW FILES DISTRIBUTION Aki
- [AMBER] Query regarding format issue of prepc and frcmod Saikat Pal
- [AMBER] AMBER 18 and A100? Neale, Christopher Andrew
- Re: [AMBER] MMPBSA.py PB calculation not working Ray Luo
- Re: [AMBER] PySander availability in PyTraj David A Case
- Re: [AMBER] A5000 vs 2080 Ti Jason Hogrefe
- Re: [AMBER] PySander availability in PyTraj Hai Nguyen
- Re: [AMBER] MDGX Error Problem with Recognizing Torsion Type David Cerutti
- Re: [AMBER] MDGX Error Problem with Recognizing Torsion Type David Cerutti
- Re: [AMBER] A5000 vs 2080 Ti Fabian Glaser
Wednesday, 6 April 2022
- [AMBER] Imaging issue in DNA with cations - cpptraj Sathyaseelan C
- Re: [AMBER] MMPBSA.py PB calculation not working Richard Kullmann
- [AMBER] Using amber force field in NAMD Hrishikesh Dhondge
- Re: [AMBER] Water bridge formed between protein and ligand Shakuntala Dhurua
- Re: [AMBER] Using amber force field in NAMD Vlad Cojocaru
- Re: [AMBER] Using amber force field in NAMD David A Case
- Re: [AMBER] Using amber force field in NAMD Hrishikesh Dhondge
- Re: [AMBER] Query regarding format issue of prepc and frcmod Dr. Anselm Horn
- Re: [AMBER] Imaging issue in DNA with cations - cpptraj Dr. Anselm Horn
- Re: [AMBER] Water bridge formed between protein and ligand Daniel Roe
- Re: [AMBER] Imaging issue in DNA with cations - cpptraj Daniel Roe
- [AMBER] Centering structure in box Boris Gomaz
- Re: [AMBER] Centering structure in box Daniel Roe
- Re: [AMBER] CUDART lib not found during install Daniel Roe
- Re: [AMBER] Query regarding format issue of prepc and frcmod Saikat Pal
- [AMBER] Amber20 installation on Ubuntu 21.10 Hamed S. Hayatshahi
- Re: [AMBER] MMPBSA.py PB calculation not working Ray Luo
- Re: [AMBER] CUDART lib not found during install Charlotta Lebedenko
- Re: [AMBER] problem with using amber Feng Su
- Re: [AMBER] Query regarding format issue of prepc and frcmod David A Case
- Re: [AMBER] Amber20 installation on Ubuntu 21.10 David A Case
- [AMBER] Error during production run - AMBER20 Sathyaseelan C
- [AMBER] cpptraj unable to strip/save topology and trajectory Vaibhav Dixit
Thursday, 7 April 2022
- Re: [AMBER] Error during production run - AMBER20 David A Case
- Re: [AMBER] cpptraj unable to strip/save topology and trajectory Daniel Roe
- [AMBER] Adapting AMBER parameters to Gaussian16 input Kovács Richárd Dezső
- Re: [AMBER] Adapting AMBER parameters to Gaussian16 input David A Case
- Re: [AMBER] Adapting AMBER parameters to Gaussian16 input Erdem Yeler
- Re: [AMBER] Adapting AMBER parameters to Gaussian16 input Matthew Guberman-Pfeffer
- [AMBER] What atom is atom type C1, C2 and C3 Maximilian Ebert
- [AMBER] Output forces or gradients in sqm Jinzhe Zeng
Friday, 8 April 2022
- Re: [AMBER] cpptraj unable to strip/save topology and trajectory Vaibhav Dixit
- Re: [AMBER] Output forces or gradients in sqm David A Case
- Re: [AMBER] What atom is atom type C1, C2 and C3 Jason Swails
- Re: [AMBER] Imaging issue in DNA with cations - cpptraj Daniel Roe
- [AMBER] pysander and external QM Kristoffer Lundgren
- Re: [AMBER] Amber20 installation on Ubuntu 21.10 Hamed S. Hayatshahi
- [AMBER] Barostat not working (?) Artur Hermano
- Re: [AMBER] Barostat not working (?) Carlos Simmerling
- Re: [AMBER] What atom is atom type C1, C2 and C3 Maximilian Ebert
- Re: [AMBER] MMPBSA.py PB calculation not working Ray Luo
Saturday, 9 April 2022
- [AMBER] CPPTRAJ, how to write first solvent shell trajectory Matthew Guberman-Pfeffer
- [AMBER] Ubuntu 20.4 make install error? "Error: bad value (‘tigerlake’) for ‘-mtune=’ switch" Matthew Noto
- Re: [AMBER] Ubuntu 20.4 make install error? "Error: bad value (‘tigerlake’) for ‘-mtune=’ switch" Daniel Roe
- Re: [AMBER] Ubuntu 20.4 make install error? "Error: bad value (‘tigerlake’) for ‘-mtune=’ switch" Matthew Noto
- Re: [AMBER] {SPAM?} Re: CPPTRAJ, how to write first solvent shell trajectory Matthew Guberman-Pfeffer
Sunday, 10 April 2022
- Re: [AMBER] Barostat not working (?) Artur Hermano
- Re: [AMBER] Barostat not working (?) Artur Hermano
- [AMBER] Script starts but then stops w/o error message erik zuiderweg
- [AMBER] Amber force field for polymers rsaha.icredd.hokudai.ac.jp
- Re: [AMBER] Adapting AMBER parameters to Gaussian16 input Kovács Richárd Dezső
Monday, 11 April 2022
- Re: [AMBER] Script starts but then stops w/o error message Carlos Simmerling
- [AMBER] Amber 20 / AmberTools 21 on Centos 9 / Cmake Error Giorgos Lambrinidis
- Re: [AMBER] Script starts but then stops w/o error message David A Case
- Re: [AMBER] Amber 20 / AmberTools 21 on Centos 9 / Cmake Error David A Case
- [AMBER] Reg: Modified LYS - Trimethylated Lara rajam
- Re: [AMBER] Script starts but then stops w/o error message Erik Zuiderweg
Wednesday, 13 April 2022
- [AMBER] REMD Juliette Newell
- Re: [AMBER] REMD Carlos Simmerling
- [AMBER] Fitting RESP charges to carbocations, Antechamber warns "bond-type" wrong. Kovács Richárd Dezső
Thursday, 14 April 2022
- Re: [AMBER] Fitting RESP charges to carbocations, Antechamber warns "bond-type" wrong. Erdem Yeler
- Re: [AMBER] Amber force field for polymers rsaha.icredd.hokudai.ac.jp
Friday, 15 April 2022
- Re: [AMBER] AMBER/TeraChem interface Vinicius Wilian Cruzeiro
Saturday, 16 April 2022
- [AMBER] Regarding metal cofactor replacement Sruthi Sudhakar
- Re: [AMBER] Regarding metal cofactor replacement David A Case
- Re: [AMBER] Regarding metal cofactor replacement Sruthi Sudhakar
- [AMBER] QM+cutoff larger than box error -Qm/Mm simulation keerthi vaasan
- Re: [AMBER] MMPBSA module error Ray Luo
Tuesday, 19 April 2022
- Re: [AMBER] MMPBSA module error Ryan Pavlovicz
- Re: [AMBER] MMPBSA module error Ray Luo
Thursday, 21 April 2022
- [AMBER] P-O-P angle of pyrophosphoric acid becomes 180 degree after being optimized by sander with DFTB Suitian Lai
- [AMBER] Problem in forcefield generation for polymer with two bond connection between the monomers rsaha.icredd.hokudai.ac.jp
Saturday, 23 April 2022
- [AMBER] Segmentation fault (core dumped) amber Tleap İmren Bayıl
Tuesday, 26 April 2022
- [AMBER] Compiling Amber18 on Scientific Linux 7.7 (CentOS 7) with gcc-7.5.0 and cuda-10.0 / cuda-11.4 Gerald Keller
Thursday, 28 April 2022
- [AMBER] Release of Amber22 and AmberTools22 David A Case
Friday, 29 April 2022
- Re: [AMBER] QM restrains David A Case
- Re: [AMBER] How to get and install latest CPPTRAJ aishen

Last message date: Sat Apr 30 2022 - 02:00:02 PDT
Archived on: Wed Apr 17 2024 - 05:56:02 PDT