Amber Archive Mar 2019: by subject

[AMBER] 1/2 term in dihdral
- David A Case (Thu Mar 07 2019 - 08:54:17 PST)
- Mayank Dixit (Fri Mar 01 2019 - 14:27:36 PST)
[AMBER] [error] The system has extended beyond the extent of the virtual box
- David A Case (Tue Mar 05 2019 - 06:35:42 PST)
- Bill Ross (Sun Mar 03 2019 - 03:18:30 PST)
- Xiaocong Wang (Sun Mar 03 2019 - 02:17:15 PST)
- Bill Ross (Sun Mar 03 2019 - 01:20:06 PST)
- Xiaocong Wang (Sun Mar 03 2019 - 00:37:41 PST)
[AMBER] [MGMS-DS]: Molecular Modelling Workshop + Tim Clark Birthday Symposium: April 08-11, 2019 in Erlangen, Germany
- Dr. Anselm Horn (Thu Mar 14 2019 - 02:24:46 PDT)
[AMBER] A confused question about calculate the binding free energy from MMPBSA.py
- Ray Luo (Fri Mar 29 2019 - 07:38:02 PDT)
- bjyx20090941 (Thu Mar 28 2019 - 05:29:53 PDT)
- bjyx20090941 (Sun Mar 17 2019 - 18:13:28 PDT)
[AMBER] AMBER 18 error in QM region of QMMM
- Abhilash J (Tue Mar 26 2019 - 23:02:49 PDT)
- Abhilash J (Tue Mar 26 2019 - 19:21:31 PDT)
- Goetz, Andreas (Tue Mar 26 2019 - 14:49:26 PDT)
- Abhilash J (Tue Mar 26 2019 - 06:33:03 PDT)
- Bill Ross (Tue Mar 26 2019 - 03:39:46 PDT)
- Szymon Żaczek (Tue Mar 26 2019 - 02:45:10 PDT)
- Abhilash J (Tue Mar 26 2019 - 02:27:05 PDT)
[AMBER] Amber Installation
- David A Case (Tue Mar 19 2019 - 06:50:10 PDT)
[AMBER] Amber18 pmemd TI
- Hosein Geraili Daronkola (Tue Mar 05 2019 - 06:12:43 PST)
[AMBER] Amber18 STSM
- Feng Pan (Sun Mar 17 2019 - 21:48:00 PDT)
- 李耀 (Sat Mar 16 2019 - 06:38:45 PDT)
[AMBER] Amber18: Adaptively Biased MD (Metadynalmics)
- Feng Pan (Sun Mar 24 2019 - 20:37:50 PDT)
- 李耀 (Thu Mar 21 2019 - 08:49:56 PDT)
[AMBER] Amber18: cv_min and cv_max for periodic cv in ABMD
- 李耀 (Wed Mar 20 2019 - 09:25:26 PDT)
[AMBER] antechamber bcc error
- Michael Shokhen (Tue Mar 12 2019 - 06:16:19 PDT)
- David A Case (Mon Mar 11 2019 - 07:36:40 PDT)
- Michael Shokhen (Mon Mar 11 2019 - 04:09:32 PDT)
[AMBER] Assigning protonation states manually to the amino vs CpH MD simulation
- Carlos Simmerling (Mon Mar 18 2019 - 07:05:15 PDT)
- Bharat Manna (Mon Mar 18 2019 - 11:50:23 PDT)
[AMBER] Atom type of Calcium
- Pengfei Li (Sat Mar 02 2019 - 19:14:17 PST)
- Sunita Patel (Fri Mar 01 2019 - 23:26:23 PST)
- Daniel Roe (Fri Mar 01 2019 - 07:10:01 PST)
[AMBER] Building pmemd.cuda.MPI error in amber18
- David Case (Fri Mar 29 2019 - 04:15:39 PDT)
- Meng Wu (Fri Mar 29 2019 - 01:13:48 PDT)
- Meng Wu (Thu Mar 28 2019 - 04:11:23 PDT)
[AMBER] calculate RDF using COM
- Daniel Roe (Mon Mar 11 2019 - 11:12:25 PDT)
- Saikat Pal (Thu Mar 07 2019 - 22:57:51 PST)
[AMBER] CEMD protcnt meaning
- Feng, Zimin (Thu Mar 21 2019 - 10:18:48 PDT)
- Cruzeiro,Vinicius Wilian D (Thu Mar 21 2019 - 09:41:42 PDT)
- Feng, Zimin (Thu Mar 21 2019 - 09:31:40 PDT)
[AMBER] charged residue mutation free energy
- Hosein Geraili Daronkola (Fri Mar 15 2019 - 06:32:43 PDT)
[AMBER] chi1 angle of amino acids not having a CG atom
- Daniel Roe (Mon Mar 11 2019 - 12:07:20 PDT)
- Rosellen, Martin (Wed Mar 06 2019 - 09:21:34 PST)
[AMBER] Chirality Restraint on a Part of Replica
- Ikuo KURISAKI (Wed Mar 06 2019 - 22:19:51 PST)
[AMBER] Closest command in cpptraj for non aqeous solvents
- Daniel Roe (Tue Mar 26 2019 - 08:32:06 PDT)
- Debarati DasGupta (Fri Mar 22 2019 - 13:40:58 PDT)
- Debarati DasGupta (Fri Mar 22 2019 - 13:09:10 PDT)
- Daniel Roe (Fri Mar 22 2019 - 12:32:04 PDT)
- Debarati DasGupta (Fri Mar 22 2019 - 12:23:32 PDT)
[AMBER] Converting Charmm forcefileld to Amber
- Jason Swails (Tue Mar 05 2019 - 15:02:19 PST)
- Daniel Roe (Tue Mar 05 2019 - 06:21:29 PST)
- Hadi Rahmaninejad (Mon Mar 04 2019 - 12:43:49 PST)
- Daniel Roe (Mon Mar 04 2019 - 11:36:03 PST)
- Hadi Rahmaninejad (Mon Mar 04 2019 - 09:23:26 PST)
[AMBER] CPPTRAJ grid unknown command
- Daniel Roe (Mon Mar 11 2019 - 12:17:28 PDT)
- Debarati DasGupta (Fri Mar 01 2019 - 09:41:16 PST)
- Debarati DasGupta (Fri Mar 01 2019 - 09:23:50 PST)
- Debarati DasGupta (Fri Mar 01 2019 - 09:17:44 PST)
- Daniel Roe (Fri Mar 01 2019 - 07:08:17 PST)
[AMBER] CPPTRAJ Grid with COM
- Daniel Roe (Wed Mar 13 2019 - 10:03:09 PDT)
- Kung, Ryan (Wed Mar 13 2019 - 09:57:16 PDT)
- Daniel Roe (Wed Mar 13 2019 - 09:08:55 PDT)
- Kung, Ryan (Wed Mar 13 2019 - 09:03:55 PDT)
[AMBER] CPPTRAJ SPAM error while executing the input file
- Daniel Roe (Tue Mar 05 2019 - 09:09:44 PST)
- Daniel Roe (Tue Mar 05 2019 - 05:41:17 PST)
- Daniel Roe (Mon Mar 04 2019 - 11:31:25 PST)
- Debarati DasGupta (Mon Mar 04 2019 - 09:14:52 PST)
[AMBER] CUDA COM distance restraint (v18 with patch.7 applied)
- Charles Lin (Mon Mar 11 2019 - 08:05:29 PDT)
- Pratul Agarwal (Sun Mar 10 2019 - 16:19:06 PDT)
- Kellon Belfon (Sun Mar 10 2019 - 13:44:31 PDT)
- Pratul Agarwal (Sun Mar 10 2019 - 13:38:51 PDT)
- Stephan Schott (Sun Mar 10 2019 - 12:10:57 PDT)
- Pratul Agarwal (Sun Mar 10 2019 - 11:48:33 PDT)
[AMBER] cuda test failing after installation
- Ravi Abrol (Sun Mar 24 2019 - 22:35:49 PDT)
- David Case (Sun Mar 24 2019 - 05:35:00 PDT)
- Ravi Abrol (Wed Mar 20 2019 - 10:09:32 PDT)
[AMBER] Design of graphene quantum dots
- pavel.banas.upol.cz (Wed Mar 27 2019 - 01:35:55 PDT)
- RITUPARNA ROY (Tue Mar 26 2019 - 20:50:50 PDT)
[AMBER] DFTB3/MM simulations of CCCC zinc finger
- Pengfei Li (Thu Mar 28 2019 - 09:09:44 PDT)
- Dreab, Ana (Thu Mar 28 2019 - 08:27:33 PDT)
- Pengfei Li (Sat Mar 23 2019 - 12:35:59 PDT)
- Dreab, Ana (Thu Mar 21 2019 - 09:18:35 PDT)
[AMBER] Directly Set Restraint for Chilarity to Prmtop File
- David Case (Wed Mar 13 2019 - 08:39:54 PDT)
- Ikuo KURISAKI (Tue Mar 12 2019 - 18:16:01 PDT)
[AMBER] distance restraint
- Sunita Patel (Thu Mar 07 2019 - 20:12:15 PST)
- Sundar (Thu Mar 07 2019 - 06:29:09 PST)
- Sunita Patel (Wed Mar 06 2019 - 19:58:55 PST)
- Sundar (Wed Mar 06 2019 - 07:57:38 PST)
- Sunita Patel (Sat Mar 02 2019 - 04:00:15 PST)
[AMBER] Doubt regarding input files in NMR refinement
- Christina Bergonzo (Fri Mar 01 2019 - 06:51:30 PST)
- RITUPARNA ROY (Fri Mar 01 2019 - 06:34:13 PST)
[AMBER] DSSP residue vs time graph
- Myriam Hanna (Thu Mar 14 2019 - 06:44:14 PDT)
- Daniel Roe (Thu Mar 14 2019 - 05:20:47 PDT)
- Myriam Hanna (Wed Mar 13 2019 - 09:54:12 PDT)
- Premila Samuel Mohan Dass (Wed Mar 13 2019 - 09:18:21 PDT)
- Myriam Hanna (Wed Mar 13 2019 - 08:30:27 PDT)
[AMBER] Error in `sander': malloc(): smallbin double linked list corrupted:
- Margarita I. Bernal-Uruchurtu (Tue Mar 26 2019 - 14:53:00 PDT)
[AMBER] Error in Minimization
- Zhonghua Xia (Fri Mar 15 2019 - 09:48:21 PDT)
- Zhonghua Xia (Fri Mar 15 2019 - 08:37:48 PDT)
- David A Case (Fri Mar 08 2019 - 06:13:54 PST)
- Bill Ross (Fri Mar 08 2019 - 02:21:21 PST)
- Zhonghua Xia (Fri Mar 08 2019 - 01:18:57 PST)
[AMBER] Error in REMD with pmemd.cuda.MPI
- Ikuo KURISAKI (Wed Mar 06 2019 - 22:05:10 PST)
- Cruzeiro,Vinicius Wilian D (Wed Mar 06 2019 - 06:58:25 PST)
- Ikuo KURISAKI (Wed Mar 06 2019 - 00:24:07 PST)
[AMBER] FEW amber- LIE analysis
- Sowmya Indrakumar (Wed Mar 27 2019 - 03:36:06 PDT)
- Sowmya Indrakumar (Thu Mar 21 2019 - 06:38:37 PDT)
[AMBER] gaff2 parameters of c3-c3-os-c3
- Träg, Johannes (Mon Mar 18 2019 - 03:41:46 PDT)
- David Case (Fri Mar 15 2019 - 12:20:19 PDT)
- Träg, Johannes (Fri Mar 15 2019 - 08:21:05 PDT)
[AMBER] Gpu illegal memory code accessed
- David A Case (Thu Mar 21 2019 - 11:38:16 PDT)
- Debarati DasGupta (Thu Mar 21 2019 - 07:03:35 PDT)
- Brian Radak (Wed Mar 20 2019 - 07:53:17 PDT)
- Debarati DasGupta (Wed Mar 20 2019 - 07:39:25 PDT)
[AMBER] Help regarding protein DNA MD in AMBER
- David A Case (Thu Mar 07 2019 - 06:09:15 PST)
- Vikram Dalal (Thu Mar 07 2019 - 03:25:19 PST)
[AMBER] Homodimerization of IRF3 protein
- Debarati DasGupta (Sat Mar 16 2019 - 14:38:05 PDT)
[AMBER] How can I generate of force field parameter for nano-material?
- xmgign.126.com (Sun Mar 03 2019 - 22:00:57 PST)
[AMBER] How the instantaneous temperature is calculated in Amber ?
- Bill Ross (Sun Mar 31 2019 - 21:51:19 PDT)
- Bill Ross (Sun Mar 31 2019 - 17:57:02 PDT)
[AMBER] how to get unbiased trajectories from biased trajectories
- Mayank Dixit (Wed Mar 27 2019 - 07:33:36 PDT)
[AMBER] how to make sure .prmtop is the same for NEB calculation when using explicit solvent?
- Ghoreishi, Delaram (Sun Mar 03 2019 - 23:11:02 PST)
- 郭昱 (Sun Mar 03 2019 - 19:06:08 PST)
[AMBER] huge reference.frc in MMPBSA
- Ray Luo (Sun Mar 31 2019 - 13:51:03 PDT)
- Antoine MARION (Sun Mar 31 2019 - 10:44:56 PDT)
[AMBER] Hyaluronic acid using Glycam06
- Casalini Tommaso (Wed Mar 20 2019 - 04:00:26 PDT)
- monia kam (Tue Mar 19 2019 - 08:15:18 PDT)
[AMBER] improper dihedral
- David Case (Thu Mar 07 2019 - 06:17:07 PST)
- Mayank Dixit (Tue Mar 05 2019 - 08:59:58 PST)
[AMBER] Incorrect electric field
- Bill Ross (Mon Mar 25 2019 - 12:18:47 PDT)
- Charles Lin (Mon Mar 25 2019 - 08:28:12 PDT)
- Bill Ross (Fri Mar 22 2019 - 00:40:31 PDT)
- Ashutosh Mishra (Thu Mar 21 2019 - 23:48:05 PDT)
- Bill Ross (Thu Mar 21 2019 - 23:45:34 PDT)
- Ashutosh Mishra (Thu Mar 21 2019 - 23:43:27 PDT)
- Bill Ross (Thu Mar 21 2019 - 23:40:21 PDT)
- Ashutosh Mishra (Thu Mar 21 2019 - 23:26:14 PDT)
[AMBER] Input Reservoir REMD
- koushik kasavajhala (Tue Mar 19 2019 - 02:47:31 PDT)
- Raimon Fabregat (Tue Mar 19 2019 - 01:17:13 PDT)
[AMBER] Installation error AmberTools18 - [test.rism1d] Error
- Daniel Roe (Thu Mar 21 2019 - 07:50:03 PDT)
- David A Case (Wed Mar 20 2019 - 13:25:08 PDT)
- Mariana Simões Ferreira (Wed Mar 20 2019 - 10:02:37 PDT)
[AMBER] Installation of AmberTools18 in macOS Mojave
- Gustaf Olsson (Fri Mar 29 2019 - 08:15:17 PDT)
- Daniel Roe (Fri Mar 29 2019 - 07:41:49 PDT)
- Gustaf Olsson (Fri Mar 29 2019 - 07:22:10 PDT)
- Reza Esmaeeli (Thu Mar 28 2019 - 08:21:37 PDT)
- Gustaf Olsson (Thu Mar 28 2019 - 08:18:33 PDT)
- Gustaf Olsson (Thu Mar 28 2019 - 07:58:26 PDT)
- Reza Esmaeeli (Thu Mar 28 2019 - 07:15:01 PDT)
- Gustaf Olsson (Thu Mar 28 2019 - 07:08:46 PDT)
- Gustaf Olsson (Thu Mar 28 2019 - 04:32:42 PDT)
- Reza Esmaeeli (Wed Mar 27 2019 - 23:59:26 PDT)
- Gustaf Olsson (Wed Mar 27 2019 - 23:41:42 PDT)
- David Case (Wed Mar 27 2019 - 19:02:52 PDT)
- Reza Esmaeeli (Wed Mar 27 2019 - 11:48:21 PDT)
[AMBER] Installation Problem
- Bill Ross (Mon Mar 18 2019 - 05:18:51 PDT)
- Gerardo Zerbetto De Palma (Mon Mar 18 2019 - 05:08:11 PDT)
- Bill Ross (Mon Mar 18 2019 - 05:00:04 PDT)
[AMBER] Installation problem AMBER16
- David A Case (Tue Mar 19 2019 - 06:51:50 PDT)
[AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid?
- Cruzeiro,Vinicius Wilian D (Fri Mar 01 2019 - 14:38:17 PST)
- Feng, Zimin (Fri Mar 01 2019 - 12:35:23 PST)
- Feng, Zimin (Fri Mar 01 2019 - 12:32:39 PST)
- Feng, Zimin (Fri Mar 01 2019 - 12:28:39 PST)
- Cruzeiro,Vinicius Wilian D (Fri Mar 01 2019 - 12:00:31 PST)
- Feng, Zimin (Fri Mar 01 2019 - 07:47:20 PST)
[AMBER] Jar pulling
- Gerardo Zerbetto De Palma (Fri Mar 15 2019 - 05:00:28 PDT)
- Stephan Schott (Fri Mar 15 2019 - 07:15:17 PDT)
- Pratul Agarwal (Wed Mar 13 2019 - 13:46:49 PDT)
- Gerardo Zerbetto De Palma (Wed Mar 13 2019 - 10:21:47 PDT)
[AMBER] Job position
- David Case (Sat Mar 30 2019 - 13:30:02 PDT)
- Ganesh Kamath (Thu Mar 28 2019 - 18:31:02 PDT)
[AMBER] Job terminated during TI calculation in pmemd.cuda
- 강무석 (Wed Mar 13 2019 - 01:13:42 PDT)
[AMBER] Ligand autoimaging issue Amber18
- David A Case (Fri Mar 01 2019 - 05:41:03 PST)
[AMBER] locating the single probe out of 80000 snapshots
- Debarati DasGupta (Wed Mar 27 2019 - 07:02:18 PDT)
- Daniel Roe (Wed Mar 27 2019 - 06:42:56 PDT)
- Debarati DasGupta (Wed Mar 27 2019 - 06:24:59 PDT)
- Daniel Roe (Wed Mar 27 2019 - 06:23:30 PDT)
- Debarati DasGupta (Wed Mar 27 2019 - 06:12:45 PDT)
- Daniel Roe (Tue Mar 26 2019 - 17:36:02 PDT)
- Debarati DasGupta (Tue Mar 26 2019 - 14:05:36 PDT)
- Daniel Roe (Tue Mar 26 2019 - 12:12:30 PDT)
- Debarati DasGupta (Mon Mar 25 2019 - 07:58:20 PDT)
[AMBER] Message-ID: <20190301134103.u232i6wjibdt4cav@godel.rutgers.edu>
- Daniel Roe (Mon Mar 04 2019 - 12:00:06 PST)
- zaid kamal (Mon Mar 04 2019 - 00:37:49 PST)
[AMBER] metal parameters
- Marcelo Andrade Chagas (Sat Mar 16 2019 - 08:49:45 PDT)
- Pengfei Li (Sat Mar 16 2019 - 08:19:13 PDT)
- Fabian Glaser (Tue Mar 12 2019 - 07:00:06 PDT)
[AMBER] Metal parameters method
- Fabian Glaser (Tue Mar 12 2019 - 09:09:27 PDT)
[AMBER] metal-oxide-metal interactions
- Arun Srikanth (Tue Mar 26 2019 - 15:34:21 PDT)
[AMBER] MM/PBSA topfile question
- David A Case (Tue Mar 05 2019 - 06:38:01 PST)
- Manyi Yang (Sun Mar 03 2019 - 17:35:51 PST)
[AMBER] MMPBSA
- Prabir Khatua (Sat Mar 30 2019 - 16:12:36 PDT)
- Wesley Michael Botello-Smith (Sat Mar 30 2019 - 12:58:42 PDT)
- Wesley Michael Botello-Smith (Sat Mar 30 2019 - 12:43:38 PDT)
- Prabir Khatua (Sat Mar 30 2019 - 09:39:40 PDT)
- Abhilash J (Sat Mar 30 2019 - 01:42:49 PDT)
- Prabir Khatua (Fri Mar 29 2019 - 22:46:23 PDT)
- Elvis Martis (Fri Mar 29 2019 - 21:38:19 PDT)
- Prabir Khatua (Fri Mar 29 2019 - 14:14:33 PDT)
[AMBER] MMPBSA.py Calculation error
- Rinsha Chk (Fri Mar 08 2019 - 06:21:05 PST)
- David A Case (Fri Mar 08 2019 - 06:06:45 PST)
- Rinsha Chk (Thu Mar 07 2019 - 21:52:40 PST)
[AMBER] MMPBSA.py.MPI error
- Prabir Khatua (Thu Mar 14 2019 - 15:24:21 PDT)
[AMBER] Nastruct vs 3DNA
- Daniel Roe (Mon Mar 18 2019 - 12:33:47 PDT)
- Jason Imamoto (Mon Mar 18 2019 - 12:14:24 PDT)
- Daniel Roe (Mon Mar 18 2019 - 10:37:04 PDT)
- Jason Imamoto (Mon Mar 18 2019 - 10:12:37 PDT)
[AMBER] Nastruct vs 3DNA: Files used for analysis and the output
- Daniel Roe (Wed Mar 20 2019 - 12:23:59 PDT)
- Jason Imamoto (Wed Mar 20 2019 - 11:00:51 PDT)
[AMBER] nativecontacs in ccptraj
- Daniel Roe (Sat Mar 30 2019 - 06:03:30 PDT)
- Debarati DasGupta (Fri Mar 29 2019 - 10:49:51 PDT)
[AMBER] NFE error: Cannot read &abmd namelist
- Feng Pan (Sat Mar 30 2019 - 20:52:49 PDT)
- Jason Imamoto (Sat Mar 30 2019 - 04:26:33 PDT)
[AMBER] nmode_com.96
- 高含露 (Wed Mar 13 2019 - 01:24:58 PDT)
[AMBER] NMR order parameters from MD trajectories
- George M. Giambasu (Wed Mar 27 2019 - 19:36:50 PDT)
- giulia palermo (Wed Mar 27 2019 - 18:41:09 PDT)
[AMBER] Occupancy values in pseudo PDB from CPPRAJ grid analysis
- Daniel Roe (Tue Mar 26 2019 - 05:34:54 PDT)
- anu chandra (Fri Mar 22 2019 - 14:42:04 PDT)
[AMBER] One query about SPAM type calculations
- Daniel Roe (Mon Mar 11 2019 - 12:15:14 PDT)
- Debarati DasGupta (Tue Mar 05 2019 - 09:45:26 PST)
[AMBER] parameters for cc and cd
- David Case (Wed Mar 13 2019 - 16:46:18 PDT)
- Träg, Johannes (Wed Mar 13 2019 - 10:27:19 PDT)
[AMBER] PCA analysis of NM
- Daniel Roe (Tue Mar 26 2019 - 12:09:37 PDT)
- maya nair (Mon Mar 25 2019 - 05:05:01 PDT)
[AMBER] pdb file with 4 atoms coordinates of water molecules with TIP4PFB model
- Daniel Roe (Mon Mar 18 2019 - 05:49:47 PDT)
- bjyx20090941 (Mon Mar 18 2019 - 05:41:16 PDT)
[AMBER] PNEB simulation transition
- Ashutosh Shandilya (Thu Mar 14 2019 - 12:11:39 PDT)
- Ghoreishi, Delaram (Thu Mar 14 2019 - 11:23:14 PDT)
- Ashutosh Shandilya (Thu Mar 14 2019 - 09:04:18 PDT)
[AMBER] Potential bug in sander/LMOD
- Scott Brozell (Fri Mar 08 2019 - 18:02:40 PST)
- Charles Lin (Fri Mar 08 2019 - 11:05:50 PST)
[AMBER] Problem with distance restraints in membrane system with pmemd.cuda
- Charles Lin (Mon Mar 11 2019 - 08:44:58 PDT)
- David Bickel (Mon Mar 11 2019 - 05:10:32 PDT)
- David Case (Sat Mar 09 2019 - 06:01:53 PST)
- David Bickel (Fri Mar 08 2019 - 07:29:28 PST)
- David Bickel (Wed Mar 06 2019 - 01:18:40 PST)
[AMBER] Problems calculating density over distance
- Daniel Roe (Tue Mar 26 2019 - 12:08:03 PDT)
- Lucas Bandeira (Mon Mar 25 2019 - 10:41:48 PDT)
[AMBER] Protein - Ligand simulation on amber and PBSA
- Prasanth G, Research Scholar (Wed Mar 06 2019 - 05:35:34 PST)
[AMBER] Quantitative measurement of hydrophobic and polar contacts
- Rakesh Srivastava (Wed Mar 13 2019 - 00:13:07 PDT)
[AMBER] Query about metal RMSD regarding residue number or atom number
- Dr. Anselm Horn (Thu Mar 07 2019 - 04:09:55 PST)
- shahid khan (Thu Mar 07 2019 - 03:21:39 PST)
[AMBER] Query about plotting/visualizing the lifetime curve from H-Bond analysis using CPPTRAJ
- Daniel Roe (Fri Mar 29 2019 - 07:34:55 PDT)
- SATYAJIT KHATUA (Fri Mar 29 2019 - 07:12:27 PDT)
[AMBER] Query about protein DNA MD
- David A Case (Fri Mar 08 2019 - 11:00:35 PST)
- Vikram Dalal (Fri Mar 08 2019 - 09:29:34 PST)
[AMBER] Query regarding secondary structure
- Daniel Roe (Wed Mar 20 2019 - 05:09:21 PDT)
- Saikat Pal (Tue Mar 19 2019 - 22:08:42 PDT)
[AMBER] Question about Amber TUTORIAL B5: Simulating the Green Fluorescent Protein
- David A Case (Wed Mar 27 2019 - 04:28:35 PDT)
- Debarati DasGupta (Tue Mar 26 2019 - 10:17:13 PDT)
- A K (Tue Mar 26 2019 - 10:12:13 PDT)
[AMBER] Reference energies in CpHMD (constant pH MD) for HIP
- Brian Radak (Sat Mar 02 2019 - 08:39:54 PST)
- Jason Swails (Sat Mar 02 2019 - 06:54:39 PST)
[AMBER] regarding simulation
- Carlos Simmerling (Fri Mar 29 2019 - 04:43:17 PDT)
- angad sharma (Thu Mar 28 2019 - 23:59:05 PDT)
[AMBER] Regarding solvated interaction energy (SIE) method in Amber 16
- Fulbabu Sk (Thu Mar 28 2019 - 03:27:00 PDT)
[AMBER] Research Programmer for VMD/NAMD at UIUC
- João Ribeiro (Tue Mar 12 2019 - 11:33:01 PDT)
[AMBER] Restraint and ambmask syntax issue
- David Case (Fri Mar 15 2019 - 12:29:20 PDT)
- Xiaoyu Wang (Fri Mar 15 2019 - 11:36:13 PDT)
[AMBER] Retrieving topology file
- Daniel Roe (Tue Mar 26 2019 - 12:16:08 PDT)
- emanuele falbo (Mon Mar 04 2019 - 06:57:27 PST)
- Daniel Roe (Mon Mar 04 2019 - 05:53:38 PST)
- emanuele falbo (Mon Mar 04 2019 - 02:08:01 PST)
[AMBER] Running a MMPBSA calculation on only the structure
- Keiran Corbett (Thu Mar 07 2019 - 06:32:17 PST)
[AMBER] Setbox and ChBox
- Lin Song (Thu Mar 07 2019 - 09:48:14 PST)
[AMBER] simulating a box of pure TIP3P water
- Daniel Roe (Mon Mar 11 2019 - 12:31:50 PDT)
- Daniel Roe (Mon Mar 11 2019 - 12:30:28 PDT)
- Debarati DasGupta (Tue Mar 05 2019 - 07:32:16 PST)
[AMBER] Simulation of spherical macroion system
- Rakesh Srivastava (Mon Mar 25 2019 - 06:17:24 PDT)
[AMBER] Single point energy calculation SCC-DFTB
- David A Case (Mon Mar 25 2019 - 07:33:45 PDT)
- Setyanto Md (Mon Mar 25 2019 - 05:47:53 PDT)
- Anthony Bogetti (Mon Mar 25 2019 - 05:40:28 PDT)
[AMBER] Solvate with methanol and acetone using free energy methods?
- Stephan Schott (Sat Mar 30 2019 - 14:47:07 PDT)
- Debarati DasGupta (Tue Mar 26 2019 - 09:53:33 PDT)
- Defrese, Matthew (Tue Mar 26 2019 - 08:27:31 PDT)
[AMBER] Solvating a Lipid bilayer in Amber
- Souvik Dey (Sun Mar 03 2019 - 18:13:59 PST)
[AMBER] SPAM analysis
- Daniel Roe (Mon Mar 11 2019 - 12:14:34 PDT)
- Debarati DasGupta (Tue Mar 05 2019 - 14:05:41 PST)
[AMBER] system explosion
- David A Case (Fri Mar 08 2019 - 06:04:02 PST)
- Hadi Rahmaninejad (Thu Mar 07 2019 - 15:18:30 PST)
[AMBER] the question of calculate the binding free energy by MMPBSA.py
- bjyx20090941 (Fri Mar 15 2019 - 00:28:05 PDT)
[AMBER] TI atom limit
- accuratefreeenergy.gmail.com (Wed Mar 27 2019 - 06:27:26 PDT)
- Andrea Cavalli (Wed Mar 27 2019 - 05:37:46 PDT)
- accuratefreeenergy.gmail.com (Wed Mar 27 2019 - 04:53:19 PDT)
- Andrea Cavalli (Wed Mar 27 2019 - 01:14:32 PDT)
[AMBER] TIP4P Ice1h phase initial structure
- Mohd moid khan (Tue Mar 26 2019 - 13:11:14 PDT)
[AMBER] Two dimensional replica exchange MD: Success rate
- Daniel Roe (Mon Mar 04 2019 - 11:58:09 PST)
[AMBER] Use of amber force field in gromacs
- David A Case (Tue Mar 05 2019 - 06:46:23 PST)
- Mayank Dixit (Tue Mar 05 2019 - 06:16:49 PST)
- Akshay Prabhakant (Tue Mar 05 2019 - 01:39:49 PST)
[AMBER] using amber parameters in namd
- David A Case (Thu Mar 21 2019 - 11:34:07 PDT)
- Akshay Prabhakant (Thu Mar 21 2019 - 06:27:22 PDT)
[AMBER] ValueError: invalid literal for int() with base 10: '-3.0'
- Daniel Roe (Thu Mar 14 2019 - 05:26:50 PDT)
- SATYAJIT KHATUA (Wed Mar 13 2019 - 21:19:19 PDT)
- SATYAJIT KHATUA (Thu Mar 07 2019 - 20:29:11 PST)
[AMBER] varying pressure conditions?
- David Case (Sat Mar 30 2019 - 13:53:00 PDT)
- Shayna Hilburg (Mon Mar 25 2019 - 11:06:06 PDT)
[AMBER] velocities from and velocityautocorr
- Ruth Helena Tichauer (Mon Mar 18 2019 - 00:36:08 PDT)
- Daniel Roe (Fri Mar 15 2019 - 12:30:59 PDT)
- Ruth Helena Tichauer (Fri Mar 15 2019 - 07:08:02 PDT)
- Ruth Helena Tichauer (Wed Mar 13 2019 - 13:56:51 PDT)
- Daniel Roe (Wed Mar 13 2019 - 10:17:47 PDT)
- Ruth Helena Tichauer (Wed Mar 13 2019 - 09:25:43 PDT)
- Ruth Helena Tichauer (Wed Mar 13 2019 - 09:07:37 PDT)
[AMBER] What does "0 Kb value" mean in dihedrals
- Erdem Yeler (Sat Mar 09 2019 - 05:47:12 PST)
- David Case (Wed Mar 06 2019 - 14:27:08 PST)
- Erdem Yeler (Tue Mar 05 2019 - 11:35:33 PST)
[AMBER] write equilibrium bond lengths, angles and dihedrals from a ligand structure file to a frcmod file
- Thomas Evangelidis (Sun Mar 10 2019 - 03:49:56 PDT)
- Dickson, Callum (Sat Mar 09 2019 - 19:03:29 PST)
- Thomas Evangelidis (Fri Mar 08 2019 - 10:08:14 PST)

Amber Archive Mar 2019 by subject