Amber Archive Oct 2021 by thread
- [AMBER] buffer overflow in tleap, AmberTools21, gcc 9.3 Alessandro Contini (Fri Oct 01 2021 - 03:02:44 PDT)
- Re: [AMBER] Error installing amber macOS M1 David A Case (Fri Oct 01 2021 - 05:13:42 PDT)
- [AMBER] Postdoctoral fellowship Computational Drug Discovery Marawan Hussien (Fri Oct 01 2021 - 10:50:10 PDT)
- [AMBER] How to reshuffle traj frames Matthew Guberman-Pfeffer (Fri Oct 01 2021 - 20:51:41 PDT)
- Re: [AMBER] How to combine the coordinate and parm7 files of the glycolipid into a protein complex system neildancer (Fri Oct 01 2021 - 21:09:32 PDT)
- [AMBER] Distanced-based atom selection from the center of mass Umesh Roy (Sat Oct 02 2021 - 05:01:20 PDT)
- Re: [AMBER] parmed for 12-6-4 LJ (Geng Dong) Pengfei Li (Sat Oct 02 2021 - 17:47:19 PDT)
- [AMBER] TI for DG when only cofactor charge changes Vaibhav Dixit (Sat Oct 02 2021 - 23:21:35 PDT)
- [AMBER] Question of Amber_ Sasaki Shiho Ohno (Mon Oct 04 2021 - 01:34:16 PDT)
- [AMBER] Ligand is unstable in simulations Midhun K Madhu (Mon Oct 04 2021 - 05:10:24 PDT)
- [AMBER] How to superpose the solvated box to the original pdb structure? Gao Zhenting (Mon Oct 04 2021 - 20:32:48 PDT)
- [AMBER] FixCondaShebang Error Satya Pal Singh (Mon Oct 04 2021 - 23:15:37 PDT)
- Re: [AMBER] Cpptraj hbond criteria Daniel Roe (Tue Oct 05 2021 - 05:43:48 PDT)
- Re: [AMBER] Restart/Reference file for targeted MD Daniel Roe (Tue Oct 05 2021 - 05:47:08 PDT)
- [AMBER] Restraint COM between two proteins Mohamed Aboelnga (Tue Oct 05 2021 - 06:19:23 PDT)
- [AMBER] Zn sim Cato, Lee (Tue Oct 05 2021 - 07:05:10 PDT)
- [AMBER] The silver ion parameter nali (Tue Oct 05 2021 - 10:01:14 PDT)
- [AMBER] Regarding xleap error Archana (Wed Oct 06 2021 - 08:17:25 PDT)
- [AMBER] CPPTRAJ Rana Rehan Khalid (Wed Oct 06 2021 - 09:11:45 PDT)
- [AMBER] Symmetrical voids during heating stage Nagar, Hemant (Wed Oct 06 2021 - 16:38:09 PDT)
- [AMBER] Question of Amber_ Sasaki Shiho Ohno (Wed Oct 06 2021 - 17:08:07 PDT)
- [AMBER] Tohoku Medical and Pharmaceutical University Sasaki It's resolved Shiho Ohno (Wed Oct 06 2021 - 17:45:36 PDT)
- [AMBER] parameters for ions in Amber Małgorzata Kogut (Wed Oct 06 2021 - 23:57:58 PDT)
- [AMBER] parameters for ions Małgorzata Kogut (Thu Oct 07 2021 - 00:14:01 PDT)
- [AMBER] Help with carbohydrate nomenclature Daniel Roe (Thu Oct 07 2021 - 16:09:28 PDT)
- [AMBER] Calculating viscosity, thermal conductivity and self-diffusion coefficient Chloe Jaiswal (Fri Oct 08 2021 - 02:31:48 PDT)
- [AMBER] How to set multiple positional restraints during minimization Sadaf Rani (Fri Oct 08 2021 - 08:25:06 PDT)
- [AMBER] Restraining the distance between two groups of residues? Gustavo Seabra (Fri Oct 08 2021 - 11:34:46 PDT)
- [AMBER] VDWAALS = ************* in minimization Sadaf Rani (Sat Oct 09 2021 - 10:59:56 PDT)
- [AMBER] Rotation Matrix mohamed marzouk (Sat Oct 09 2021 - 18:58:13 PDT)
- [AMBER] How many complex trajectories for mmpbsa computations ? Cenk Andac (Sun Oct 10 2021 - 13:20:30 PDT)
- [AMBER] FixCondaShebang persists German P. Barletta (Mon Oct 11 2021 - 04:10:37 PDT)
- [AMBER] How to generate different velocities for same structure during equilibration Sadaf Rani (Mon Oct 11 2021 - 04:20:32 PDT)
- [AMBER] How to turn H-bonding point charges Matthew Guberman-Pfeffer (Mon Oct 11 2021 - 05:59:05 PDT)
- [AMBER] On Ion Distribution and "Replicates" Robert Molt (Mon Oct 11 2021 - 07:26:39 PDT)
- [AMBER] Accelerated dissociation events in MD simulation by temperature increase? Liao (Mon Oct 11 2021 - 12:33:53 PDT)
- [AMBER] How to depict Atomic Fluctuations of a specific residue Versus Frames by CPPTRAJ Maghsoud, Yazdan (Tue Oct 12 2021 - 14:23:11 PDT)
- [AMBER] Amber20/AmberTools21 Installation Test Errors Ravi Abrol (Wed Oct 13 2021 - 00:23:21 PDT)
- [AMBER] How to minimize average structure (pdb) using Amber 16 priya murugan (Wed Oct 13 2021 - 09:23:48 PDT)
- [AMBER] How to characterize Binding Sites with cpptraj Matthew Guberman-Pfeffer (Wed Oct 13 2021 - 11:07:47 PDT)
- Re: [AMBER] Explicit water molecules in MMPBSA.py: OPC vs TIP3P Lennart Gundelach (Thu Oct 14 2021 - 00:58:38 PDT)
- [AMBER] parmed for two atom type with the same LJ parameters Qinghua Liao (Thu Oct 14 2021 - 05:27:33 PDT)
- [AMBER] Automated capping of missing loops? Brian Radak (Thu Oct 14 2021 - 13:54:34 PDT)
- [AMBER] Protein-protein binding free energy MMPBSA Rana Rehan Khalid (Thu Oct 14 2021 - 15:43:43 PDT)
- [AMBER] Mutation by pdb4amber mohamed marzouk (Fri Oct 15 2021 - 05:41:50 PDT)
- [AMBER] MMGBSA error help Debarati DasGupta (Fri Oct 15 2021 - 06:50:37 PDT)
- [AMBER] Unwanted water protein interaction mohamed marzouk (Sat Oct 16 2021 - 08:15:04 PDT)
- [AMBER] Regarding entropy calculations in MMPBSA.py when enthalpy is either from GBSA or PBSA? Liao (Sat Oct 16 2021 - 09:43:52 PDT)
- [AMBER] cpptraj RMSD reference Mac Kevin Braza (Sat Oct 16 2021 - 16:16:54 PDT)
- [AMBER] trajectory of mutation generation (Geng Dong) 东庚 (Sun Oct 17 2021 - 02:32:48 PDT)
- [AMBER] Meaning of 3D-RISM output files? Gao Zhenting (Sun Oct 17 2021 - 03:42:43 PDT)
- [AMBER] What is the default value of tishake Suitian Lai (Mon Oct 18 2021 - 07:48:19 PDT)
- [AMBER] Parameters for non-standard residues Nagar, Hemant (Mon Oct 18 2021 - 13:07:04 PDT)
- [AMBER] How I can Remove dna form .rst files Rana Rehan Khalid (Mon Oct 18 2021 - 14:00:16 PDT)
- [AMBER] Error with PDB4AMBER Rangarajan, Amith (Tue Oct 19 2021 - 11:28:29 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Rangarajan, Amith (Tue Oct 19 2021 - 12:08:42 PDT)
- [AMBER] Restraining ligand for TI Delwakkada Liyanage, Senal Dinuka (Tue Oct 19 2021 - 15:34:13 PDT)
- [AMBER] Fwd: topology file and co-ordinate file making by amber tool (gaff.dat) vivek rabha (Wed Oct 20 2021 - 02:58:09 PDT)
- [AMBER] Freeze DNA during simulation. Rana Rehan Khalid (Wed Oct 20 2021 - 12:34:43 PDT)
- [AMBER] Query regarding missing oxygen atom in RNA sequence Saikat Pal (Wed Oct 20 2021 - 15:10:26 PDT)
- [AMBER] Ambertools18 tleap scripts not working when run on Ambertools21 Daniel Fowles (Thu Oct 21 2021 - 04:21:32 PDT)
- [AMBER] Query regarding not integral charge in RNA Saikat Pal (Thu Oct 21 2021 - 08:44:38 PDT)
- [AMBER] Maximizing GROMACS Throughput with Multiple Simulations per GPU Using MPS and MIG James Kress (Thu Oct 21 2021 - 13:29:16 PDT)
- [AMBER] ZAFF Simulation Error Daniel Hall (Thu Oct 21 2021 - 13:48:27 PDT)
- [AMBER] RMSD of residues within 3A of ligand Sadaf Rani (Fri Oct 22 2021 - 06:56:41 PDT)
- [AMBER] Amber20 benchmarks for RTX A4000 Vaibhav Dixit (Fri Oct 22 2021 - 09:14:00 PDT)
- [AMBER] Query regarding ZAFF Modeling Tutorial Saikat Pal (Fri Oct 22 2021 - 14:58:03 PDT)
- [AMBER] How can I download amber 18？ Hecate Me (Sat Oct 23 2021 - 01:09:25 PDT)
- [AMBER] Fwd: Ambertools21 installation problems Victor Nazarychev (Sat Oct 23 2021 - 05:46:43 PDT)
- [AMBER] LINMIN ERROR Sumon Naskar (Sat Oct 23 2021 - 13:07:25 PDT)
- [AMBER] reasonable GIST griddim values Christian Seitz (Sun Oct 24 2021 - 13:27:07 PDT)
- [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 priya murugan (Sun Oct 24 2021 - 19:23:06 PDT)
- [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16 priya murugan (Sun Oct 24 2021 - 20:27:09 PDT)
- [AMBER] Can I used AMBER 16 CPPTRAJ to perform dynamic cross correlation map? priya murugan (Sun Oct 24 2021 - 20:35:21 PDT)
- [AMBER] How is correlation computed in cpptraj Matthew Guberman-Pfeffer (Mon Oct 25 2021 - 01:45:55 PDT)
- [AMBER] Several postdoctoral positions available in EU Jan Brezovsky (Mon Oct 25 2021 - 09:19:37 PDT)
- [AMBER] bug in pmemd/src/cuda/gpu.cpp line 2852? Thomas Zeiser (Mon Oct 25 2021 - 12:47:41 PDT)
- [AMBER] Reg: Cpptraj-Hierarchical Agglomerative Reference paper for methodology and result analysis Lara rajam (Mon Oct 25 2021 - 18:01:23 PDT)
- [AMBER] Amber21 installation using Docker will be Parallel or Serial? Erdem Yeler (Tue Oct 26 2021 - 06:32:10 PDT)
- [AMBER] Regarding Amber20 installation Rajarshi Roy (Tue Oct 26 2021 - 06:59:33 PDT)
- [AMBER] Organometallic RESP charge derivation for use with AmberTools Sam Walsworth (Researcher) (Tue Oct 26 2021 - 11:58:00 PDT)
- [AMBER] Atom type does not shown up in PARMCHK.DAT Rohanizeidanlou, Sahar (Tue Oct 26 2021 - 16:38:13 PDT)
- [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces Umesh Roy (Wed Oct 27 2021 - 00:08:33 PDT)
- [AMBER] How to minimize a pdb format file in Amber 16 priya murugan (Wed Oct 27 2021 - 21:52:36 PDT)
- [AMBER] How to handle Ca2+ ion with 8 coordination Geometry in lectin domain for MD simulation. Bhat Zahoor (Thu Oct 28 2021 - 01:20:17 PDT)
- [AMBER] Regarding area calculation of protein cavity Athena N (Thu Oct 28 2021 - 04:12:15 PDT)
- [AMBER] mm_pbsa and MMPBSA.py zmatovic.kg.ac.rs (Thu Oct 28 2021 - 06:57:15 PDT)
- [AMBER] Multiple Replicate Trajectories Li,Haoxi (Thu Oct 28 2021 - 08:21:17 PDT)
- [AMBER] Wrong Angel Given by Cpptraj? Matthew Guberman-Pfeffer (Fri Oct 29 2021 - 03:38:16 PDT)
- [AMBER] Constant pH MD simulation Divya Rai (Fri Oct 29 2021 - 07:19:15 PDT)
- [AMBER] weired Ligand conformation during simulation Sadaf Rani (Fri Oct 29 2021 - 19:10:22 PDT)
- [AMBER] unable to get response from mailing list Sadaf Rani (Fri Oct 29 2021 - 19:20:21 PDT)
- [AMBER] Fwd: Constant pH MD simulation Divya Rai (Sat Oct 30 2021 - 12:21:19 PDT)
- [AMBER] Problem measuring angle in CPPTRAJ Matthew Guberman-Pfeffer (Sat Oct 30 2021 - 13:14:13 PDT)
- [AMBER] How to Compare RDFs for different systems Matthew Guberman-Pfeffer (Sat Oct 30 2021 - 14:15:01 PDT)
- [AMBER] MMPBSA (Unable to read script file because of error: invalid option argument "-O") Rana Rehan Khalid (Sat Oct 30 2021 - 15:40:00 PDT)
- Last message date: Sun Oct 31 2021 - 13:30:02 PDT
- Archived on: Fri Dec 20 2024 - 05:56:09 PST
