Amber Archive Mar 2017 by thread
- [AMBER] Holes/bubbles in water during NVT (fix atoms) Neha Gandhi (Tue Feb 28 2017 - 23:35:53 PST)
- Re: [AMBER] MM energy contributions of atoms in a molecule Bruno Falcone (Wed Mar 01 2017 - 06:43:33 PST)
- [AMBER] pmemd.cuda and taskset on K80 Diego Gomes (Wed Mar 01 2017 - 08:10:24 PST)
- Re: [AMBER] Methods to count the different species Daniel Roe (Wed Mar 01 2017 - 08:13:56 PST)
- Re: [AMBER] cpptraj: dihcovar and projection need trajin to work properly? Daniel Roe (Wed Mar 01 2017 - 08:26:10 PST)
- [AMBER] Distance between benzene ring of one molecule and centre of mass of other molecule konda003 . (Wed Mar 01 2017 - 13:54:53 PST)
- Re: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue Junmei Wang (Thu Mar 02 2017 - 08:13:04 PST)
- [AMBER] REMD processor number Andreas Tosstorff (Thu Mar 02 2017 - 09:04:47 PST)
- [AMBER] H-bonds matrix giulia palermo (Thu Mar 02 2017 - 09:26:11 PST)
- [AMBER] 1-4 VDW and 1-4 EEL Energy Components in mm-gbsa Atila Petrosian (Fri Mar 03 2017 - 01:01:24 PST)
- Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Eric Lang (Fri Mar 03 2017 - 06:33:24 PST)
- Re: [AMBER] When does cpptraj use information from the original pdb file? Daniel Roe (Fri Mar 03 2017 - 07:02:11 PST)
- [AMBER] How to make rst file by using ptraj Vishal Nemaysh (Sat Mar 04 2017 - 07:24:09 PST)
- [AMBER] Amber 16 MD simulation Problems 杨满意 (Sat Mar 04 2017 - 20:11:03 PST)
- [AMBER] dUMP parameters Mrinal Arandhara (Sun Mar 05 2017 - 07:20:35 PST)
- [AMBER] prepare prepin file from MCPB results Abhilash J (Mon Mar 06 2017 - 00:34:14 PST)
- [AMBER] reg "rel delta G binding computation using TIMD" Smriti Sharma (Mon Mar 06 2017 - 02:12:32 PST)
- Re: [AMBER] rdf_with_center_in_cpptraj_16 Daniel Roe (Mon Mar 06 2017 - 05:21:05 PST)
- [AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type. Nikolay N. Kuzmich (Mon Mar 06 2017 - 09:16:33 PST)
- [AMBER] Query regarding extension of Molecular dynamics simulation from 50ns to 100ns Lovika Mittal (Mon Mar 06 2017 - 20:26:12 PST)
- Re: [AMBER] problems with heating Alicia Merlino (Mon Mar 06 2017 - 20:44:37 PST)
- [AMBER] error explicit solvent CpHMD production run EGIDEA PUTI DEVINA (Mon Mar 06 2017 - 22:05:05 PST)
- [AMBER] how to use TImerge to do TI simulations Sowmya Indrakumar (Tue Mar 07 2017 - 06:55:53 PST)
- [AMBER] Application of external electric field with QM/MM in Amber Kshatresh Dutta Dubey (Tue Mar 07 2017 - 12:47:15 PST)
- [AMBER] Error in Cobalt parameters in CO-METHYLCOBALAMIN with MCPB.py Abhilash J (Wed Mar 08 2017 - 01:45:50 PST)
- [AMBER] OPEN SHELL MOLECULES Stellamaris Sotomayor Burneo (Wed Mar 08 2017 - 14:19:29 PST)
- [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered kungking Hanpaibool (Thu Mar 09 2017 - 01:59:04 PST)
- [AMBER] Accelerated MD Beale, John (Thu Mar 09 2017 - 02:51:12 PST)
- [AMBER] Generate psf file for chamber Shanghaitech University WuMeng (Thu Mar 09 2017 - 02:56:23 PST)
- [AMBER] AmberTools compilation Tom Dreyfus (Thu Mar 09 2017 - 05:04:44 PST)
- [AMBER] anionic Ser ? Michael Shokhen (Thu Mar 09 2017 - 05:23:25 PST)
- Re: [AMBER] Distance constraint Thakur, Abhishek (Thu Mar 09 2017 - 07:53:35 PST)
- [AMBER] hydophobic Thakur, Abhishek (Thu Mar 09 2017 - 12:28:58 PST)
- [AMBER] Question about the implementation of the Steered MD abdennour braka (Thu Mar 09 2017 - 23:26:36 PST)
- [AMBER] Problem in configuring+compiling cpptraj development version with Sander compiled with AmberTools16 SHAILESH KUMAR (Fri Mar 10 2017 - 02:50:34 PST)
- [AMBER] Boron's parameter jinfeng liu (Fri Mar 10 2017 - 04:35:54 PST)
- [AMBER] Potential on QM atoms - details about cutoff Elisa Pieri (Fri Mar 10 2017 - 07:13:19 PST)
- [AMBER] maximum distance for protein-ligand interactions in MM/GBSA Thomas Evangelidis (Sat Mar 11 2017 - 07:34:05 PST)
- [AMBER] Memory footprint goes on increasing: pytraj traj.iterchunk used, distances between bonds calculation SHAILESH KUMAR (Sun Mar 12 2017 - 13:17:30 PDT)
- [AMBER] How to use MCPB.py to generate OH parameters Alice Zeng (Sun Mar 12 2017 - 21:25:36 PDT)
- [AMBER] Unperturbed charge of the unit is not zero Eugene Cha (Mon Mar 13 2017 - 07:09:29 PDT)
- Re: [AMBER] Error for reading the amber rst file David Case (Mon Mar 13 2017 - 08:02:23 PDT)
- [AMBER] Installing AmberTools16 - ld library issue Giannis Gl (Mon Mar 13 2017 - 10:32:43 PDT)
- [AMBER] Installing AmberTools16 - Sierra MacOs Giannis Gl (Mon Mar 13 2017 - 12:10:49 PDT)
- [AMBER] Discrepancy between gaff.dat and leaprc.gaff hybridization Maral Aminpour (Mon Mar 13 2017 - 13:17:52 PDT)
- [AMBER] A problem about the frcmod produced by ParmChk JinpengYang (Mon Mar 13 2017 - 18:07:16 PDT)
- [AMBER] Error when running QM/MM MD for actinide and lanthanide system by amber 鲁俊波 (Mon Mar 13 2017 - 19:22:19 PDT)
- [AMBER] problem with solvation Maryam Hamzehee (Tue Mar 14 2017 - 00:21:18 PDT)
- [AMBER] Intel Xeon Phi 7120P Sofia Vasilakaki (Tue Mar 14 2017 - 07:26:43 PDT)
- [AMBER] prepc vs prepi Yong Duan (Tue Mar 14 2017 - 12:36:07 PDT)
- [AMBER] How to generate inputfile 杨满意 (Tue Mar 14 2017 - 20:37:08 PDT)
- [AMBER] How to get parmed.py script? Sowmya Indrakumar (Wed Mar 15 2017 - 02:31:05 PDT)
- [AMBER] Help with reconstructing pH-based mdcrd (trajectory) files Ingvild Isaksen (Wed Mar 15 2017 - 05:13:32 PDT)
- [AMBER] Problems in using Parmchk2 杨满意 (Wed Mar 15 2017 - 07:08:58 PDT)
- [AMBER] About PCA with cpptraj Elvis Martis (Wed Mar 15 2017 - 09:34:00 PDT)
- [AMBER] Issues running TI simulations Sowmya Indrakumar (Thu Mar 16 2017 - 02:10:04 PDT)
- [AMBER] distance calculations - Protein-RNA Sidhu, Khushwant (Dr.) (Thu Mar 16 2017 - 03:36:26 PDT)
- [AMBER] Generating topology from Gaussian 09 Vijay Achari (Thu Mar 16 2017 - 05:08:25 PDT)
- [AMBER] converting trajectory file from NAMD to AMBER Oleksii Zdorevskyi (Thu Mar 16 2017 - 07:43:12 PDT)
- [AMBER] timerge question Adrian Roitberg (Thu Mar 16 2017 - 07:48:09 PDT)
- [AMBER] RE : suitable basis sets for QM/MM Budhathoki, Dipesh (Thu Mar 16 2017 - 10:49:00 PDT)
- Re: [AMBER] How to generate inputfile (???) David Poole (Thu Mar 16 2017 - 12:08:50 PDT)
- [AMBER] Generate DNA sequence with a mismatch diego.soler.uam.es (Fri Mar 17 2017 - 04:39:43 PDT)
- [AMBER] MM/GBSA residual decomposition issue Bharatham, Nagakumar (Fri Mar 17 2017 - 05:29:57 PDT)
- [AMBER] issues generating parameter files for the ligands- FEW Sowmya Indrakumar (Fri Mar 17 2017 - 08:13:03 PDT)
- [AMBER] MM/GBSA residual decomposition issue nagakumarb.ccamp.res.in (Fri Mar 17 2017 - 08:13:20 PDT)
- [AMBER] C/Fortran compilation Kanin Wichapong (Fri Mar 17 2017 - 08:42:27 PDT)
- [AMBER] NMODE ERROR MESSAGE konda003 . (Fri Mar 17 2017 - 09:02:46 PDT)
- [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit Vasantha Kumar (Fri Mar 17 2017 - 23:33:42 PDT)
- [AMBER] 2D rms plot doubt Mary Varughese (Sat Mar 18 2017 - 02:56:00 PDT)
- [AMBER] pmemd.MPI error on lonestar5 super comp. Miguel Rivera (Sun Mar 19 2017 - 15:48:00 PDT)
- [AMBER] Issue regarding ligand parameterization Nirupma Singh (Sun Mar 19 2017 - 22:55:18 PDT)
- [AMBER] install AMBER16 GTX480 Kanin Wichapong (Mon Mar 20 2017 - 06:46:54 PDT)
- [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16? paul (Mon Mar 20 2017 - 07:02:10 PDT)
- [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16? paul (Mon Mar 20 2017 - 07:12:48 PDT)
- [AMBER] Antechamber Error luca maggi (Mon Mar 20 2017 - 23:56:51 PDT)
- [AMBER] Issue generating parameter files - FEW Sowmya Indrakumar (Tue Mar 21 2017 - 08:06:10 PDT)
- [AMBER] help in RDF Robin Jain (Tue Mar 21 2017 - 08:19:44 PDT)
- [AMBER] Questions about Amber TI tutorial Sadegh Faramarzi Ganjabad (Tue Mar 21 2017 - 12:50:28 PDT)
- [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Scott Brozell (Tue Mar 21 2017 - 12:52:34 PDT)
- [AMBER] Select specific frames within cpptraj? Kenneth Huang (Tue Mar 21 2017 - 13:03:03 PDT)
- Re: [AMBER] Nmode using MMPBSA.py konda003 . (Tue Mar 21 2017 - 14:06:36 PDT)
- [AMBER] Error Importing pytraj to Python 2.7 Program Samuel Bowerman (Tue Mar 21 2017 - 14:20:40 PDT)
- [AMBER] unable to solvate a polymer Jon Mujika (Tue Mar 21 2017 - 16:00:19 PDT)
- [AMBER] Difficulty using noshakemask in Amber15 Chase Zagorec-Marks (Tue Mar 21 2017 - 16:43:03 PDT)
- [AMBER] Problem with keyboard in xleap Miguel Garavís (Wed Mar 22 2017 - 03:59:30 PDT)
- [AMBER] CpHMD: how is the charged system treated? Elisa Pieri (Wed Mar 22 2017 - 06:33:30 PDT)
- [AMBER] 来自zengxitao的邮件 zengxitao (Wed Mar 22 2017 - 10:28:16 PDT)
- [AMBER] AWS GPU node crashes with AMBER 16 Arnoult, Eric [JRDUS] (Wed Mar 22 2017 - 10:35:11 PDT)
- [AMBER] Chamber error; No NONBONDED Sadegh Faramarzi Ganjabad (Wed Mar 22 2017 - 11:34:47 PDT)
- [AMBER] Count number of water molecules in minor groove of DNA The Cromicus Productions (Wed Mar 22 2017 - 12:33:02 PDT)
- [AMBER] DU issue with Antechamber Abhilash J (Wed Mar 22 2017 - 21:21:37 PDT)
- [AMBER] Why molecular dynamics simulation was stopped without giving any error Garima Singh (Wed Mar 22 2017 - 23:36:01 PDT)
- [AMBER] cpptraj distance between centroid of a ring and an atom Neha Gandhi (Thu Mar 23 2017 - 00:41:54 PDT)
- [AMBER] How to perform Newton-Raphson minimization to protein 巩梦雪 (Thu Mar 23 2017 - 05:22:59 PDT)
- [AMBER] 发自刘兰茹的邮件 刘兰茹 (Fri Mar 24 2017 - 01:42:12 PDT)
- [AMBER] residue contribution for covalent inhibitor nagakumarb.ccamp.res.in (Fri Mar 24 2017 - 06:54:34 PDT)
- [AMBER] renumber residues Thakur, Abhishek (Fri Mar 24 2017 - 07:15:15 PDT)
- [AMBER] Restraint on Z-projection of a distance Chitrak Gupta (Fri Mar 24 2017 - 11:44:53 PDT)
- [AMBER] Installation issue George Tzotzos (Sat Mar 25 2017 - 05:37:03 PDT)
- [AMBER] Force/energy vs extension curve in steered MD Ramin Salimi (Sat Mar 25 2017 - 10:02:22 PDT)
- [AMBER] Force/Energy vs extension curve from Steered MD Ramin Salimi (Sat Mar 25 2017 - 10:36:15 PDT)
- [AMBER] Force/Energy vs extension curve from Steered MD Ramin Salimi (Sat Mar 25 2017 - 10:50:05 PDT)
- [AMBER] restarting Amber calculations gives abnormal structures Sadegh Faramarzi Ganjabad (Sat Mar 25 2017 - 20:53:09 PDT)
- [AMBER] Thermodynamic integration simulations issues Szymon Żaczek (Sun Mar 26 2017 - 13:02:04 PDT)
- [AMBER] surf cpptraj non-standard residue Andreas Tosstorff (Mon Mar 27 2017 - 05:29:01 PDT)
- [AMBER] FEW- issues generating parameter files for MD Sowmya Indrakumar (Mon Mar 27 2017 - 06:57:49 PDT)
- Re: [AMBER-Developers] web site inaccessible? David Case (Mon Mar 27 2017 - 07:31:14 PDT)
- [AMBER] water bridge Ming Tang (Tue Mar 28 2017 - 02:24:20 PDT)
- [AMBER] RDF plot Sowmya Indrakumar (Tue Mar 28 2017 - 03:35:39 PDT)
- [AMBER] Linkage problem in branched oligosaccharide Manju Sah (Tue Mar 28 2017 - 05:36:34 PDT)
- Re: [AMBER] Question about the propagation of error in MM/PBSA binding free energy calculation. Adrian Roitberg (Tue Mar 28 2017 - 10:11:17 PDT)
- [AMBER] Preparation of ligand enantiomers George Tzotzos (Tue Mar 28 2017 - 10:14:45 PDT)
- [AMBER] what hardware is required for gou peer-ro-peer an how imporant is gpu-to-gpu nvlink Chris Neale (Tue Mar 28 2017 - 17:38:22 PDT)
- [AMBER] Error: FATAL: Atom .R<ZN 2>.A<ZN 1> does not have a type. Aishani Prem (Tue Mar 28 2017 - 18:22:06 PDT)
- [AMBER] Cpptraj problems 杨满意 (Tue Mar 28 2017 - 20:43:52 PDT)
- [AMBER] Split a Large trajectory into smaller trajectory Vishal Nemaysh (Tue Mar 28 2017 - 21:30:33 PDT)
- [AMBER] Oligosaccharide linkage breaking problem during Solvent minimization Manju Sah (Wed Mar 29 2017 - 02:53:19 PDT)
- [AMBER] Dimer trajectory analysis Andreas Tosstorff (Wed Mar 29 2017 - 09:34:23 PDT)
- [AMBER] constraint residues while enhanced sampling simulation Kat G (Wed Mar 29 2017 - 13:40:43 PDT)
- [AMBER] Questions about MCPB.py Mingyuan_xu (Wed Mar 29 2017 - 18:57:03 PDT)
- [AMBER] autoimage for a protein filament Baker, Joseph (Wed Mar 29 2017 - 19:10:08 PDT)
- [AMBER] Installing Amber14 and AmberTools15 Error Erma Fatiha Muhammad (Wed Mar 29 2017 - 19:59:11 PDT)
- [AMBER] Water molecules show three bonds in VMD 吴萌 (Thu Mar 30 2017 - 04:04:57 PDT)
- [AMBER] Amber Mailing List problem George Tzotzos (Thu Mar 30 2017 - 06:59:43 PDT)
- [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphälinger (Thu Mar 30 2017 - 07:57:04 PDT)
- [AMBER] coordinates in restraint mast Thomas Evangelidis (Fri Mar 31 2017 - 06:13:37 PDT)
- [AMBER] Issues Regaring the PDB files from Trajectory frames Ramin Salimi (Fri Mar 31 2017 - 14:23:52 PDT)
- Last message date: Fri Mar 31 2017 - 16:30:03 PDT
- Archived on: Wed Dec 25 2024 - 05:55:29 PST
