Amber Archive Jun 2020 by thread
- Re: [AMBER] AMBER Digest, Vol 3019, Issue 1 Gao J (Sun May 31 2020 - 19:05:05 PDT)
- Re: [AMBER] igb for non-aqueous solvent? David A Case (Mon Jun 01 2020 - 07:00:00 PDT)
- Re: [AMBER] COM position Daniel Roe (Mon Jun 01 2020 - 12:26:00 PDT)
- Re: [AMBER] AMBER Digest, Vol 3020, Issue 1 Gao J (Mon Jun 01 2020 - 18:17:05 PDT)
- [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? Amanda Buyan (Tue Jun 02 2020 - 20:54:59 PDT)
- [AMBER] suggestion for generation of prmtop and inpcrd file at different pH Vikram Dalal (Wed Jun 03 2020 - 14:04:52 PDT)
- [AMBER] MC barostat Debarati DasGupta (Thu Jun 04 2020 - 07:25:10 PDT)
- [AMBER] help with building an amino acid based surfactant molecule Billiot, Eugene (Thu Jun 04 2020 - 08:01:18 PDT)
- [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? Erdem Yeler (Thu Jun 04 2020 - 08:34:26 PDT)
- [AMBER] protein on gold surface Raik Grünberg (Thu Jun 04 2020 - 11:26:15 PDT)
- [AMBER] using PLUMED with pmemd.cuda? Amanda Buyan (Thu Jun 04 2020 - 19:48:31 PDT)
- [AMBER] ambertools19 Renato Araujo (Fri Jun 05 2020 - 18:39:28 PDT)
- [AMBER] Converting Amber trajectory NetCDF file to Desmond readable Nada Afiva (Sun Jun 07 2020 - 03:38:11 PDT)
- [AMBER] MM/PBSA and GBSA fails Thakur, Abhishek (Sun Jun 07 2020 - 16:02:48 PDT)
- Re: [AMBER] clustering parameter files Ranim Maaieh (Sun Jun 07 2020 - 16:43:21 PDT)
- [AMBER] Gold in PARMCHK.dat Antechamber. anirudh mantri (Mon Jun 08 2020 - 01:59:25 PDT)
- [AMBER] tleap splitting the lipid zhiyi wu (Mon Jun 08 2020 - 02:58:22 PDT)
- [AMBER] MCPB.py problem to make step 1 works Barak Alnami (Mon Jun 08 2020 - 04:19:56 PDT)
- [AMBER] error installation mpi Renato Araujo (Mon Jun 08 2020 - 07:18:21 PDT)
- [AMBER] residue renumbering in trajectory files Ranim Maaieh (Mon Jun 08 2020 - 13:40:51 PDT)
- [AMBER] Individual water lifetimes within a distance cutoff? Kenneth Huang (Mon Jun 08 2020 - 16:18:17 PDT)
- [AMBER] steered MD with restraints on a selection Baker, Joseph (Mon Jun 08 2020 - 19:44:03 PDT)
- [AMBER] Charge parameters in GAFF Stefan Menzel (Mon Jun 08 2020 - 22:52:45 PDT)
- [AMBER] Parameters for sphingomyelin Jianguo Li (Tue Jun 09 2020 - 02:11:55 PDT)
- [AMBER] Steered MD with highly charged species Delwakkada Liyanage, Senal Dinuka (Tue Jun 09 2020 - 08:55:06 PDT)
- [AMBER] Xleap - disappearance of selection when trying to relax selection Billiot, Eugene (Tue Jun 09 2020 - 11:18:43 PDT)
- [AMBER] tleap - extract ion molecules and save it as pdb HOCHEOL LIM (Tue Jun 09 2020 - 16:14:02 PDT)
- [AMBER] atom type in a substituted pyrimidine Sofia Vasilakaki (Wed Jun 10 2020 - 00:10:50 PDT)
- [AMBER] tiMerge error with ff19SB HOCHEOL LIM (Wed Jun 10 2020 - 01:30:47 PDT)
- [AMBER] Python related problem running MMPBSA.py.MPI Casalini Tommaso (Wed Jun 10 2020 - 07:36:18 PDT)
- [AMBER] Parameters for Implicit Membrane in MMPBSA.py Li,Haoxi (Wed Jun 10 2020 - 12:08:14 PDT)
- [AMBER] Setting custom parameters for CpHMD simulations Jade Shi (Wed Jun 10 2020 - 15:38:59 PDT)
- [AMBER] Cellulose-lignin interaction Pinky Mazumder (Wed Jun 10 2020 - 21:25:36 PDT)
- [AMBER] Amber parameters for sphingomyelin Jianguo Li (Thu Jun 11 2020 - 01:00:14 PDT)
- Re: [AMBER] amber20 output header Baker, Joseph (Thu Jun 11 2020 - 06:47:05 PDT)
- [AMBER] GLYCAM and scaling of electrostatic and nonbonded interactions Jordi Bujons (Thu Jun 11 2020 - 09:17:29 PDT)
- [AMBER] Epot value in Amber TI output Eric Chen (Fri Jun 12 2020 - 10:24:20 PDT)
- [AMBER] Error with MMPBSA - per residue decomposition Prasanth G, Research Scholar (Sat Jun 13 2020 - 00:51:15 PDT)
- [AMBER] adding a new covalently-linked ligand abhisek Mondal (Sat Jun 13 2020 - 03:39:57 PDT)
- [AMBER] question 闫芳芳 (Sun Jun 14 2020 - 07:08:52 PDT)
- [AMBER] planarity issue during md Sofia Vasilakaki (Mon Jun 15 2020 - 00:23:42 PDT)
- [AMBER] MMPBSA.py error Oanh Thuy Ngoc Tran (Mon Jun 15 2020 - 14:57:20 PDT)
- [AMBER] mmgbsa question MYRIAN TORRES RICO (Tue Jun 16 2020 - 02:16:37 PDT)
- [AMBER] generating parameters for methane angad sharma (Tue Jun 16 2020 - 02:37:55 PDT)
- [AMBER] OPLS-AA/M force field Rosellen, Martin (Tue Jun 16 2020 - 03:35:36 PDT)
- [AMBER] Error while using Parmchk2 Sodiq Waheed (Tue Jun 16 2020 - 09:51:22 PDT)
- [AMBER] Adiabatic Mapping Info Request Bowleg, Jerrano (Tue Jun 16 2020 - 10:02:23 PDT)
- [AMBER] Average structure of production run Sruthi Sudhakar (Tue Jun 16 2020 - 10:26:44 PDT)
- [AMBER] how to combine several stripped trajectory netcdf files Nada Afiva (Tue Jun 16 2020 - 20:09:05 PDT)
- [AMBER] junmaozb.foxmail.com 毛君 (Tue Jun 16 2020 - 21:11:16 PDT)
- [AMBER] About two amber REMD simulation problems 毛君 (Wed Jun 17 2020 - 00:26:42 PDT)
- [AMBER] Error: Could not determine format of topology Jag Silwal (Wed Jun 17 2020 - 06:36:26 PDT)
- [AMBER] tleap PDB file in ORCA Benedikt Flöser (Thu Jun 18 2020 - 00:22:46 PDT)
- [AMBER] error: installing amber18 on MacOS gaohanlu (Thu Jun 18 2020 - 07:29:58 PDT)
- [AMBER] Hoogsteen H-bond Jisha B (Fri Jun 19 2020 - 22:20:58 PDT)
- [AMBER] Cluster analysis: the result was strange Nada Afiva (Sat Jun 20 2020 - 01:57:48 PDT)
- [AMBER] Incompatibility of coordinate file with topology after minimization Houcemeddine Othman (Sat Jun 20 2020 - 06:16:13 PDT)
- [AMBER] Tutorials unavailable Sruthi Sudhakar (Sat Jun 20 2020 - 08:33:32 PDT)
- [AMBER] How to install Ambertools 20 using Cygwin and CMake on windows 7? Ibrahim Mohamed (Sat Jun 20 2020 - 14:32:32 PDT)
- [AMBER] How to use Ambertools20 parmed.py? Ibrahim Mohamed (Sun Jun 21 2020 - 00:53:49 PDT)
- [AMBER] pH-REMD error Kolattukudy P. Santo (Sun Jun 21 2020 - 09:35:12 PDT)
- Re: [AMBER] contents of AMBER Digest, Vol 3040, Issue 1, message 1 gaohanlu (Sun Jun 21 2020 - 18:59:39 PDT)
- [AMBER] GPU error in the heating step of PMEMD.CUDA rosaester.forgione.unina.it (Mon Jun 22 2020 - 04:05:51 PDT)
- [AMBER] RAMD implementation in the new Amber 20 package Richter, Stefan (Mon Jun 22 2020 - 08:12:36 PDT)
- [AMBER] generating methane parameters angad sharma (Mon Jun 22 2020 - 08:56:55 PDT)
- [AMBER] nmropt vs infe Gard Nelson (Mon Jun 22 2020 - 14:56:17 PDT)
- [AMBER] Regarding Amber 20 License Suchetana Gupta (Tue Jun 23 2020 - 03:09:47 PDT)
- [AMBER] Truncated NMODE calculation with MMPBSA.py.MPI Wan, Shunzhou (Tue Jun 23 2020 - 09:34:57 PDT)
- [AMBER] Minimization erro Renato Araujo (Tue Jun 23 2020 - 12:05:59 PDT)
- [AMBER] Steered MD in AMBER using GPU Souvik Dey (Tue Jun 23 2020 - 19:30:02 PDT)
- [AMBER] Amber installation error ankita mehta (Wed Jun 24 2020 - 06:41:57 PDT)
- Re: [AMBER] nativecontacts Daniel Roe (Wed Jun 24 2020 - 08:52:56 PDT)
- Re: [AMBER] How to get the eigenvalues from PCA Daniel Roe (Wed Jun 24 2020 - 08:58:00 PDT)
- Re: [AMBER] Energy values from mdout files (excluding solvent molecules) Daniel Roe (Wed Jun 24 2020 - 09:04:15 PDT)
- Re: [AMBER] Problem in calculating pairwise interaction with CPPTRAJ Daniel Roe (Wed Jun 24 2020 - 09:07:22 PDT)
- Re: [AMBER] CPPtraj PCA error Daniel Roe (Wed Jun 24 2020 - 09:13:47 PDT)
- [AMBER] Amber20 update failure on RHEL7/CentOS7 Peng Wang (Wed Jun 24 2020 - 11:14:29 PDT)
- [AMBER] restraint 10 kcal/mol Debarati DasGupta (Wed Jun 24 2020 - 11:35:38 PDT)
- [AMBER] pmemd.cuda for heating and equilibration? Nada Afiva (Wed Jun 24 2020 - 18:27:34 PDT)
- [AMBER] Problems with Make install Amber 18 Joanna Michelle E. Chua (Wed Jun 24 2020 - 20:26:44 PDT)
- [AMBER] Compiling Amber18 AmberTools19 on CentOS 7 Gustaf Olsson (Thu Jun 25 2020 - 02:02:03 PDT)
- [AMBER] ERROR:nfft1 must be in the range of 6 to 512! Rinsha Chk (Thu Jun 25 2020 - 02:28:26 PDT)
- [AMBER] bulding a monosaccharide with N-acetylation rosaester.forgione.unina.it (Thu Jun 25 2020 - 06:34:36 PDT)
- [AMBER] nastruct command query Athena N (Thu Jun 25 2020 - 12:25:31 PDT)
- [AMBER] Help GPU support information Renato Araujo (Thu Jun 25 2020 - 13:45:10 PDT)
- [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies Nada Afiva (Thu Jun 25 2020 - 15:08:24 PDT)
- [AMBER] generating methane parameters angad sharma (Fri Jun 26 2020 - 00:28:56 PDT)
- [AMBER] Error in Antechamber Shreeramesh (Fri Jun 26 2020 - 07:38:55 PDT)
- [AMBER] Problems with RMSF calculations kartik.lakshmi.gmail.com (Fri Jun 26 2020 - 11:48:47 PDT)
- [AMBER] restraining surfactant tails in micelles intact Billiot, Eugene (Fri Jun 26 2020 - 12:55:41 PDT)
- [AMBER] Ligand movement w.r.t protein backbone Prasanth G, Research Scholar (Sat Jun 27 2020 - 02:29:21 PDT)
- [AMBER] Error Message while using GPU Sivanandam Magudeeswaran (Sat Jun 27 2020 - 22:53:34 PDT)
- [AMBER] Is there a method that can calculate the angle between two planes? xmgign.126.com (Sun Jun 28 2020 - 02:59:25 PDT)
- [AMBER] Steered Molecular Dynamics Simulation Vishal Singh (Sun Jun 28 2020 - 11:55:13 PDT)
- [AMBER] ff14SBonlysc + OPC3 Fabian Glaser (Mon Jun 29 2020 - 05:40:11 PDT)
- [AMBER] error message create parameters Renato Araujo (Mon Jun 29 2020 - 05:49:42 PDT)
- [AMBER] Error in Installing Amber 20 on GPU Suchetana Gupta (Mon Jun 29 2020 - 05:55:25 PDT)
- [AMBER] CPPTRAJ: Time Correlation Function (TCF) emanuele falbo (Mon Jun 29 2020 - 06:26:06 PDT)
- [AMBER] centos 7 install Ambertools20 error, final link failed: Bad value He DC (Mon Jun 29 2020 - 07:50:32 PDT)
- [AMBER] pmemd.MPI and minization trajectories Seibold, Steve Allan (Mon Jun 29 2020 - 08:09:07 PDT)
- [AMBER] An Error with MMPBSA.py in AmberTools 17 Ibrahim Mohamed (Mon Jun 29 2020 - 15:23:34 PDT)
- [AMBER] add NO3- ions 费俊文 (Mon Jun 29 2020 - 23:29:48 PDT)
- [AMBER] "Does not have a type" error in tleap Jatin Kashyap (Tue Jun 30 2020 - 00:00:30 PDT)
- [AMBER] Zwitter ionic form of a residue Sunita Patel (Tue Jun 30 2020 - 04:20:44 PDT)
- [AMBER] interaction entropy calculation Hector A. Baldoni (Tue Jun 30 2020 - 12:41:22 PDT)
- Last message date: Tue Jun 30 2020 - 13:30:03 PDT
- Archived on: Sun Nov 24 2024 - 05:56:11 PST
