Amber Archive Apr 2022 by thread
117 messages
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Starting
Fri Apr 01 2022 - 02:30:02 PDT,
Ending
Sat Apr 30 2022 - 02:00:02 PDT
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[AMBER] Pd (palladium not "pd" for p) lost bonds after minimization and seem as "P" atom
Erdem Yeler
(Fri Apr 01 2022 - 02:17:04 PDT)
Re: [AMBER] Pd (palladium not "pd" for p) lost bonds after minimization and seem as "P" atom
Erdem Yeler
(Fri Apr 01 2022 - 02:18:16 PDT)
Re: [AMBER] Pd (palladium not "pd" for p) lost bonds after minimization and seem as "P" atom
David A Case
(Fri Apr 01 2022 - 05:18:09 PDT)
Re: [AMBER] Pd (palladium not "pd" for p) lost bonds after minimization and seem as "P" atom
Erdem Yeler
(Fri Apr 01 2022 - 06:28:30 PDT)
[AMBER] Announcing new Fast AF MD in Amber
Jason Swails
(Fri Apr 01 2022 - 03:59:12 PDT)
Re: [AMBER] Announcing new Fast AF MD in Amber
Matias Machado
(Fri Apr 01 2022 - 08:53:58 PDT)
Re: [AMBER] Announcing new Fast AF MD in Amber
Matias Machado
(Fri Apr 01 2022 - 09:37:37 PDT)
Re: [AMBER] Announcing new Fast AF MD in Amber
ABEL Stephane
(Fri Apr 01 2022 - 09:06:40 PDT)
Re: [AMBER] Announcing new Fast AF MD in Amber
Scott Brozell
(Fri Apr 01 2022 - 09:27:47 PDT)
[AMBER] MDGX Error Problem with Recognizing Torsion Type
Eken, Yigitcan
(Fri Apr 01 2022 - 12:13:16 PDT)
Re: [AMBER] MDGX Error Problem with Recognizing Torsion Type
Erdem Yeler
(Fri Apr 01 2022 - 21:19:21 PDT)
Re: [AMBER] MDGX Error Problem with Recognizing Torsion Type
David Cerutti
(Tue Apr 05 2022 - 16:15:42 PDT)
Re: [AMBER] MDGX Error Problem with Recognizing Torsion Type
David Cerutti
(Tue Apr 05 2022 - 17:08:22 PDT)
Re: [AMBER] PySander availability in PyTraj
Jason Swails
(Fri Apr 01 2022 - 15:12:00 PDT)
Re: [AMBER] PySander availability in PyTraj
David A Case
(Tue Apr 05 2022 - 06:31:15 PDT)
Re: [AMBER] PySander availability in PyTraj
David A Case
(Tue Apr 05 2022 - 11:42:48 PDT)
Re: [AMBER] PySander availability in PyTraj
Hai Nguyen
(Tue Apr 05 2022 - 12:50:57 PDT)
Re: [AMBER] mmpbsa divalent ion bug
Jason Swails
(Sat Apr 02 2022 - 05:26:16 PDT)
Re: [AMBER] MMPBSA.py.MPI and pytraj bugs
David A Case
(Sat Apr 02 2022 - 06:47:56 PDT)
Re: [AMBER] MMPBSA.py.MPI and pytraj bugs
Hai Nguyen
(Sat Apr 02 2022 - 19:26:49 PDT)
[AMBER] PySander availability in PyTraj
David Poole
(Sat Apr 02 2022 - 17:52:10 PDT)
Re: [AMBER] PySander availability in PyTraj
Hai Nguyen
(Sat Apr 02 2022 - 19:24:50 PDT)
Re: [AMBER] PySander availability in PyTraj
Hai Nguyen
(Sat Apr 02 2022 - 19:39:07 PDT)
[AMBER] MMPBSA.py PB calculation not working
Richard Kullmann
(Mon Apr 04 2022 - 03:01:24 PDT)
Re: [AMBER] MMPBSA.py PB calculation not working
Ray Luo
(Mon Apr 04 2022 - 08:33:16 PDT)
Re: [AMBER] MMPBSA.py PB calculation not working
Ray Luo
(Fri Apr 08 2022 - 20:18:54 PDT)
Re: [AMBER] MMPBSA.py PB calculation not working
Richard Kullmann
(Tue Apr 05 2022 - 08:38:16 PDT)
Re: [AMBER] MMPBSA.py PB calculation not working
Ray Luo
(Tue Apr 05 2022 - 11:42:37 PDT)
Re: [AMBER] MMPBSA.py PB calculation not working
Richard Kullmann
(Wed Apr 06 2022 - 02:44:57 PDT)
Re: [AMBER] MMPBSA.py PB calculation not working
Ray Luo
(Wed Apr 06 2022 - 10:13:25 PDT)
[AMBER] Water bridge formed between protein and ligand
Shakuntala Dhurua
(Mon Apr 04 2022 - 06:38:53 PDT)
Re: [AMBER] Water bridge formed between protein and ligand
Daniel Roe
(Mon Apr 04 2022 - 07:25:54 PDT)
Re: [AMBER] Water bridge formed between protein and ligand
Shakuntala Dhurua
(Mon Apr 04 2022 - 10:23:40 PDT)
Re: [AMBER] Water bridge formed between protein and ligand
Daniel Roe
(Wed Apr 06 2022 - 06:43:34 PDT)
Re: [AMBER] Water bridge formed between protein and ligand
Shakuntala Dhurua
(Wed Apr 06 2022 - 03:11:20 PDT)
[AMBER] FEW FILES DISTRIBUTION
Aki
(Mon Apr 04 2022 - 09:48:16 PDT)
Re: [AMBER] FEW FILES DISTRIBUTION
Aki
(Tue Apr 05 2022 - 08:45:22 PDT)
Re: [AMBER] CUDART lib not found during install
Charlotta Lebedenko
(Mon Apr 04 2022 - 12:24:43 PDT)
Re: [AMBER] WSL2 failing at netcdf configure step
David A Case
(Tue Apr 05 2022 - 06:15:46 PDT)
Re: [AMBER] CUDART lib not found during install
Daniel Roe
(Wed Apr 06 2022 - 07:22:10 PDT)
Re: [AMBER] CUDART lib not found during install
Charlotta Lebedenko
(Wed Apr 06 2022 - 12:48:26 PDT)
[AMBER] A5000 vs 2080 Ti
Fabian Glaser
(Tue Apr 05 2022 - 06:25:34 PDT)
Re: [AMBER] A5000 vs 2080 Ti
Stephan Schott
(Tue Apr 05 2022 - 07:42:42 PDT)
Re: [AMBER] A5000 vs 2080 Ti
Fabian Glaser
(Tue Apr 05 2022 - 22:50:23 PDT)
Re: [AMBER] A5000 vs 2080 Ti
Jason Hogrefe
(Tue Apr 05 2022 - 11:57:40 PDT)
[AMBER] Query regarding format issue of prepc and frcmod
Saikat Pal
(Tue Apr 05 2022 - 10:07:03 PDT)
Re: [AMBER] Query regarding format issue of prepc and frcmod
Dr. Anselm Horn
(Wed Apr 06 2022 - 06:21:21 PDT)
Re: [AMBER] Query regarding format issue of prepc and frcmod
Saikat Pal
(Wed Apr 06 2022 - 08:43:46 PDT)
Re: [AMBER] Query regarding format issue of prepc and frcmod
David A Case
(Wed Apr 06 2022 - 18:44:57 PDT)
[AMBER] AMBER 18 and A100?
Neale, Christopher Andrew
(Tue Apr 05 2022 - 11:38:36 PDT)
[AMBER] Imaging issue in DNA with cations - cpptraj
Sathyaseelan C
(Wed Apr 06 2022 - 01:06:40 PDT)
Re: [AMBER] Imaging issue in DNA with cations - cpptraj
Dr. Anselm Horn
(Wed Apr 06 2022 - 06:35:08 PDT)
Re: [AMBER] Imaging issue in DNA with cations - cpptraj
Daniel Roe
(Wed Apr 06 2022 - 06:47:51 PDT)
Re: [AMBER] Imaging issue in DNA with cations - cpptraj
Daniel Roe
(Fri Apr 08 2022 - 07:10:23 PDT)
[AMBER] Using amber force field in NAMD
Hrishikesh Dhondge
(Wed Apr 06 2022 - 03:03:43 PDT)
Re: [AMBER] Using amber force field in NAMD
Vlad Cojocaru
(Wed Apr 06 2022 - 05:06:49 PDT)
Re: [AMBER] Using amber force field in NAMD
David A Case
(Wed Apr 06 2022 - 05:52:42 PDT)
Re: [AMBER] Using amber force field in NAMD
Hrishikesh Dhondge
(Wed Apr 06 2022 - 05:59:47 PDT)
[AMBER] Centering structure in box
Boris Gomaz
(Wed Apr 06 2022 - 06:56:44 PDT)
Re: [AMBER] Centering structure in box
Daniel Roe
(Wed Apr 06 2022 - 07:12:41 PDT)
[AMBER] Amber20 installation on Ubuntu 21.10
Hamed S. Hayatshahi
(Wed Apr 06 2022 - 10:09:55 PDT)
Re: [AMBER] Amber20 installation on Ubuntu 21.10
David A Case
(Wed Apr 06 2022 - 18:55:24 PDT)
Re: [AMBER] Amber20 installation on Ubuntu 21.10
Hamed S. Hayatshahi
(Fri Apr 08 2022 - 12:52:26 PDT)
Re: [AMBER] problem with using amber
Feng Su
(Wed Apr 06 2022 - 17:52:16 PDT)
[AMBER] Error during production run - AMBER20
Sathyaseelan C
(Wed Apr 06 2022 - 20:42:57 PDT)
Re: [AMBER] Error during production run - AMBER20
David A Case
(Thu Apr 07 2022 - 03:53:56 PDT)
[AMBER] cpptraj unable to strip/save topology and trajectory
Vaibhav Dixit
(Wed Apr 06 2022 - 20:46:30 PDT)
Re: [AMBER] cpptraj unable to strip/save topology and trajectory
Daniel Roe
(Thu Apr 07 2022 - 05:23:23 PDT)
Re: [AMBER] cpptraj unable to strip/save topology and trajectory
Vaibhav Dixit
(Fri Apr 08 2022 - 00:22:38 PDT)
[AMBER] Adapting AMBER parameters to Gaussian16 input
Kovács Richárd Dezső
(Thu Apr 07 2022 - 07:36:14 PDT)
Re: [AMBER] Adapting AMBER parameters to Gaussian16 input
David A Case
(Thu Apr 07 2022 - 09:58:36 PDT)
Re: [AMBER] Adapting AMBER parameters to Gaussian16 input
Erdem Yeler
(Thu Apr 07 2022 - 10:29:47 PDT)
Re: [AMBER] Adapting AMBER parameters to Gaussian16 input
Matthew Guberman-Pfeffer
(Thu Apr 07 2022 - 10:34:52 PDT)
Re: [AMBER] Adapting AMBER parameters to Gaussian16 input
Kovács Richárd Dezső
(Sun Apr 10 2022 - 20:13:49 PDT)
[AMBER] What atom is atom type C1, C2 and C3
Maximilian Ebert
(Thu Apr 07 2022 - 13:29:36 PDT)
Re: [AMBER] What atom is atom type C1, C2 and C3
Jason Swails
(Fri Apr 08 2022 - 06:35:49 PDT)
Re: [AMBER] What atom is atom type C1, C2 and C3
Maximilian Ebert
(Fri Apr 08 2022 - 17:01:12 PDT)
[AMBER] Output forces or gradients in sqm
Jinzhe Zeng
(Thu Apr 07 2022 - 14:16:33 PDT)
Re: [AMBER] Output forces or gradients in sqm
David A Case
(Fri Apr 08 2022 - 06:35:02 PDT)
[AMBER] pysander and external QM
Kristoffer Lundgren
(Fri Apr 08 2022 - 07:25:05 PDT)
[AMBER] Barostat not working (?)
Artur Hermano
(Fri Apr 08 2022 - 13:46:41 PDT)
Re: [AMBER] Barostat not working (?)
Carlos Simmerling
(Fri Apr 08 2022 - 14:27:59 PDT)
Re: [AMBER] Barostat not working (?)
Artur Hermano
(Sun Apr 10 2022 - 08:26:04 PDT)
Re: [AMBER] Barostat not working (?)
Artur Hermano
(Sun Apr 10 2022 - 13:11:35 PDT)
[AMBER] CPPTRAJ, how to write first solvent shell trajectory
Matthew Guberman-Pfeffer
(Sat Apr 09 2022 - 02:59:05 PDT)
[AMBER] Ubuntu 20.4 make install error? "Error: bad value (‘tigerlake’) for ‘-mtune=’ switch"
Matthew Noto
(Sat Apr 09 2022 - 13:04:10 PDT)
Re: [AMBER] Ubuntu 20.4 make install error? "Error: bad value (‘tigerlake’) for ‘-mtune=’ switch"
Daniel Roe
(Sat Apr 09 2022 - 14:07:34 PDT)
Re: [AMBER] Ubuntu 20.4 make install error? "Error: bad value (‘tigerlake’) for ‘-mtune=’ switch"
Matthew Noto
(Sat Apr 09 2022 - 14:33:19 PDT)
Re: [AMBER] {SPAM?} Re: CPPTRAJ, how to write first solvent shell trajectory
Matthew Guberman-Pfeffer
(Sat Apr 09 2022 - 18:26:17 PDT)
[AMBER] Script starts but then stops w/o error message
erik zuiderweg
(Sun Apr 10 2022 - 13:35:21 PDT)
Re: [AMBER] Script starts but then stops w/o error message
Carlos Simmerling
(Mon Apr 11 2022 - 05:20:08 PDT)
Re: [AMBER] Script starts but then stops w/o error message
David A Case
(Mon Apr 11 2022 - 10:28:02 PDT)
Re: [AMBER] Script starts but then stops w/o error message
Erik Zuiderweg
(Mon Apr 11 2022 - 15:55:21 PDT)
[AMBER] Amber force field for polymers
rsaha.icredd.hokudai.ac.jp
(Sun Apr 10 2022 - 20:00:29 PDT)
[AMBER] Amber 20 / AmberTools 21 on Centos 9 / Cmake Error
Giorgos Lambrinidis
(Mon Apr 11 2022 - 08:55:46 PDT)
Re: [AMBER] Amber 20 / AmberTools 21 on Centos 9 / Cmake Error
David A Case
(Mon Apr 11 2022 - 10:51:37 PDT)
[AMBER] Reg: Modified LYS - Trimethylated
Lara rajam
(Mon Apr 11 2022 - 12:23:52 PDT)
[AMBER] REMD
Juliette Newell
(Wed Apr 13 2022 - 02:01:14 PDT)
Re: [AMBER] REMD
Carlos Simmerling
(Wed Apr 13 2022 - 06:54:30 PDT)
[AMBER] Fitting RESP charges to carbocations, Antechamber warns "bond-type" wrong.
Kovács Richárd Dezső
(Wed Apr 13 2022 - 08:23:01 PDT)
Re: [AMBER] Fitting RESP charges to carbocations, Antechamber warns "bond-type" wrong.
Erdem Yeler
(Thu Apr 14 2022 - 15:27:55 PDT)
Re: [AMBER] Amber force field for polymers
rsaha.icredd.hokudai.ac.jp
(Thu Apr 14 2022 - 18:23:02 PDT)
Re: [AMBER] AMBER/TeraChem interface
Vinicius Wilian Cruzeiro
(Fri Apr 15 2022 - 08:53:05 PDT)
[AMBER] Regarding metal cofactor replacement
Sruthi Sudhakar
(Sat Apr 16 2022 - 04:42:51 PDT)
Re: [AMBER] Regarding metal cofactor replacement
David A Case
(Sat Apr 16 2022 - 04:53:03 PDT)
Re: [AMBER] Regarding metal cofactor replacement
Sruthi Sudhakar
(Sat Apr 16 2022 - 05:11:28 PDT)
[AMBER] QM+cutoff larger than box error -Qm/Mm simulation
keerthi vaasan
(Sat Apr 16 2022 - 05:41:32 PDT)
Re: [AMBER] MMPBSA module error
Ray Luo
(Sat Apr 16 2022 - 07:58:45 PDT)
Re: [AMBER] MMPBSA module error
Ryan Pavlovicz
(Tue Apr 19 2022 - 10:15:28 PDT)
Re: [AMBER] MMPBSA module error
Ray Luo
(Tue Apr 19 2022 - 16:55:43 PDT)
[AMBER] P-O-P angle of pyrophosphoric acid becomes 180 degree after being optimized by sander with DFTB
Suitian Lai
(Thu Apr 21 2022 - 20:13:08 PDT)
[AMBER] Problem in forcefield generation for polymer with two bond connection between the monomers
rsaha.icredd.hokudai.ac.jp
(Thu Apr 21 2022 - 23:58:11 PDT)
[AMBER] Segmentation fault (core dumped) amber Tleap
İmren Bayıl
(Sat Apr 23 2022 - 22:02:15 PDT)
[AMBER] Compiling Amber18 on Scientific Linux 7.7 (CentOS 7) with gcc-7.5.0 and cuda-10.0 / cuda-11.4
Gerald Keller
(Tue Apr 26 2022 - 00:18:20 PDT)
[AMBER] Release of Amber22 and AmberTools22
David A Case
(Thu Apr 28 2022 - 04:16:50 PDT)
Re: [AMBER] QM restrains
David A Case
(Fri Apr 29 2022 - 18:53:42 PDT)
Re: [AMBER] How to get and install latest CPPTRAJ
aishen
(Fri Apr 29 2022 - 23:42:02 PDT)
Last message date
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Sat Apr 30 2022 - 02:00:02 PDT
Archived on
: Wed Dec 25 2024 - 05:56:11 PST
117 messages
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