Amber Archive Aug 2019 by thread
326 messages
:
Starting
Thu Aug 01 2019 - 04:00:02 PDT,
Ending
Sat Aug 31 2019 - 10:30:02 PDT
This period
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[AMBER] error in Cuda installtion
Karim Mahnam
(Thu Aug 01 2019 - 03:41:04 PDT)
Re: [AMBER] error in Cuda installtion
Daniel Roe
(Thu Aug 01 2019 - 04:57:57 PDT)
Re: [AMBER] error in Cuda installtion
David A Case
(Thu Aug 01 2019 - 05:23:48 PDT)
[AMBER] 1-4 EvdW and 1-4 EEL
Lod King
(Thu Aug 01 2019 - 14:24:56 PDT)
Re: [AMBER] 1-4 EvdW and 1-4 EEL
David A Case
(Fri Aug 02 2019 - 05:42:17 PDT)
Re: [AMBER] 1-4 EvdW and 1-4 EEL
David Cerutti
(Fri Aug 02 2019 - 11:51:42 PDT)
Re: [AMBER] 1-4 EvdW and 1-4 EEL
Lod King
(Fri Aug 02 2019 - 11:54:43 PDT)
[AMBER] RTX 5000 cards and AMBER 16 compatibility
Laura Furge
(Fri Aug 02 2019 - 14:17:05 PDT)
Re: [AMBER] RTX 5000 cards and AMBER 16 compatibility
Hashemi, Mohtadin
(Fri Aug 02 2019 - 20:38:12 PDT)
Re: [AMBER] Constant pH MD + HMR
Jason Swails
(Fri Aug 02 2019 - 21:50:07 PDT)
[AMBER] Simulations without PME
Tom Kurtzman
(Mon Aug 05 2019 - 12:45:49 PDT)
Re: [AMBER] Simulations without PME
David Case
(Mon Aug 05 2019 - 18:18:50 PDT)
Re: [AMBER] Simulations without PME
Bill Ross
(Mon Aug 05 2019 - 18:43:09 PDT)
Re: [AMBER] Simulations without PME
Tom Kurtzman
(Tue Aug 06 2019 - 09:03:27 PDT)
Re: [AMBER] gaff2 parameters of c3-c3-os-c3
Song, Lin
(Mon Aug 05 2019 - 12:51:36 PDT)
Re: [AMBER] gaff2 parameters of c3-c3-os-c3
David Cerutti
(Mon Aug 05 2019 - 13:04:28 PDT)
Re: [AMBER] gaff2 parameters of c3-c3-os-c3
David Case
(Mon Aug 05 2019 - 18:27:36 PDT)
Re: [AMBER] gaff2 parameters of c3-c3-os-c3
Song, Lin
(Fri Aug 09 2019 - 08:30:28 PDT)
Re: [AMBER] gaff2 parameters of c3-c3-os-c3
Junmei Wang
(Fri Aug 09 2019 - 13:03:14 PDT)
Re: [AMBER] GaMD Not Running in GPU
ATUL KUMAR
(Mon Aug 05 2019 - 22:13:49 PDT)
[AMBER] $AMBERHOME vs $AMBER_PREFIX
Pete Biggs
(Tue Aug 06 2019 - 01:23:19 PDT)
Re: [AMBER] $AMBERHOME vs $AMBER_PREFIX
Hai Nguyen
(Tue Aug 06 2019 - 04:55:15 PDT)
Re: [AMBER] $AMBERHOME vs $AMBER_PREFIX
Pete Biggs
(Tue Aug 06 2019 - 08:40:59 PDT)
[AMBER] error during the calculation of MMPBSA
Jeyaram R A
(Tue Aug 06 2019 - 06:03:44 PDT)
Re: [AMBER] error during the calculation of MMPBSA
rluo.uci.edu
(Tue Aug 06 2019 - 06:50:54 PDT)
Re: [AMBER] error during the calculation of MMPBSA
Jeyaram R A
(Tue Aug 06 2019 - 08:24:47 PDT)
Re: [AMBER] error during the calculation of MMPBSA
Thomas Gaillard
(Wed Aug 07 2019 - 02:30:47 PDT)
Re: [AMBER] error during the calculation of MMPBSA
Elvis Martis
(Tue Aug 06 2019 - 06:54:02 PDT)
Re: [AMBER] error during the calculation of MMPBSA
Jeyaram R A
(Tue Aug 06 2019 - 08:14:22 PDT)
Re: [AMBER] error during the calculation of MMPBSA
Elvis Martis
(Tue Aug 06 2019 - 08:21:33 PDT)
Re: [AMBER] error during the calculation of MMPBSA
Jeyaram R A
(Tue Aug 06 2019 - 08:26:31 PDT)
Re: [AMBER] error during the calculation of MMPBSA
Jeyaram R A
(Tue Aug 06 2019 - 09:50:38 PDT)
Re: [AMBER] error during the calculation of MMPBSA
Jeyaram R A
(Tue Aug 06 2019 - 09:51:51 PDT)
Re: [AMBER] error during the calculation of MMPBSA
Elvis Martis
(Tue Aug 06 2019 - 19:33:31 PDT)
Re: [AMBER] error during the calculation of MMPBSA
Jeyaram R A
(Tue Aug 06 2019 - 22:33:25 PDT)
Re: [AMBER] error during the calculation of MMPBSA
Elvis Martis
(Tue Aug 06 2019 - 22:37:57 PDT)
[AMBER] T-leap.
Parviz Seifpanahi Shabane
(Tue Aug 06 2019 - 07:01:25 PDT)
Re: [AMBER] T-leap.
David A Case
(Tue Aug 06 2019 - 09:24:16 PDT)
[AMBER] Specifying size of truncated octahedron box manually
Bellesis, Andrew G
(Tue Aug 06 2019 - 07:29:57 PDT)
Re: [AMBER] Specifying size of truncated octahedron box manually
David Case
(Tue Aug 20 2019 - 19:33:01 PDT)
Re: [AMBER] Specifying size of truncated octahedron box manually
Matias Machado
(Fri Aug 23 2019 - 13:32:20 PDT)
[AMBER] Alanine scan issue
YOGESH NARKHEDE
(Tue Aug 06 2019 - 10:59:51 PDT)
[AMBER] How to generate Free energy landscape for amber trajectory?
M RCC
(Tue Aug 06 2019 - 22:10:14 PDT)
Re: [AMBER] How to generate Free energy landscape for amber trajectory?
Carlos Simmerling
(Wed Aug 07 2019 - 04:58:07 PDT)
Re: [AMBER] How to generate Free energy landscape for amber trajectory?
Daniel Roe
(Thu Aug 08 2019 - 05:00:21 PDT)
[AMBER] Imaging-rst file error
Hira Jabeen
(Wed Aug 07 2019 - 03:34:59 PDT)
Re: [AMBER] Imaging-rst file error
Carlos Simmerling
(Wed Aug 07 2019 - 04:41:27 PDT)
Re: [AMBER] Imaging-rst file error
Hira Jabeen
(Wed Aug 07 2019 - 05:56:44 PDT)
Re: [AMBER] Imaging-rst file error
Carlos Simmerling
(Wed Aug 07 2019 - 06:19:59 PDT)
Re: [AMBER] Imaging-rst file error
Hira Jabeen
(Wed Aug 07 2019 - 06:51:30 PDT)
Re: [AMBER] Imaging-rst file error
Daniel Roe
(Thu Aug 08 2019 - 05:38:38 PDT)
Re: [AMBER] Imaging-rst file error
David A Case
(Thu Aug 08 2019 - 08:41:50 PDT)
Re: [AMBER] Imaging-rst file error
Daniel Roe
(Thu Aug 08 2019 - 10:31:46 PDT)
[AMBER] Lazy Question: File conversion NCRST to RST
Gustaf Olsson
(Wed Aug 07 2019 - 04:40:51 PDT)
Re: [AMBER] Lazy Question: File conversion NCRST to RST
Carlos Simmerling
(Wed Aug 07 2019 - 04:41:58 PDT)
Re: [AMBER] Lazy Question: File conversion NCRST to RST
Daniel Roe
(Wed Aug 07 2019 - 05:06:37 PDT)
Re: [AMBER] Lazy Question: File conversion NCRST to RST
Gustaf Olsson
(Wed Aug 07 2019 - 05:58:53 PDT)
Re: [AMBER] Lazy Question: File conversion NCRST to RST
Gustaf Olsson
(Wed Aug 07 2019 - 06:43:41 PDT)
Re: [AMBER] Lazy Question: File conversion NCRST to RST
Daniel Roe
(Mon Aug 12 2019 - 11:05:31 PDT)
Re: [AMBER] Lazy Question: File conversion NCRST to RST
Gustaf Olsson
(Mon Aug 12 2019 - 22:42:01 PDT)
Re: [AMBER] Lazy Question: File conversion NCRST to RST
Gustaf Olsson
(Wed Aug 14 2019 - 02:32:32 PDT)
Re: [AMBER] Lazy Question: File conversion NCRST to RST
Daniel Roe
(Wed Aug 14 2019 - 04:30:10 PDT)
Re: [AMBER] Lazy Question: File conversion NCRST to RST
Gustaf Olsson
(Wed Aug 14 2019 - 05:28:44 PDT)
Re: [AMBER] Lazy Question: File conversion NCRST to RST
Gustaf Olsson
(Wed Aug 14 2019 - 06:06:35 PDT)
[AMBER] Difference in velocity values between parmed and pytraj
Irfan Alibay
(Wed Aug 07 2019 - 08:13:12 PDT)
Re: [AMBER] Difference in velocity values between parmed and pytraj
Hai Nguyen
(Wed Aug 07 2019 - 08:47:37 PDT)
Re: [AMBER] Difference in velocity values between parmed and pytraj
Irfan Alibay
(Thu Aug 08 2019 - 12:06:34 PDT)
Re: [AMBER] Difference in velocity values between parmed and pytraj
Hai Nguyen
(Thu Aug 08 2019 - 12:14:26 PDT)
Re: [AMBER] Difference in velocity values between parmed and pytraj
Daniel Roe
(Thu Aug 08 2019 - 12:23:05 PDT)
Re: [AMBER] MCPB.py showing error in the step: MCPB.py -i 1OKL.in -s 2
Pengfei Li
(Wed Aug 07 2019 - 19:49:23 PDT)
Re: [AMBER] modelling of a penta coordination around zinc ion (+2) using MCPB.py
Pengfei Li
(Wed Aug 07 2019 - 19:56:47 PDT)
[AMBER] problems with Miniconda installation
Elvis Martis
(Wed Aug 07 2019 - 23:52:40 PDT)
Re: [AMBER] problems with Miniconda installation
David A Case
(Thu Aug 08 2019 - 08:39:10 PDT)
Re: [AMBER] problems with Miniconda installation
Elvis Martis
(Thu Aug 08 2019 - 08:50:07 PDT)
Re: [AMBER] problems with Miniconda installation
Sunita Patel
(Thu Aug 08 2019 - 23:43:27 PDT)
Re: [AMBER] problems with Miniconda installation
Sunita Patel
(Fri Aug 09 2019 - 01:52:59 PDT)
Re: [AMBER] problems with Miniconda installation
Elvis Martis
(Fri Aug 09 2019 - 03:44:09 PDT)
Re: [AMBER] problems with Miniconda installation
Sunita Patel
(Fri Aug 09 2019 - 04:44:39 PDT)
[AMBER] Transcription factor DNA binding - Gibbs of activation
charalamm.cheng.auth.gr
(Wed Aug 07 2019 - 23:58:27 PDT)
[AMBER] ΑΠ: Transcription factor DNA binding - Gibbs of activation
Antonios Kolocouris
(Thu Aug 08 2019 - 00:41:43 PDT)
Re: [AMBER] Transcription factor DNA binding - Gibbs of activation
Kevin Hauser
(Thu Aug 08 2019 - 07:38:03 PDT)
[AMBER-Developers] AMBER developer job opening and TI/FEP calculation postdoc opening coming up
Christian Schafmeister
(Thu Aug 08 2019 - 10:17:44 PDT)
[AMBER] Issues in AMBER-18 Installation
Deepika Sardana
(Fri Aug 09 2019 - 00:25:40 PDT)
[AMBER] How to calculate the tilt angle of TM helix
Maria Bzówka
(Fri Aug 09 2019 - 01:17:53 PDT)
Re: [AMBER] How to calculate the tilt angle of TM helix
Dickson, Callum
(Fri Aug 09 2019 - 13:49:44 PDT)
Re: [AMBER] How to calculate the tilt angle of TM helix
Prajwal Nandekar
(Fri Aug 09 2019 - 21:56:17 PDT)
Re: [AMBER] How to calculate the tilt angle of TM helix
Daniel Roe
(Sat Aug 10 2019 - 06:25:38 PDT)
Re: [AMBER] How to calculate the tilt angle of TM helix
Maria Bzówka
(Mon Aug 12 2019 - 01:57:36 PDT)
Re: [AMBER] How to calculate the tilt angle of TM helix
Stephan Schott
(Mon Aug 12 2019 - 03:37:26 PDT)
Re: [AMBER] How to calculate the tilt angle of TM helix
Maria Bzówka
(Mon Aug 12 2019 - 04:22:47 PDT)
[AMBER] T-leap "does not have a type"
Parviz Seifpanahi Shabane
(Fri Aug 09 2019 - 09:47:14 PDT)
Re: [AMBER] T-leap "does not have a type"
Matias Machado
(Sat Aug 10 2019 - 12:39:12 PDT)
Re: [AMBER] T-leap "does not have a type"
Matias Machado
(Sat Aug 10 2019 - 13:18:17 PDT)
Re: [AMBER] T-leap "does not have a type"
David Case
(Sun Aug 11 2019 - 05:36:06 PDT)
[AMBER] DNA force field.
Parviz Seifpanahi Shabane
(Fri Aug 09 2019 - 09:54:06 PDT)
Re: [AMBER] DNA force field.
Matias Machado
(Sat Aug 10 2019 - 13:01:51 PDT)
[AMBER] MM-PBSA Alanine scanning issue
YOGESH NARKHEDE
(Fri Aug 09 2019 - 10:44:00 PDT)
Re: [AMBER] MM-PBSA Alanine scanning issue
Elvis Martis
(Fri Aug 09 2019 - 21:23:18 PDT)
[AMBER] MD on small molecules, The file contained 8 atoms not in residue templates
Amen Shamim
(Fri Aug 09 2019 - 11:17:52 PDT)
Re: [AMBER] MD on small molecules, The file contained 8 atoms not in residue templates
David Case
(Tue Aug 20 2019 - 19:29:47 PDT)
[AMBER] Installaiton of pmemd for Amber16
Ryoichi Utsumi
(Sat Aug 10 2019 - 04:18:40 PDT)
Re: [AMBER] Installaiton of pmemd for Amber16
David Case
(Wed Aug 14 2019 - 18:32:57 PDT)
[AMBER] Error iin running mmpbsa
shivangi agarwal
(Sat Aug 10 2019 - 09:36:39 PDT)
[AMBER] Question about DFTB3 method with dispersion correction
Rajiv
(Sun Aug 11 2019 - 09:55:33 PDT)
Re: [AMBER] Question about DFTB3 method with dispersion correction
Pavlína Pokorná
(Mon Aug 12 2019 - 07:43:40 PDT)
[AMBER] sander engine problem
Rui Chen
(Mon Aug 12 2019 - 07:24:43 PDT)
Re: [AMBER] sander engine problem
Pratul Agarwal
(Mon Aug 12 2019 - 07:28:24 PDT)
[AMBER] atom numbering in cpptraj and pytraj
Rosellen, Martin
(Mon Aug 12 2019 - 07:38:29 PDT)
Re: [AMBER] atom numbering in cpptraj and pytraj
Hai Nguyen
(Mon Aug 12 2019 - 07:45:44 PDT)
Re: [AMBER] atom numbering in cpptraj and pytraj
Hai Nguyen
(Mon Aug 12 2019 - 07:49:09 PDT)
[AMBER] OpenMPI 4 and pmemd.cuda.MPI
Jose Christian Flores Canales
(Tue Aug 13 2019 - 04:20:31 PDT)
Re: [AMBER] OpenMPI 4 and pmemd.cuda.MPI
Jose Christian Flores Canales
(Tue Aug 13 2019 - 04:22:58 PDT)
Re: [AMBER] OpenMPI 4 and pmemd.cuda.MPI
David Case
(Tue Aug 13 2019 - 06:25:54 PDT)
[AMBER] NH-pi interaction using ff14SB forcefield
Saikat Pal
(Tue Aug 13 2019 - 04:44:50 PDT)
Re: [AMBER] NH-pi interaction using ff14SB forcefield
Carlos Simmerling
(Tue Aug 13 2019 - 06:56:35 PDT)
[AMBER] Problem for the frcmod file from the amber tutorial
辛志宏
(Tue Aug 13 2019 - 09:14:27 PDT)
Re: [AMBER] Problem for the frcmod file from the amber tutorial
David Case
(Tue Aug 20 2019 - 19:24:16 PDT)
[AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues
viktor drobot
(Tue Aug 13 2019 - 13:28:50 PDT)
Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues
David Case
(Wed Aug 14 2019 - 18:12:48 PDT)
Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues
viktor drobot
(Thu Aug 15 2019 - 07:26:49 PDT)
Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues
viktor drobot
(Fri Aug 16 2019 - 06:57:58 PDT)
Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues
David Case
(Fri Aug 16 2019 - 13:54:31 PDT)
Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues
Tyler Luchko (Lists)
(Fri Aug 16 2019 - 16:54:35 PDT)
Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues
viktor drobot
(Sat Aug 17 2019 - 03:29:38 PDT)
Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues
David Case
(Sat Aug 17 2019 - 06:03:37 PDT)
Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues
viktor drobot
(Sat Aug 17 2019 - 06:29:57 PDT)
[AMBER] Amber16 + AmberTools19
Jose Javier Muñoz Criollo
(Wed Aug 14 2019 - 08:39:27 PDT)
Re: [AMBER] Amber16 + AmberTools19
David Case
(Wed Aug 14 2019 - 18:06:57 PDT)
Re: [AMBER] Amber16 + AmberTools19
Jose Javier Muñoz Criollo
(Fri Aug 16 2019 - 05:29:05 PDT)
Re: [AMBER] Amber16 + AmberTools19
David Case
(Fri Aug 16 2019 - 13:56:44 PDT)
[AMBER] How can I calculate RDF only in a specific region of my system?
Lucas Bandeira
(Wed Aug 14 2019 - 09:57:28 PDT)
Re: [AMBER] How can I calculate RDF only in a specific region of my system?
emanuele falbo
(Wed Aug 14 2019 - 10:16:30 PDT)
[AMBER] Segmentation Fault
Parviz Seifpanahi Shabane
(Wed Aug 14 2019 - 13:53:15 PDT)
Re: [AMBER] Segmentation Fault
Bill Ross
(Wed Aug 14 2019 - 14:16:22 PDT)
Re: [AMBER] Segmentation Fault
David Case
(Wed Aug 14 2019 - 18:20:51 PDT)
Re: [AMBER] Force field for Cecl3, Lacl3 and Prcl3
Pengfei Li
(Wed Aug 14 2019 - 19:15:07 PDT)
[AMBER] probelm -- QMMM-MD with ZN（Znic atom）in QM region
东庚
(Wed Aug 14 2019 - 23:20:20 PDT)
[AMBER] probelm -- QMMM-MD with ZN（Znic atom）in QM region
东庚
(Fri Aug 16 2019 - 19:10:11 PDT)
Re: [AMBER] probelm -- QMMM-MD with ZN（Znic atom）in QM region
Pengfei Li
(Fri Aug 16 2019 - 20:12:00 PDT)
[AMBER] 答复: probelm -- QMMM-MD with ZN（Znic atom）in QM region
东庚
(Sat Aug 17 2019 - 19:20:03 PDT)
[AMBER] 答复: probelm -- QMMM-MD with ZN（Znic atom）in QM region
东庚
(Mon Aug 19 2019 - 01:51:21 PDT)
Re: [AMBER] 答复: probelm -- QMMM-MD with ZN（Znic atom）in QM region
Pengfei Li
(Tue Aug 20 2019 - 12:28:59 PDT)
Re: [AMBER] 答复: probelm -- QMMM-MD with ZN（Znic atom）in QM region
Pengfei Li
(Mon Aug 26 2019 - 14:55:58 PDT)
[AMBER] Problem Running Antechamber for GTP
Akinpelu Olayinka
(Thu Aug 15 2019 - 00:21:48 PDT)
Re: [AMBER] Problem Running Antechamber for GTP
Elvis Martis
(Thu Aug 15 2019 - 00:47:32 PDT)
Re: [AMBER] Problem Running Antechamber for GTP
Gustaf Olsson
(Thu Aug 15 2019 - 01:14:40 PDT)
[AMBER] Installing Amber parallel option
Roy Ashworth
(Thu Aug 15 2019 - 04:00:40 PDT)
Re: [AMBER] Installing Amber parallel option
Elvis Martis
(Thu Aug 15 2019 - 04:08:38 PDT)
Re: [AMBER] Installing Amber parallel option
Roy Ashworth
(Thu Aug 15 2019 - 07:45:27 PDT)
Re: [AMBER] Installing Amber parallel option
Elvis Martis
(Thu Aug 15 2019 - 07:48:44 PDT)
Re: [AMBER] Installing Amber parallel option
David Case
(Thu Aug 15 2019 - 18:05:43 PDT)
[AMBER] Lateral diffusion of lipid head groups
Maria Bzówka
(Thu Aug 15 2019 - 04:12:21 PDT)
[AMBER] mmPBSA error in Amber19 suite
jacky zhao
(Thu Aug 15 2019 - 10:10:25 PDT)
Re: [AMBER] mmPBSA error in Amber19 suite
jacky zhao
(Sat Aug 17 2019 - 04:40:29 PDT)
Re: [AMBER] mmPBSA error in Amber19 suite
David Case
(Sat Aug 17 2019 - 06:11:31 PDT)
Re: [AMBER] mmPBSA error in Amber19 suite
Lei Zhao
(Sat Aug 17 2019 - 19:55:45 PDT)
Re: [AMBER] mmPBSA error in Amber19 suite
jacky zhao
(Sat Aug 17 2019 - 22:12:33 PDT)
Re: [AMBER] problem with building cpptraj in AmberTools19
A K
(Thu Aug 15 2019 - 13:04:03 PDT)
Re: [AMBER] problem with building cpptraj in AmberTools19
Daniel Roe
(Mon Aug 19 2019 - 06:40:34 PDT)
[AMBER] WaterBox is getting distorted while running PMF
Airy Sanjeev
(Thu Aug 15 2019 - 21:17:45 PDT)
Re: [AMBER] WaterBox is getting distorted while running PMF
David Cerutti
(Fri Aug 16 2019 - 10:10:56 PDT)
Re: [AMBER] WaterBox is getting distorted while running PMF
Airy Sanjeev
(Sun Aug 18 2019 - 23:50:37 PDT)
[AMBER] Error in MMPBSA calculation
shivangi agarwal
(Fri Aug 16 2019 - 01:14:43 PDT)
Re: [AMBER] Error in MMPBSA calculation
Ray Luo
(Fri Aug 16 2019 - 02:27:20 PDT)
Re: [AMBER] Error in MMPBSA calculation
shivangi agarwal
(Fri Aug 16 2019 - 04:52:13 PDT)
Re: [AMBER] Error in MMPBSA calculation
Elvis Martis
(Fri Aug 16 2019 - 05:17:46 PDT)
Re: [AMBER] Error in MMPBSA calculation
shivangi agarwal
(Fri Aug 16 2019 - 05:40:39 PDT)
Re: [AMBER] Error in MMPBSA calculation
RAY LUO, Ph.D.
(Fri Aug 16 2019 - 13:29:34 PDT)
Re: [AMBER] Error in MMPBSA calculation
jacky zhao
(Sat Aug 17 2019 - 04:44:03 PDT)
Re: [AMBER] Error in MMPBSA calculation
rluo.uci.edu
(Sat Aug 17 2019 - 06:21:04 PDT)
Re: [AMBER] Error in MMPBSA calculation
Lei Zhao
(Sat Aug 17 2019 - 19:57:54 PDT)
Re: [AMBER] Error in MMPBSA calculation
Ray Luo
(Sun Aug 18 2019 - 07:08:27 PDT)
[AMBER] error with CPPTRAj
Mohammad Salem
(Fri Aug 16 2019 - 03:44:50 PDT)
Re: [AMBER] error with CPPTRAj
Mohammad Salem
(Fri Aug 16 2019 - 04:25:01 PDT)
[AMBER] volume in pytraj?
Shayna Hilburg
(Fri Aug 16 2019 - 14:56:12 PDT)
Re: [AMBER] volume in pytraj?
Hai Nguyen
(Fri Aug 16 2019 - 15:29:58 PDT)
Re: [AMBER] volume in pytraj?
Shayna Hilburg
(Sun Aug 18 2019 - 18:03:44 PDT)
Re: [AMBER] volume in pytraj?
Hai Nguyen
(Sun Aug 18 2019 - 21:28:43 PDT)
Re: [AMBER] volume in pytraj?
Shayna Hilburg
(Mon Aug 19 2019 - 06:51:13 PDT)
Re: [AMBER] volume in pytraj?
Hai Nguyen
(Mon Aug 19 2019 - 09:06:45 PDT)
[AMBER] Question about running MMPBSA.py with a mask to exclude certain residues
A K
(Fri Aug 16 2019 - 17:05:26 PDT)
Re: [AMBER] Question about running MMPBSA.py with a mask to exclude certain residues
A K
(Fri Aug 23 2019 - 09:22:53 PDT)
Re: [AMBER] Question about running MMPBSA.py with a mask to exclude certain residues
A K
(Fri Aug 23 2019 - 14:03:55 PDT)
Re: [AMBER] Question about running MMPBSA.py with a mask to exclude certain residues
David Case
(Fri Aug 23 2019 - 18:58:53 PDT)
Re: [AMBER] Question about running MMPBSA.py with a mask to exclude certain residues
A K
(Fri Aug 23 2019 - 20:03:32 PDT)
Re: [AMBER] Question about running MMPBSA.py with a mask to exclude certain residues
Supriyo Bhattacharya
(Fri Aug 23 2019 - 11:07:03 PDT)
[AMBER] mismatch between parm files from CHARMM-GUI and chamber
Quynh Vo
(Fri Aug 16 2019 - 17:13:52 PDT)
[AMBER] Error searching for compatible GPU in Amber18
Karim Mahnam
(Sat Aug 17 2019 - 00:47:18 PDT)
Re: [AMBER] Error searching for compatible GPU in Amber18
James Kress
(Sat Aug 17 2019 - 09:16:20 PDT)
Re: [AMBER] Error searching for compatible GPU in Amber18
Karim Mahnam
(Sun Aug 18 2019 - 19:22:38 PDT)
Re: [AMBER] Error searching for compatible GPU in Amber18
Daniel Roe
(Mon Aug 19 2019 - 05:13:12 PDT)
Re: [AMBER] Error searching for compatible GPU in Amber18
Karim Mahnam
(Mon Aug 19 2019 - 06:44:43 PDT)
Re: [AMBER] Error searching for compatible GPU in Amber18
Ross Walker
(Mon Aug 19 2019 - 19:59:54 PDT)
[AMBER] Restraint ramp
Dhananjay
(Sat Aug 17 2019 - 09:58:03 PDT)
Re: [AMBER] Restraint ramp
David Case
(Sat Aug 17 2019 - 18:16:40 PDT)
[AMBER] MMPBSA using amberTools19
shivangi agarwal
(Sun Aug 18 2019 - 00:39:28 PDT)
Re: [AMBER] MMPBSA using amberTools19
Ray Luo
(Sun Aug 18 2019 - 07:10:58 PDT)
Re: [AMBER] MMPBSA using amberTools19
Hai Nguyen
(Sun Aug 18 2019 - 08:27:14 PDT)
[AMBER] Amber installation error
Vivek Junghare
(Mon Aug 19 2019 - 00:57:09 PDT)
Re: [AMBER] Amber installation error
Daniel Roe
(Mon Aug 19 2019 - 05:35:33 PDT)
[AMBER] Graphene residue name Tleap
Nora Kremer
(Mon Aug 19 2019 - 01:03:12 PDT)
Re: [AMBER] Graphene residue name Tleap
Matias Machado
(Fri Aug 23 2019 - 10:57:33 PDT)
[AMBER] Regarding restarting from RST files using pmemd.cuda
Midhun K Madhu
(Mon Aug 19 2019 - 03:53:03 PDT)
Re: [AMBER] Regarding restarting from RST files using pmemd.cuda
Daniel Roe
(Mon Aug 19 2019 - 05:22:51 PDT)
Re: [AMBER] Regarding restarting from RST files using pmemd.cuda
Akinpelu Olayinka
(Mon Aug 19 2019 - 06:39:03 PDT)
Re: [AMBER] Regarding restarting from RST files using pmemd.cuda
David Cerutti
(Mon Aug 19 2019 - 09:55:18 PDT)
[AMBER] AccelleratedMD production
Giulia Paiardi
(Mon Aug 19 2019 - 04:01:36 PDT)
Re: [AMBER] AccelleratedMD production
Jacopo Sgrignani
(Mon Aug 19 2019 - 04:06:50 PDT)
Re: [AMBER] AccelleratedMD production
Giulia Paiardi
(Mon Aug 19 2019 - 05:55:03 PDT)
Re: [AMBER] AccelleratedMD production
David Cerutti
(Mon Aug 19 2019 - 09:59:37 PDT)
Re: [AMBER] AccelleratedMD production
Elvis Martis
(Mon Aug 19 2019 - 10:15:09 PDT)
[AMBER] CHARMM forcefield
Hira Jabeen
(Mon Aug 19 2019 - 06:59:31 PDT)
Re: [AMBER] CHARMM forcefield
David Case
(Tue Aug 20 2019 - 19:20:00 PDT)
[AMBER] How does PMEMD handle duplicates in GROUP?
Quynh N. Vo
(Mon Aug 19 2019 - 12:04:01 PDT)
Re: [AMBER] How does PMEMD handle duplicates in GROUP?
David Case
(Tue Aug 20 2019 - 19:17:02 PDT)
[AMBER] Could not import Amber Python modules! error during parallel test of Amber18
Sunita Patel
(Mon Aug 19 2019 - 22:41:59 PDT)
Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18
Bill Ross
(Mon Aug 19 2019 - 22:49:40 PDT)
Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18
Sunita Patel
(Mon Aug 19 2019 - 22:54:23 PDT)
Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18
David A Case
(Tue Aug 20 2019 - 05:21:19 PDT)
Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18
Sunita Patel
(Tue Aug 20 2019 - 22:26:41 PDT)
Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18
Sunita Patel
(Tue Aug 20 2019 - 22:41:08 PDT)
Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18
Hai Nguyen
(Tue Aug 20 2019 - 23:10:51 PDT)
Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18
Sunita Patel
(Wed Aug 21 2019 - 01:20:21 PDT)
Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18
Sunita Patel
(Wed Aug 21 2019 - 04:52:06 PDT)
Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18
Hai Nguyen
(Wed Aug 21 2019 - 05:33:39 PDT)
[AMBER] Amberff99sb topology for phosphorylated tyrosine residue in GROMACS
Seketoulie Keretsu
(Tue Aug 20 2019 - 02:22:09 PDT)
Re: [AMBER] Amberff99sb topology for phosphorylated tyrosine residue in GROMACS
David A Case
(Tue Aug 20 2019 - 05:24:42 PDT)
[AMBER] Not able to load Amber trajectories in VMD
shivangi agarwal
(Tue Aug 20 2019 - 09:50:35 PDT)
Re: [AMBER] Not able to load Amber trajectories in VMD
Daniel Roe
(Tue Aug 20 2019 - 10:15:20 PDT)
[AMBER] vlimit exceeded for step
Sadaf Rani
(Tue Aug 20 2019 - 15:54:12 PDT)
Re: [AMBER] vlimit exceeded for step
David Case
(Tue Aug 20 2019 - 19:12:58 PDT)
Re: [AMBER] vlimit exceeded for step
Sadaf Rani
(Wed Aug 21 2019 - 02:02:36 PDT)
Re: [AMBER] MMPBSA.py code Error: unknown keyword or invalid value: --closureorder
David Case
(Tue Aug 20 2019 - 19:30:46 PDT)
[AMBER] PDB file carbohydrates naming problem
Rui Chen
(Tue Aug 20 2019 - 20:43:45 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Rui Chen
(Tue Aug 20 2019 - 20:49:26 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Lachele Foley
(Tue Aug 20 2019 - 21:07:18 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Rui Chen
(Tue Aug 20 2019 - 21:32:14 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Lachele Foley
(Tue Aug 20 2019 - 22:32:14 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Rui Chen
(Wed Aug 21 2019 - 16:02:22 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Lachele Foley
(Wed Aug 21 2019 - 18:35:32 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Rui Chen
(Wed Aug 21 2019 - 19:17:53 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Lachele Foley
(Thu Aug 22 2019 - 07:24:07 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Rui Chen
(Thu Aug 22 2019 - 08:45:11 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Rui Chen
(Thu Aug 22 2019 - 19:21:03 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Lachele Foley
(Fri Aug 23 2019 - 05:59:04 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Rui Chen
(Fri Aug 23 2019 - 21:44:51 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Rui Chen
(Fri Aug 23 2019 - 21:53:24 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Lachele Foley
(Mon Aug 26 2019 - 11:30:22 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Rui Chen
(Mon Aug 26 2019 - 12:23:20 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Rui Chen
(Fri Aug 30 2019 - 14:37:52 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Lachele Foley
(Sat Aug 31 2019 - 02:51:35 PDT)
Re: [AMBER] PDB file carbohydrates naming problem
Rui Chen
(Sat Aug 31 2019 - 09:59:27 PDT)
[AMBER] Preparation of trajectory for stfc diffusion calculations
Maria Bzówka
(Wed Aug 21 2019 - 06:37:34 PDT)
Re: [AMBER] R . E. D
Lachele Foley
(Wed Aug 21 2019 - 12:34:09 PDT)
Re: [AMBER] Non-integer charge problem with tleap using GLYCAM_06EPb but not GLYCAM_06j-1
Lachele Foley
(Wed Aug 21 2019 - 12:36:10 PDT)
Re: [AMBER] Glycan naming problem
Lachele Foley
(Wed Aug 21 2019 - 12:40:17 PDT)
Re: [AMBER] Glycan naming problem
Rui Chen
(Wed Aug 21 2019 - 12:51:37 PDT)
Re: [AMBER] Glycan naming problem
Lachele Foley
(Wed Aug 21 2019 - 12:53:42 PDT)
[AMBER] Did I miss anyone? Sorry I was gone so long
Lachele Foley
(Wed Aug 21 2019 - 12:44:58 PDT)
[AMBER] Regarding heating equilibration
Midhun K Madhu
(Wed Aug 21 2019 - 16:11:09 PDT)
Re: [AMBER] Regarding heating equilibration
David A Case
(Thu Aug 22 2019 - 06:31:00 PDT)
[AMBER] CHARMM 3 extra energy terms in AMBER dynamic engines (SANDER&PMEMD)
Lod King
(Wed Aug 21 2019 - 20:52:39 PDT)
Re: [AMBER] CHARMM 3 extra energy terms in AMBER dynamic engines (SANDER&PMEMD)
David A Case
(Thu Aug 22 2019 - 06:35:19 PDT)
Re: [AMBER] CHARMM 3 extra energy terms in AMBER dynamic engines (SANDER&PMEMD)
Lod King
(Thu Aug 22 2019 - 08:14:46 PDT)
[AMBER] mdgx, improper terms and multifit
viktor drobot
(Thu Aug 22 2019 - 10:23:06 PDT)
Re: [AMBER] mdgx, improper terms and multifit
David Cerutti
(Thu Aug 22 2019 - 10:45:22 PDT)
[AMBER] Error in running simulation in HPC using AMBER-18
Deepika Sardana
(Thu Aug 22 2019 - 21:48:23 PDT)
Re: [AMBER] Error in running simulation in HPC using AMBER-18
Elvis Martis
(Thu Aug 22 2019 - 23:07:48 PDT)
[AMBER] Glycolipid Simulation
Rajarshi Roy
(Fri Aug 23 2019 - 05:07:40 PDT)
Re: [AMBER] Glycolipid Simulation
Lachele Foley
(Sat Aug 24 2019 - 13:17:52 PDT)
Re: [AMBER] Glycolipid Simulation
Horn, Anselm
(Tue Aug 27 2019 - 00:28:31 PDT)
Re: [AMBER] Glycolipid Simulation
Rajarshi Roy
(Tue Aug 27 2019 - 04:27:46 PDT)
[AMBER] PIMD is not compatible with the MC Barostat
jinfeng liu
(Fri Aug 23 2019 - 17:29:19 PDT)
Re: [AMBER] PIMD is not compatible with the MC Barostat
David Case
(Fri Aug 23 2019 - 19:07:28 PDT)
[AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true?
Erdem Yeler
(Sat Aug 24 2019 - 04:18:49 PDT)
Re: [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true?
Bill Ross
(Sat Aug 24 2019 - 04:44:18 PDT)
Re: [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true?
Bill Ross
(Sat Aug 24 2019 - 04:57:15 PDT)
Re: [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true?
Erdem Yeler
(Tue Aug 27 2019 - 14:32:59 PDT)
Re: [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true?
Bill Ross
(Tue Aug 27 2019 - 16:06:55 PDT)
Re: [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true?
Erdem Yeler
(Thu Aug 29 2019 - 13:42:26 PDT)
[AMBER] MAWS_Amber/antechamber assistance
Bruno Cramer
(Sun Aug 25 2019 - 13:06:23 PDT)
Re: [AMBER] MAWS_Amber/antechamber assistance
Gerald Monard
(Mon Aug 26 2019 - 06:49:18 PDT)
[AMBER] Regarding setting up FEP calculations in AMBER18
Debarati DasGupta
(Mon Aug 26 2019 - 11:59:52 PDT)
[AMBER] Error "forrtl: severe (174) : SIGSEGV, segmentation fault" while running MD simulation production run
Leena Aggarwal
(Tue Aug 27 2019 - 07:02:15 PDT)
Re: [AMBER] Error "forrtl: severe (174) : SIGSEGV, segmentation fault" while running MD simulation production run
Andrew Sugarman
(Tue Aug 27 2019 - 08:13:16 PDT)
Re: [AMBER] Error "forrtl: severe (174) : SIGSEGV, segmentation fault" while running MD simulation production run
Leena Aggarwal
(Wed Aug 28 2019 - 00:31:31 PDT)
Re: [AMBER] Error "forrtl: severe (174) : SIGSEGV, segmentation fault" while running MD simulation production run
Horn, Anselm
(Wed Aug 28 2019 - 01:56:06 PDT)
Re: [AMBER] Error "forrtl: severe (174) : SIGSEGV, segmentation fault" while running MD simulation production run
Leena Aggarwal
(Wed Aug 28 2019 - 04:49:01 PDT)
[AMBER] Combining sevaral frcmods into single file
viktor drobot
(Tue Aug 27 2019 - 07:16:13 PDT)
Re: [AMBER] Combining sevaral frcmods into single file
Matias Machado
(Tue Aug 27 2019 - 08:20:28 PDT)
Re: [AMBER] Combining sevaral frcmods into single file
viktor drobot
(Tue Aug 27 2019 - 08:31:58 PDT)
[AMBER] Fwd: evec.pev file in essential dynamics analysis
Shirin Jamshidi
(Tue Aug 27 2019 - 08:39:24 PDT)
Re: [AMBER] Fwd: evec.pev file in essential dynamics analysis
Daniel Roe
(Tue Aug 27 2019 - 10:29:50 PDT)
Re: [AMBER] evec.pev file in essential dynamics analysis
Shirin Jamshidi
(Thu Aug 29 2019 - 03:24:49 PDT)
Re: [AMBER] evec.pev file in essential dynamics analysis
Shirin Jamshidi
(Thu Aug 29 2019 - 08:14:44 PDT)
[AMBER] building amber 16 parallel with MPI
Sadaf Rani
(Tue Aug 27 2019 - 09:57:42 PDT)
Re: [AMBER] building amber 16 parallel with MPI
Gustaf Olsson
(Tue Aug 27 2019 - 22:43:39 PDT)
[AMBER] MAWS/Amber and python program adjustment
Bruno Cramer
(Tue Aug 27 2019 - 15:53:53 PDT)
[AMBER] Calculation of ΔG from PMF
Airy Sanjeev
(Tue Aug 27 2019 - 21:41:06 PDT)
Re: [AMBER] Calculation of ΔG from PMF
Carlos Simmerling
(Wed Aug 28 2019 - 08:19:14 PDT)
Re: [AMBER] Calculation of ΔG from PMF
David A Case
(Wed Aug 28 2019 - 08:35:29 PDT)
[AMBER] MMPBS.py error: IOError: [Errno 2] No such file or directory
maryam azimzadehirani
(Wed Aug 28 2019 - 00:48:45 PDT)
[AMBER] nmropt problems
Andrea H. Kasun
(Wed Aug 28 2019 - 06:50:38 PDT)
Re: [AMBER] nmropt problems
David A Case
(Wed Aug 28 2019 - 08:15:12 PDT)
Re: [AMBER] nmropt problems
Andrea H. Kasun
(Thu Aug 29 2019 - 09:02:06 PDT)
[AMBER] using accelerated MD on membrane proteins?
Homeo Morphism
(Wed Aug 28 2019 - 09:09:15 PDT)
Re: [AMBER] using accelerated MD on membrane proteins?
Robin Betz
(Wed Aug 28 2019 - 10:39:36 PDT)
[AMBER] question about bond command in tleap
Rui Chen
(Wed Aug 28 2019 - 13:47:11 PDT)
Re: [AMBER] question about bond command in tleap
Matias Machado
(Wed Aug 28 2019 - 14:33:44 PDT)
[AMBER] per residue decompose energy error
Nisha Amarnath Jonniya
(Thu Aug 29 2019 - 02:07:09 PDT)
[AMBER] periodic box size
Rui Chen
(Thu Aug 29 2019 - 17:58:54 PDT)
Re: [AMBER] periodic box size
David A Case
(Fri Aug 30 2019 - 04:30:27 PDT)
Re: [AMBER] periodic box size
Rui Chen
(Fri Aug 30 2019 - 08:42:13 PDT)
[AMBER] Small molecule break after minimization
Amen Shamim
(Fri Aug 30 2019 - 06:16:46 PDT)
[AMBER] equilirbration at constant volume
Sadaf Rani
(Fri Aug 30 2019 - 07:48:24 PDT)
Re: [AMBER] equilirbration at constant volume
David A Case
(Fri Aug 30 2019 - 09:30:19 PDT)
[AMBER] Constant PH simulations for non-proteins and nonstandard residues
Kolattukudy P. Santo
(Fri Aug 30 2019 - 09:00:26 PDT)
Re: [AMBER] Constant PH simulations for non-proteins and nonstandard residues
Cruzeiro,Vinicius Wilian D
(Fri Aug 30 2019 - 11:03:56 PDT)
[AMBER] Print non bonded pair list
Song, Lin
(Fri Aug 30 2019 - 09:39:54 PDT)
Re: [AMBER] Print non bonded pair list
David Cerutti
(Fri Aug 30 2019 - 09:59:34 PDT)
[AMBER] Bug in ambpdb in anaconda distribution?
Nathan Guerin
(Fri Aug 30 2019 - 10:27:17 PDT)
Re: [AMBER] Bug in ambpdb in anaconda distribution?
viktor drobot
(Fri Aug 30 2019 - 10:36:38 PDT)
Re: [AMBER] Bug in ambpdb in anaconda distribution?
Nathan Guerin
(Fri Aug 30 2019 - 10:42:22 PDT)
Re: [AMBER] Bug in ambpdb in anaconda distribution?
Nathan Guerin
(Fri Aug 30 2019 - 10:58:25 PDT)
Re: [AMBER] Bug in ambpdb in anaconda distribution?
viktor drobot
(Fri Aug 30 2019 - 11:13:29 PDT)
[AMBER] H - bond calculations
shivangi agarwal
(Fri Aug 30 2019 - 10:20:31 PDT)
Last message date
:
Sat Aug 31 2019 - 10:30:02 PDT
Archived on
: Fri Nov 15 2024 - 05:55:55 PST
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