Amber Archive Mar 2019 by thread
- Re: [AMBER] Ligand autoimaging issue Amber18 David A Case (Fri Mar 01 2019 - 05:41:03 PST)
- [AMBER] Doubt regarding input files in NMR refinement RITUPARNA ROY (Fri Mar 01 2019 - 06:34:13 PST)
- Re: [AMBER] CPPTRAJ grid unknown command Daniel Roe (Fri Mar 01 2019 - 07:08:17 PST)
- Re: [AMBER] Atom type of Calcium Daniel Roe (Fri Mar 01 2019 - 07:10:01 PST)
- Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? Feng, Zimin (Fri Mar 01 2019 - 07:47:20 PST)
- [AMBER] 1/2 term in dihdral Mayank Dixit (Fri Mar 01 2019 - 14:27:36 PST)
- [AMBER] distance restraint Sunita Patel (Sat Mar 02 2019 - 04:00:15 PST)
- Re: [AMBER] Reference energies in CpHMD (constant pH MD) for HIP Jason Swails (Sat Mar 02 2019 - 06:54:39 PST)
- [AMBER] [error] The system has extended beyond the extent of the virtual box Xiaocong Wang (Sun Mar 03 2019 - 00:37:41 PST)
- [AMBER] MM/PBSA topfile question Manyi Yang (Sun Mar 03 2019 - 17:35:51 PST)
- [AMBER] Solvating a Lipid bilayer in Amber Souvik Dey (Sun Mar 03 2019 - 18:13:59 PST)
- [AMBER] how to make sure .prmtop is the same for NEB calculation when using explicit solvent? 郭昱 (Sun Mar 03 2019 - 19:06:08 PST)
- [AMBER] How can I generate of force field parameter for nano-material? xmgign.126.com (Sun Mar 03 2019 - 22:00:57 PST)
- [AMBER] Message-ID: <20190301134103.u232i6wjibdt4cav@godel.rutgers.edu> zaid kamal (Mon Mar 04 2019 - 00:37:49 PST)
- [AMBER] Retrieving topology file emanuele falbo (Mon Mar 04 2019 - 02:08:01 PST)
- [AMBER] CPPTRAJ SPAM error while executing the input file Debarati DasGupta (Mon Mar 04 2019 - 09:14:52 PST)
- [AMBER] Converting Charmm forcefileld to Amber Hadi Rahmaninejad (Mon Mar 04 2019 - 09:23:26 PST)
- Re: [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 Akshay Prabhakant (Tue Mar 05 2019 - 01:39:49 PST)
- [AMBER] Amber18 pmemd TI Hosein Geraili Daronkola (Tue Mar 05 2019 - 06:12:43 PST)
- [AMBER] simulating a box of pure TIP3P water Debarati DasGupta (Tue Mar 05 2019 - 07:32:16 PST)
- [AMBER] improper dihedral Mayank Dixit (Tue Mar 05 2019 - 08:59:58 PST)
- [AMBER] One query about SPAM type calculations Debarati DasGupta (Tue Mar 05 2019 - 09:45:26 PST)
- [AMBER] What does "0 Kb value" mean in dihedrals Erdem Yeler (Tue Mar 05 2019 - 11:35:33 PST)
- [AMBER] SPAM analysis Debarati DasGupta (Tue Mar 05 2019 - 14:05:41 PST)
- [AMBER] Error in REMD with pmemd.cuda.MPI Ikuo KURISAKI (Wed Mar 06 2019 - 00:24:07 PST)
- [AMBER] Problem with distance restraints in membrane system with pmemd.cuda David Bickel (Wed Mar 06 2019 - 01:18:40 PST)
- [AMBER] Protein - Ligand simulation on amber and PBSA Prasanth G, Research Scholar (Wed Mar 06 2019 - 05:35:34 PST)
- [AMBER] chi1 angle of amino acids not having a CG atom 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] Query about metal RMSD regarding residue number or atom number shahid khan (Thu Mar 07 2019 - 03:21:39 PST)
- [AMBER] Help regarding protein DNA MD in AMBER Vikram Dalal (Thu Mar 07 2019 - 03:25:19 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] system explosion Hadi Rahmaninejad (Thu Mar 07 2019 - 15:18:30 PST)
- [AMBER] ValueError: invalid literal for int() with base 10: '-3.0' SATYAJIT KHATUA (Thu Mar 07 2019 - 20:29:11 PST)
- [AMBER] MMPBSA.py Calculation error Rinsha Chk (Thu Mar 07 2019 - 21:52:40 PST)
- [AMBER] calculate RDF using COM Saikat Pal (Thu Mar 07 2019 - 22:57:51 PST)
- [AMBER] Error in Minimization Zhonghua Xia (Fri Mar 08 2019 - 01:18:57 PST)
- [AMBER] Query about protein DNA MD Vikram Dalal (Fri Mar 08 2019 - 09:29:34 PST)
- [AMBER] write equilibrium bond lengths, angles and dihedrals from a ligand structure file to a frcmod file Thomas Evangelidis (Fri Mar 08 2019 - 10:08:14 PST)
- Re: [AMBER] Potential bug in sander/LMOD Charles Lin (Fri Mar 08 2019 - 11:05:50 PST)
- [AMBER] CUDA COM distance restraint (v18 with patch.7 applied) Pratul Agarwal (Sun Mar 10 2019 - 11:48:33 PDT)
- [AMBER] antechamber bcc error Michael Shokhen (Mon Mar 11 2019 - 04:09:32 PDT)
- [AMBER] metal parameters 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] Research Programmer for VMD/NAMD at UIUC João Ribeiro (Tue Mar 12 2019 - 11:33:01 PDT)
- [AMBER] Directly Set Restraint for Chilarity to Prmtop File Ikuo KURISAKI (Tue Mar 12 2019 - 18:16:01 PDT)
- [AMBER] Quantitative measurement of hydrophobic and polar contacts Rakesh Srivastava (Wed Mar 13 2019 - 00:13:07 PDT)
- [AMBER] Job terminated during TI calculation in pmemd.cuda 강무석 (Wed Mar 13 2019 - 01:13:42 PDT)
- [AMBER] nmode_com.96 高含露 (Wed Mar 13 2019 - 01:24:58 PDT)
- [AMBER] DSSP residue vs time graph Myriam Hanna (Wed Mar 13 2019 - 08:30:27 PDT)
- [AMBER] CPPTRAJ Grid with COM Kung, Ryan (Wed Mar 13 2019 - 09:03:55 PDT)
- [AMBER] velocities from and velocityautocorr Ruth Helena Tichauer (Wed Mar 13 2019 - 09:07:37 PDT)
- [AMBER] parameters for cc and cd Träg, Johannes (Wed Mar 13 2019 - 10:27:19 PDT)
- [AMBER] Jar pulling Gerardo Zerbetto De Palma (Wed Mar 13 2019 - 10:21:47 PDT)
- [AMBER] PNEB simulation transition Ashutosh Shandilya (Thu Mar 14 2019 - 09:04:18 PDT)
- [AMBER] MMPBSA.py.MPI error Prabir Khatua (Thu Mar 14 2019 - 15:24:21 PDT)
- [AMBER] the question of calculate the binding free energy by MMPBSA.py bjyx20090941 (Fri Mar 15 2019 - 00:28:05 PDT)
- [AMBER] charged residue mutation free energy Hosein Geraili Daronkola (Fri Mar 15 2019 - 06:32:43 PDT)
- [AMBER] gaff2 parameters of c3-c3-os-c3 Träg, Johannes (Fri Mar 15 2019 - 08:21:05 PDT)
- [AMBER] Restraint and ambmask syntax issue Xiaoyu Wang (Fri Mar 15 2019 - 11:36:13 PDT)
- [AMBER] Amber18 STSM 李耀 (Sat Mar 16 2019 - 06:38:45 PDT)
- [AMBER] Homodimerization of IRF3 protein Debarati DasGupta (Sat Mar 16 2019 - 14:38:05 PDT)
- [AMBER] A confused question about calculate the binding free energy from MMPBSA.py bjyx20090941 (Sun Mar 17 2019 - 18:13:28 PDT)
- Re: [AMBER] Installation Problem Bill Ross (Mon Mar 18 2019 - 05:00:04 PDT)
- [AMBER] pdb file with 4 atoms coordinates of water molecules with TIP4PFB model bjyx20090941 (Mon Mar 18 2019 - 05:41:16 PDT)
- [AMBER] Assigning protonation states manually to the amino vs CpH MD simulation Bharat Manna (Mon Mar 18 2019 - 11:50:23 PDT)
- [AMBER] Nastruct vs 3DNA Jason Imamoto (Mon Mar 18 2019 - 10:12:37 PDT)
- [AMBER] Input Reservoir REMD Raimon Fabregat (Tue Mar 19 2019 - 01:17:13 PDT)
- Re: [AMBER] Amber Installation David A Case (Tue Mar 19 2019 - 06:50:10 PDT)
- Re: [AMBER] Installation problem AMBER16 David A Case (Tue Mar 19 2019 - 06:51:50 PDT)
- [AMBER] Hyaluronic acid using Glycam06 monia kam (Tue Mar 19 2019 - 08:15:18 PDT)
- [AMBER] Query regarding secondary structure Saikat Pal (Tue Mar 19 2019 - 22:08:42 PDT)
- [AMBER] Gpu illegal memory code accessed Debarati DasGupta (Wed Mar 20 2019 - 07:39:25 PDT)
- [AMBER] Amber18: cv_min and cv_max for periodic cv in ABMD 李耀 (Wed Mar 20 2019 - 09:25:26 PDT)
- [AMBER] Installation error AmberTools18 - [test.rism1d] Error Mariana Simões Ferreira (Wed Mar 20 2019 - 10:02:37 PDT)
- [AMBER] cuda test failing after installation Ravi Abrol (Wed Mar 20 2019 - 10:09:32 PDT)
- Re: [AMBER] Nastruct vs 3DNA: Files used for analysis and the output Jason Imamoto (Wed Mar 20 2019 - 11:00:51 PDT)
- [AMBER] using amber parameters in namd Akshay Prabhakant (Thu Mar 21 2019 - 06:27:22 PDT)
- [AMBER] FEW amber- LIE analysis Sowmya Indrakumar (Thu Mar 21 2019 - 06:38:37 PDT)
- [AMBER] Amber18: Adaptively Biased MD (Metadynalmics) 李耀 (Thu Mar 21 2019 - 08:49:56 PDT)
- [AMBER] DFTB3/MM simulations of CCCC zinc finger Dreab, Ana (Thu Mar 21 2019 - 09:18:35 PDT)
- [AMBER] CEMD protcnt meaning Feng, Zimin (Thu Mar 21 2019 - 09:31:40 PDT)
- [AMBER] Incorrect electric field Ashutosh Mishra (Thu Mar 21 2019 - 23:26:14 PDT)
- [AMBER] Closest command in cpptraj for non aqeous solvents Debarati DasGupta (Fri Mar 22 2019 - 12:23:32 PDT)
- [AMBER] Occupancy values in pseudo PDB from CPPRAJ grid analysis anu chandra (Fri Mar 22 2019 - 14:42:04 PDT)
- [AMBER] PCA analysis of NM maya nair (Mon Mar 25 2019 - 05:05:01 PDT)
- [AMBER] Single point energy calculation SCC-DFTB Anthony Bogetti (Mon Mar 25 2019 - 05:40:28 PDT)
- [AMBER] Simulation of spherical macroion system Rakesh Srivastava (Mon Mar 25 2019 - 06:17:24 PDT)
- [AMBER] locating the single probe out of 80000 snapshots Debarati DasGupta (Mon Mar 25 2019 - 07:58:20 PDT)
- [AMBER] Problems calculating density over distance Lucas Bandeira (Mon Mar 25 2019 - 10:41:48 PDT)
- [AMBER] varying pressure conditions? Shayna Hilburg (Mon Mar 25 2019 - 11:06:06 PDT)
- [AMBER] AMBER 18 error in QM region of QMMM Abhilash J (Tue Mar 26 2019 - 02:27:05 PDT)
- [AMBER] Solvate with methanol and acetone using free energy methods? Defrese, Matthew (Tue Mar 26 2019 - 08:27:31 PDT)
- [AMBER] Question about Amber TUTORIAL B5: Simulating the Green Fluorescent Protein A K (Tue Mar 26 2019 - 10:12:13 PDT)
- [AMBER] TIP4P Ice1h phase initial structure Mohd moid khan (Tue Mar 26 2019 - 13:11:14 PDT)
- [AMBER] Error in `sander': malloc(): smallbin double linked list corrupted: Margarita I. Bernal-Uruchurtu (Tue Mar 26 2019 - 14:53:00 PDT)
- [AMBER] metal-oxide-metal interactions Arun Srikanth (Tue Mar 26 2019 - 15:34:21 PDT)
- [AMBER] Design of graphene quantum dots RITUPARNA ROY (Tue Mar 26 2019 - 20:50:50 PDT)
- [AMBER] TI atom limit Andrea Cavalli (Wed Mar 27 2019 - 01:14:32 PDT)
- [AMBER] how to get unbiased trajectories from biased trajectories Mayank Dixit (Wed Mar 27 2019 - 07:33:36 PDT)
- [AMBER] Installation of AmberTools18 in macOS Mojave Reza Esmaeeli (Wed Mar 27 2019 - 11:48:21 PDT)
- [AMBER] NMR order parameters from MD trajectories giulia palermo (Wed Mar 27 2019 - 18:41:09 PDT)
- [AMBER] Regarding solvated interaction energy (SIE) method in Amber 16 Fulbabu Sk (Thu Mar 28 2019 - 03:27:00 PDT)
- [AMBER] Building pmemd.cuda.MPI error in amber18 Meng Wu (Thu Mar 28 2019 - 04:11:23 PDT)
- [AMBER] A confused question about calculate the binding free energy from MMPBSA.py bjyx20090941 (Thu Mar 28 2019 - 05:29:53 PDT)
- [AMBER] Job position Ganesh Kamath (Thu Mar 28 2019 - 18:31:02 PDT)
- [AMBER] regarding simulation angad sharma (Thu Mar 28 2019 - 23:59:05 PDT)
- [AMBER] Query about plotting/visualizing the lifetime curve from H-Bond analysis using CPPTRAJ SATYAJIT KHATUA (Fri Mar 29 2019 - 07:12:27 PDT)
- [AMBER] nativecontacs in ccptraj Debarati DasGupta (Fri Mar 29 2019 - 10:49:51 PDT)
- [AMBER] MMPBSA Prabir Khatua (Fri Mar 29 2019 - 14:14:33 PDT)
- [AMBER] NFE error: Cannot read &abmd namelist Jason Imamoto (Sat Mar 30 2019 - 04:26:33 PDT)
- [AMBER] huge reference.frc in MMPBSA Antoine MARION (Sun Mar 31 2019 - 10:44:56 PDT)
- Re: [AMBER] How the instantaneous temperature is calculated in Amber ? Bill Ross (Sun Mar 31 2019 - 17:57:02 PDT)
- Last message date: Sun Mar 31 2019 - 22:00:03 PDT
- Archived on: Sun Dec 22 2024 - 05:55:46 PST
