Amber Archive Aug 2018 by thread
- [AMBER] Constant pH simulation in explicit solvent Nikolay N. Kuzmich (Wed Aug 01 2018 - 02:32:06 PDT)
- [AMBER] Eigenvalues from PCA in cpptraj Adam Jo Elatico (Wed Aug 01 2018 - 04:39:50 PDT)
- [AMBER] asking about PBRadii in MMPBSA an other else Setyanto Md (Wed Aug 01 2018 - 04:49:16 PDT)
- [AMBER] Multiple PDB files to a MDCRD file Alechania Misturini (Wed Aug 01 2018 - 06:58:26 PDT)
- Re: [AMBER] MCBP force constants Seibold, Steve Allan (Wed Aug 01 2018 - 08:18:14 PDT)
- [AMBER] Fwd: Issue with imploding structure during heating and equilibration David Stevens (Wed Aug 01 2018 - 10:45:46 PDT)
- [AMBER] GPUs Alexandra Carvalho (Wed Aug 01 2018 - 14:11:49 PDT)
- Re: [AMBER] Possible bug on addLJType command of Parmed Jason Swails (Wed Aug 01 2018 - 14:20:07 PDT)
- Re: [AMBER] very slow implicit simulation on GPU!!! Jason Swails (Wed Aug 01 2018 - 14:22:54 PDT)
- Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM Tyler Luchko (Lists) (Wed Aug 01 2018 - 15:55:25 PDT)
- [AMBER] Reproduce part of AMBER trajectory Supriyo Bhattacharya (Wed Aug 01 2018 - 16:36:03 PDT)
- [AMBER] Calculate protein energy from simulation trajectory Adam Jo Elatico (Thu Aug 02 2018 - 01:10:28 PDT)
- [AMBER] Velocity Format in AMBER BLEY Michael (Thu Aug 02 2018 - 06:58:24 PDT)
- [AMBER] System density decrease during accelerated MD: why? Nikolay N. Kuzmich (Thu Aug 02 2018 - 07:13:59 PDT)
- Re: [AMBER] QM/MM link atoms emanuele falbo (Thu Aug 02 2018 - 07:59:08 PDT)
- [AMBER] Free energy landscape on principal components Adam Jo Elatico (Thu Aug 02 2018 - 08:34:04 PDT)
- [AMBER] MCPB.py with G09 rev. B.01 Jinfeng Chen (Thu Aug 02 2018 - 18:26:49 PDT)
- [AMBER] COM pulling in direction Meng Wu (Fri Aug 03 2018 - 02:52:24 PDT)
- [AMBER] Amber16 Installation error Sushi Shilpa (Fri Aug 03 2018 - 03:46:33 PDT)
- Re: [AMBER] eCheminfo Oxford 3-7 Sep., Training and Innovation Course in Drug Design, bursary and early-bird deadline approaching quickly Thomas Exner (Fri Aug 03 2018 - 04:07:56 PDT)
- [AMBER] Error for Amber16 and Amber tools 17 installation maryam azimzadehirani (Fri Aug 03 2018 - 05:16:11 PDT)
- [AMBER] Solute-solvent hydrogen bond lifetime ATUL KUMAR (Fri Aug 03 2018 - 06:01:36 PDT)
- [AMBER] error_antechamber (QMMM: ERROR!) Atila Petrosian (Fri Aug 03 2018 - 07:11:30 PDT)
- [AMBER] Change in boxlength during memebrane simulation somdev pahari (Fri Aug 03 2018 - 07:59:19 PDT)
- [AMBER] error_antechamber (QMMM: ERROR!) Atila Petrosian (Fri Aug 03 2018 - 08:52:17 PDT)
- Re: [AMBER] Reading grid data from standard datafile I Lőrincz (Fri Aug 03 2018 - 10:35:38 PDT)
- [AMBER] counterions_automatic Antonio Amber Carlesso (Sun Aug 05 2018 - 08:56:50 PDT)
- [AMBER] Adding box dimension Simon Kit Sang Chu (Sun Aug 05 2018 - 09:31:19 PDT)
- [AMBER] Atom Types for carbons with unsaturated bond Vijay Achari (Mon Aug 06 2018 - 01:37:22 PDT)
- [AMBER] Parameters for non-standard residues Anuja Ware (Mon Aug 06 2018 - 02:49:13 PDT)
- [AMBER] RDCs in pmemd? Thomas Pochapsky (Mon Aug 06 2018 - 09:02:32 PDT)
- Re: [AMBER] Running a small minimization with amber 16 package Debarati DasGupta (Mon Aug 06 2018 - 14:38:36 PDT)
- [AMBER] .frcmod_file_generation Antonio Amber Carlesso (Tue Aug 07 2018 - 07:57:39 PDT)
- [AMBER] max# cpu's for sander, specify which gpu runs a job David Christopher Schröder (Tue Aug 07 2018 - 09:40:56 PDT)
- [AMBER] Restraints on a system Debarati DasGupta (Tue Aug 07 2018 - 14:15:06 PDT)
- [AMBER] problem with amber 16 giovanna rogati (Wed Aug 08 2018 - 01:29:38 PDT)
- [AMBER] number of interconversions from free energy landscape (FEL) plot Chetna Tyagi (Wed Aug 08 2018 - 05:54:17 PDT)
- [AMBER] checkmolecule.c John L. Kulp, Jr. (Wed Aug 08 2018 - 06:10:13 PDT)
- [AMBER] Speeding up sqm, PM6 vs AM1 for am1-bcc John L. Kulp, Jr. (Wed Aug 08 2018 - 06:13:14 PDT)
- [AMBER] Amber18 on NVIDIA Quadro Cards mish (Wed Aug 08 2018 - 08:51:02 PDT)
- [AMBER] Erreneous PMF Stefan Ivanov (Wed Aug 08 2018 - 23:21:14 PDT)
- [AMBER] how to install PTRAJ and CPPTRAJ Subrata Paul (Thu Aug 09 2018 - 00:17:30 PDT)
- [AMBER] Cpptraj not working Subrata Paul (Thu Aug 09 2018 - 03:38:53 PDT)
- [AMBER] mistake in source-code in egb.F90 Johannes Kalliauer (Thu Aug 09 2018 - 04:15:45 PDT)
- [AMBER] PrmtopError: Inconsistent charge definition for atom Santanu Santra (Thu Aug 09 2018 - 06:40:08 PDT)
- [AMBER] miRNA-mRNA structure / NAB Atila Petrosian (Thu Aug 09 2018 - 08:59:49 PDT)
- [AMBER] cpptraj / ambpdb only selected atoms / residues Simon Kit Sang Chu (Thu Aug 09 2018 - 09:04:36 PDT)
- [AMBER] X-mer analysis or statistics ? Marek Maly (Thu Aug 09 2018 - 16:49:29 PDT)
- [AMBER] Amber Installation: MPI Error Aravind Ravichandran (Fri Aug 10 2018 - 00:07:24 PDT)
- [AMBER] command not found Sushi Shilpa (Fri Aug 10 2018 - 04:47:41 PDT)
- [AMBER] How to use filter command to find the structures of high density during PCA analysis? Markowska (Fri Aug 10 2018 - 05:08:41 PDT)
- [AMBER] Research Programmers Positions Available João Ribeiro (Fri Aug 10 2018 - 11:35:23 PDT)
- [AMBER] sander.MPI running on only one node Leena Aggarwal (Sat Aug 11 2018 - 03:01:15 PDT)
- [AMBER] # of Coordinates Mismatch in PCA Robert Molt (Sat Aug 11 2018 - 22:04:35 PDT)
- [AMBER] Warning: DISABLING BOX in topology '<name>.pdb'! Dmitry Suplatov (Sun Aug 12 2018 - 04:04:19 PDT)
- [AMBER] alkyl chain unsaturated bond Vijay Achari (Sun Aug 12 2018 - 14:58:42 PDT)
- [AMBER] MMPBSA.PY 龚乾坤 (Sun Aug 12 2018 - 19:37:37 PDT)
- [AMBER] Can I calculate the domain-domain interaction energy using the MMPBSA.py tool? maryam azimzadehirani (Mon Aug 13 2018 - 03:35:43 PDT)
- [AMBER] amber18 and amazon aws Luca Codutti (Mon Aug 13 2018 - 08:37:44 PDT)
- [AMBER] A question about tleap 龚乾坤 (Tue Aug 14 2018 - 01:01:56 PDT)
- [AMBER] tleap_protein_preparation_general_rule Antonio Amber Carlesso (Tue Aug 14 2018 - 01:06:07 PDT)
- [AMBER] QM/MM Thermodynamic Integration emanuele (Tue Aug 14 2018 - 03:44:46 PDT)
- [AMBER] Problem with QMMM with Amber/Gaussian interface. Sadra Aghajani (Tue Aug 14 2018 - 20:53:47 PDT)
- [AMBER] HOW to type a free CYS molecule MinYuan (Wed Aug 15 2018 - 06:57:13 PDT)
- [AMBER] Multiple trajectory analysis with CPPTRAJ and getting output for each of them separately Luka Bilić (Thu Aug 16 2018 - 00:06:23 PDT)
- [AMBER] implement_revised_RNA_force_field_general rule? Antonio Amber Carlesso (Thu Aug 16 2018 - 01:57:47 PDT)
- [AMBER] cpptraj segmentation fault when using avgout in cluster Charo del Genio (Thu Aug 16 2018 - 03:55:11 PDT)
- [AMBER] AM1BCC challenge with atomic types recognition and convertion of .ac to .mol2 Sergey Samsonov (Thu Aug 16 2018 - 08:05:29 PDT)
- [AMBER] About calculating entropy in MM_PB/GBSA using mm_pbsa.pl 龚乾坤 (Fri Aug 17 2018 - 00:17:32 PDT)
- [AMBER] MMPBSA.PY 龚乾坤 (Fri Aug 17 2018 - 00:21:07 PDT)
- [AMBER] Where is the source code adjusting the size of the periodic boundary condition box in NPT ensemble ? jinfeng liu (Fri Aug 17 2018 - 01:15:40 PDT)
- [AMBER] Mutation Free Energy hosein geraili (Fri Aug 17 2018 - 03:28:22 PDT)
- [AMBER] TLEAP script Keiran Corbett (Fri Aug 17 2018 - 03:58:59 PDT)
- Re: [AMBER] The instructions of the .out file Zhonghua Xia (Fri Aug 17 2018 - 06:19:34 PDT)
- [AMBER] Error in Running heating in GPU enabled AMBER kuldeep singh (Fri Aug 17 2018 - 10:50:02 PDT)
- [AMBER] SCF convergence problems and write density matrix Anaid Flores (Fri Aug 17 2018 - 15:08:39 PDT)
- [AMBER] update to Amber18's pmemd.cuda code David A Case (Sat Aug 18 2018 - 06:08:35 PDT)
- [AMBER] How to convert QM parameters to AMBER force field parameters MinYuan (Sat Aug 18 2018 - 06:40:40 PDT)
- [AMBER] cpptraj and ptraj not installed Subrata Paul (Sun Aug 19 2018 - 04:49:54 PDT)
- [AMBER] Scripting Bash to tleap Keiran Corbett (Mon Aug 20 2018 - 02:39:32 PDT)
- [AMBER] metalParm2.xml or metalParm.xml Seibold, Steve Allan (Mon Aug 20 2018 - 08:47:27 PDT)
- [AMBER] How to calculate SASA for an arbitrary solvent Kasprzak, Wojciech (NIH/NCI) [C] (Mon Aug 20 2018 - 13:37:19 PDT)
- [AMBER] Umbrella sampling run error Rakesh Srivastava (Mon Aug 20 2018 - 21:43:37 PDT)
- [AMBER] ASMD for decrease in distance between ligand and catalytic site sangita kachhap (Tue Aug 21 2018 - 03:42:04 PDT)
- [AMBER] H-bond between the substrate molecule and protein in the MD traj Meng Wu (Wed Aug 22 2018 - 01:18:13 PDT)
- [AMBER] Umbrella sampling rst file error M RCC (Wed Aug 22 2018 - 12:02:38 PDT)
- [AMBER] restraintmask input setup Lod King (Wed Aug 22 2018 - 18:26:43 PDT)
- [AMBER] Need help regarding Lifetime Curve of Hydrogen bond analysis Bharat Manna (Wed Aug 22 2018 - 22:32:25 PDT)
- [AMBER] Problems with constant pH production step Helena Damtoft Tjørnelund (Thu Aug 23 2018 - 01:18:27 PDT)
- [AMBER] Need help regarding calculation of Coordination number from RDF Profile Bharat Manna (Fri Aug 24 2018 - 03:21:02 PDT)
- [AMBER] Thank you Tai Tze Hong (Fri Aug 24 2018 - 19:10:56 PDT)
- [AMBER] Amber18 error: an illegal memory access was encountered launching kernel kNLSkinTest 李耀 (Sat Aug 25 2018 - 06:22:32 PDT)
- [AMBER] NCSU_SMD for protein-ligand complex pulling M RCC (Sat Aug 25 2018 - 08:15:08 PDT)
- [AMBER] MG Coordination System: Nonbonded Cationic Dummy Model Aravind Ravichandran (Sun Aug 26 2018 - 22:57:15 PDT)
- [AMBER] GIST calculation M RCC (Sun Aug 26 2018 - 23:32:07 PDT)
- [AMBER] Amber 18 targeted MD errorin input::atommask.f::pop_evalstack stack underflow 李耀 (Mon Aug 27 2018 - 00:24:27 PDT)
- [AMBER] Error: System density has likely changed M RCC (Mon Aug 27 2018 - 02:40:07 PDT)
- [AMBER] A part of protein molecule moving out of the box Sanjib Paul (Sun Aug 26 2018 - 23:16:36 PDT)
- [AMBER] Best Methods Leon Hardy (Mon Aug 27 2018 - 06:01:58 PDT)
- [AMBER] Are there any forcefield present of bio-organic polyphosphate in AMBER ?? Saikat Pal (Mon Aug 27 2018 - 08:10:06 PDT)
- [AMBER] Amber16 installation error Renato Araujo (Mon Aug 27 2018 - 16:50:44 PDT)
- [AMBER] Protein_ligand_preparation_general_rule Antonio Amber Carlesso (Tue Aug 28 2018 - 05:59:28 PDT)
- [AMBER] R.E.D. Server is down Anthony Bogetti (Tue Aug 28 2018 - 10:13:00 PDT)
- [AMBER] I want to calculate electrostatic and van der Waals energy Saikat Pal (Wed Aug 29 2018 - 03:44:03 PDT)
- [AMBER] How to define the speed of pulling ligand in SMD? M RCC (Wed Aug 29 2018 - 06:39:41 PDT)
- [AMBER] RED SERVER DOWN Corinn Durham (Wed Aug 29 2018 - 09:44:23 PDT)
- [AMBER] The R.E.D. server is down Bellesis, Andrew G (Wed Aug 29 2018 - 09:36:01 PDT)
- [AMBER] Heating error in complex sandeep singh (Wed Aug 29 2018 - 12:52:45 PDT)
- [AMBER] How to use cpptraj to wrap protein Yang, Tianyi (Wed Aug 29 2018 - 17:12:19 PDT)
- [AMBER] Steered molecular dynamics..... pulling force is not decreasing M RCC (Thu Aug 30 2018 - 03:01:51 PDT)
- [AMBER] CPPTRAJ issues parsing NETCDF RST file Gustaf Olsson (Thu Aug 30 2018 - 05:20:09 PDT)
- [AMBER] Normal mode calculation on a truncated system Marko Tomin (Thu Aug 30 2018 - 08:13:33 PDT)
- [AMBER] minimization restrain in Qm-mm/MD Thakur, Abhishek (Thu Aug 30 2018 - 12:05:50 PDT)
- [AMBER] Distance HH TIP3P David Sáez (Fri Aug 31 2018 - 12:55:49 PDT)
- Last message date: Fri Aug 31 2018 - 17:00:02 PDT
- Archived on: Wed Apr 17 2024 - 05:55:35 PDT
