Amber Archive Apr 2017 by thread
- [AMBER] How to perform good quality local optimization with Sander danil kutov (Sat Apr 01 2017 - 00:48:50 PDT)
- Re: [AMBER] Linkage problem in branched oligosaccharide Manju Sah (Sat Apr 01 2017 - 03:10:13 PDT)
- Re: [AMBER] coordinates in restraint mast Thomas Evangelidis (Sun Apr 02 2017 - 09:25:48 PDT)
- Re: [AMBER] restarting Amber calculations gives abnormal structures Sadegh Faramarzi Ganjabad (Sun Apr 02 2017 - 23:28:02 PDT)
- [AMBER] mmpbsa - stability calculation Mary Varughese (Mon Apr 03 2017 - 00:12:32 PDT)
- [AMBER] placing water at specified coordinates with tleap Thomas Evangelidis (Mon Apr 03 2017 - 08:14:51 PDT)
- [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Ramin Salimi (Mon Apr 03 2017 - 18:02:46 PDT)
- [AMBER] 3 GPUs ? Chris Neale (Mon Apr 03 2017 - 19:43:01 PDT)
- Re: [AMBER] distance calculations - Protein-RNA Sidhu, Khushwant (Dr.) (Tue Apr 04 2017 - 01:50:01 PDT)
- [AMBER] eChemInfo Training and Innovation Course in Drug Design Thomas Exner (Tue Apr 04 2017 - 02:51:20 PDT)
- [AMBER] mmpbsa- binding energy between ligand-receptor Anna Cebrian Prats (Tue Apr 04 2017 - 06:27:06 PDT)
- [AMBER] You won't believe what happens with maximum coordination limits... David Poole (Tue Apr 04 2017 - 07:23:11 PDT)
- [AMBER] Creating a pdb of only certain molecules from a frame Aseel Bala (Tue Apr 04 2017 - 09:46:37 PDT)
- [AMBER] Atom types for Baaden Hydronium Ion Samaneh Ghassabi Kondalaji (Tue Apr 04 2017 - 18:51:26 PDT)
- [AMBER] density plot of Na+ ions using grid Mary Varughese (Tue Apr 04 2017 - 23:17:14 PDT)
- [AMBER] How to distinguish between water molecules? Markowska (Wed Apr 05 2017 - 02:11:03 PDT)
- [AMBER] CPPTRAJ Cluster d00b46022 (Wed Apr 05 2017 - 02:26:09 PDT)
- [AMBER] ptraj hbonds Mary Varughese (Wed Apr 05 2017 - 03:33:55 PDT)
- [AMBER] Acetonitrile Water Mix Andreas Tosstorff (Wed Apr 05 2017 - 05:35:31 PDT)
- [AMBER] GPU performance Sofia Vasilakaki (Wed Apr 05 2017 - 07:27:35 PDT)
- [AMBER] Binding site volume calculation Thakur, Abhishek (Wed Apr 05 2017 - 08:45:53 PDT)
- [AMBER] parmed doesn't give any output or error message Sadegh Faramarzi Ganjabad (Wed Apr 05 2017 - 10:55:59 PDT)
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Charles Lin (Wed Apr 05 2017 - 12:46:03 PDT)
- [AMBER] Diffusion and permeability coefficients Fabrício Bracht (Thu Apr 06 2017 - 12:01:19 PDT)
- [AMBER] GTX 1080 error Jacopo Sgrignani (Thu Apr 06 2017 - 13:41:57 PDT)
- [AMBER] Tleap error. Vatsal Purohit (Thu Apr 06 2017 - 17:11:45 PDT)
- [AMBER] Periodic box error for restarting simulations with restraints Sadegh Faramarzi Ganjabad (Fri Apr 07 2017 - 00:44:28 PDT)
- [AMBER] Steered MD using two reaction coordinates Suchetana Gupta (Fri Apr 07 2017 - 21:27:26 PDT)
- [AMBER] Query regarding output of 3D-RISM in Amber. Rakesh Srivastava (Fri Apr 07 2017 - 21:48:22 PDT)
- [AMBER] cpptraj analysis of two different dsDNA strands. James Kress (Sat Apr 08 2017 - 11:31:57 PDT)
- [AMBER] Minimization fails when switching from steepest descent to conjugate gradient Andreas Tosstorff (Sat Apr 08 2017 - 16:08:36 PDT)
- [AMBER] Regarding REMD simulations of Proteins MOHD HOMAIDUR RAHMAN (Sun Apr 09 2017 - 08:35:32 PDT)
- [AMBER] MMPBSA entropy calculation help Mary Varughese (Mon Apr 10 2017 - 04:02:21 PDT)
- [AMBER] QM/MM equilibration before SMD in vacuum Samaneh Ghassabi Kondalaji (Mon Apr 10 2017 - 09:04:21 PDT)
- [AMBER] simulation energies are exploding giulia palermo (Mon Apr 10 2017 - 17:30:28 PDT)
- [AMBER] problem about amber install of MMPBSA.py.mpi 白正亚 (Tue Apr 11 2017 - 00:38:27 PDT)
- [AMBER] DNA Tutorial B1 - Temperature Drop Johannes Kalliauer (Tue Apr 11 2017 - 02:42:42 PDT)
- [AMBER] cpptraj creates pdb file it cannot read James Kress (Tue Apr 11 2017 - 12:29:13 PDT)
- [AMBER] Discrepancy in delta G total and per residues decomposition results in MMPBSA.py mish (Wed Apr 12 2017 - 01:35:32 PDT)
- [AMBER] antechamber problem Maura Malinska (Wed Apr 12 2017 - 06:59:37 PDT)
- [AMBER] using pmemd.MPI for REMD Kris Feher (Wed Apr 12 2017 - 09:48:36 PDT)
- [AMBER] reorientation in rmsd James Kress (Wed Apr 12 2017 - 10:32:31 PDT)
- [AMBER] ERROR in load_lbfgs(): YS=0. 杨满意 (Wed Apr 12 2017 - 20:46:26 PDT)
- [AMBER] problem with temperature after rst Jorgen Simonsen (Wed Apr 12 2017 - 22:03:57 PDT)
- [AMBER] AMBER umbrella sampling 吴萌 (Thu Apr 13 2017 - 02:27:20 PDT)
- [AMBER] solvateBox for large size of RNA Li, Wen (Thu Apr 13 2017 - 07:03:15 PDT)
- [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Samaneh Ghassabi Kondalaji (Thu Apr 13 2017 - 08:29:59 PDT)
- [AMBER] Incorrect ligand parameterization using GAFF Emilia Pecora-de-barros (Thu Apr 13 2017 - 10:16:07 PDT)
- [AMBER] About Tutorial B3 Hadeer ELHabashy (Thu Apr 13 2017 - 15:40:12 PDT)
- [AMBER] Compilation of MPI 3D-RISM issue in amber1 4 Rakesh Srivastava (Thu Apr 13 2017 - 21:54:07 PDT)
- [AMBER] BCC charge for my HEME Thakur, Abhishek (Fri Apr 14 2017 - 07:12:51 PDT)
- [AMBER] Format error in frcmod file of HEME Thakur, Abhishek (Fri Apr 14 2017 - 09:42:46 PDT)
- [AMBER] coordinate bond between them and S and FE Thakur, Abhishek (Fri Apr 14 2017 - 12:18:37 PDT)
- [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? nagakumarb.ccamp.res.in (Fri Apr 14 2017 - 22:02:36 PDT)
- [AMBER] weird asymmetries in solvent box Thomas Charles Pochapsky (Sat Apr 15 2017 - 05:52:11 PDT)
- [AMBER] How to calculate the solvation free energy using Amber? JinpengYang (Mon Apr 17 2017 - 01:05:07 PDT)
- [AMBER] PCA - concatenating trajectories George Tzotzos (Mon Apr 17 2017 - 06:19:03 PDT)
- [AMBER] HEME-CYS Thakur, Abhishek (Mon Apr 17 2017 - 09:45:38 PDT)
- [AMBER] Release of AmberTools17 David Case (Mon Apr 17 2017 - 18:28:04 PDT)
- [AMBER] Adding hydrogens to a ligand jacob wick (Tue Apr 18 2017 - 01:57:34 PDT)
- [AMBER] Quasi-harmonic entropy calculation ---- Vibrational component of entropy George Tzotzos (Tue Apr 18 2017 - 04:42:20 PDT)
- [AMBER] pmemd.cuda on an Amber Certified High-End workstation Li, Wen (Tue Apr 18 2017 - 09:02:52 PDT)
- [AMBER] Discussion questions regarding PyRED FF development Iqbal, Muhammad Sajid (Tue Apr 18 2017 - 10:28:40 PDT)
- [AMBER] Error with MMPSA.py calculation Praneeth Bommisetti (Tue Apr 18 2017 - 14:22:16 PDT)
- [AMBER] AmberTools17 + intel17 = bug Hector A. Baldoni (Tue Apr 18 2017 - 16:02:39 PDT)
- [AMBER] EVB with RPMD Rob Arbon (Wed Apr 19 2017 - 08:25:33 PDT)
- [AMBER] Post MD minimization Manjula Saravanan (Thu Apr 20 2017 - 02:33:48 PDT)
- [AMBER] Run NPT in a small periodic box Xiaoliu Zhang (Thu Apr 20 2017 - 07:44:37 PDT)
- [AMBER] MMPBSA - error Anna Cebrian Prats (Thu Apr 20 2017 - 08:02:45 PDT)
- [AMBER] Membrane Protein Simulation Methodology Gulsevin,Alican (Thu Apr 20 2017 - 08:53:30 PDT)
- [AMBER] Recommended LJ parameters for divalent cations used for negatively charged lipid bilayers simulations ? Marek Maly (Thu Apr 20 2017 - 09:02:08 PDT)
- [AMBER] 3D-RISM centering 0 Lucia Fusani (Thu Apr 20 2017 - 10:05:42 PDT)
- [AMBER] Internal dielectric constant and pmemd Samaneh Ghassabi Kondalaji (Thu Apr 20 2017 - 11:02:59 PDT)
- [AMBER] How to make sure there is bond in my complex Thakur, Abhishek (Thu Apr 20 2017 - 11:56:22 PDT)
- [AMBER] Minor bug with updating Amber/AmberTools with Python3 Rohith Mohan (Thu Apr 20 2017 - 13:52:35 PDT)
- [AMBER] PMEMD should halt with error exit after netcdf write failure Chris Moth (Thu Apr 20 2017 - 15:30:25 PDT)
- [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? Guqin Shi (Thu Apr 20 2017 - 15:59:14 PDT)
- [AMBER] Can't not run cpptraj Khatcharin Siriwong (Thu Apr 20 2017 - 19:13:06 PDT)
- [AMBER] Segmentation fault sylvester kisembo (Fri Apr 21 2017 - 06:35:04 PDT)
- [AMBER] residue-based dielectric model in MMGBSA Mrinda Jones (Fri Apr 21 2017 - 11:28:44 PDT)
- [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph (Fri Apr 21 2017 - 11:41:19 PDT)
- [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 Mooers, Blaine H.M. (HSC) (Fri Apr 21 2017 - 12:36:27 PDT)
- [AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc Sharon D. Morris (Sat Apr 22 2017 - 02:00:17 PDT)
- [AMBER] cpptraj configure may fail in AmberTools17 Hannes Loeffler (Sat Apr 22 2017 - 03:38:57 PDT)
- [AMBER] Query regarding convergence issue of 3D-RISM Rakesh Srivastava (Sun Apr 23 2017 - 23:28:53 PDT)
- [AMBER] Query regarding energy calcuation using 3D-RISM Vertika Gautam (Mon Apr 24 2017 - 01:50:11 PDT)
- [AMBER] Membrane Protein Simulation Methodology Gulsevin,Alican (Mon Apr 24 2017 - 04:10:18 PDT)
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Scott Brozell (Mon Apr 24 2017 - 13:26:21 PDT)
- [AMBER] antechamber convergence problem. Vatsal Purohit (Mon Apr 24 2017 - 13:32:52 PDT)
- [AMBER] Pairwise energy calculations in cpptraj Aishani Prem (Mon Apr 24 2017 - 20:07:52 PDT)
- [AMBER] Stricter convergence Criterion for stretching Ramin Salimi (Tue Apr 25 2017 - 10:57:29 PDT)
- [AMBER] Regarding gaussian namelist error Budhathoki, Dipesh (Tue Apr 25 2017 - 16:35:45 PDT)
- [AMBER] Trouble with simple MD simulation of short peptide and Cu2+ ion Eugene Cha (Tue Apr 25 2017 - 20:34:27 PDT)
- [AMBER] consult about LEaP in amber 张壮壮 (Tue Apr 25 2017 - 20:49:48 PDT)
- [AMBER] intra-residue water bridge with cpptraj Joanna Sarzynska (Wed Apr 26 2017 - 07:27:36 PDT)
- [AMBER] Release of AmberTools17 binary Hai Nguyen (Wed Apr 26 2017 - 07:30:04 PDT)
- [AMBER] Post Doc position in Munich, German required Andreas Tosstorff (Wed Apr 26 2017 - 09:01:44 PDT)
- [AMBER] barostat=1 error at Stampede Tarsis (Wed Apr 26 2017 - 13:10:05 PDT)
- [AMBER] Tutorial - 3 / MM-PBSA Marcelo Andrade Chagas (Wed Apr 26 2017 - 14:19:55 PDT)
- [AMBER] Error with 'surf' and acetonitrile-water solvent mixture Marcel Passon (Thu Apr 27 2017 - 01:21:32 PDT)
- [AMBER] tleap input file that fails following upgrade to AmberTools17 Adams, John E. (Thu Apr 27 2017 - 08:45:51 PDT)
- [AMBER] Announcement: Release of DOCK 6.8 Scott Brozell (Thu Apr 27 2017 - 13:23:57 PDT)
- [AMBER] Quenstions about Constraints in AMBER Pengfei Li (Thu Apr 27 2017 - 21:05:26 PDT)
- [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber. Miguel Rivera (Fri Apr 28 2017 - 15:12:18 PDT)
- [AMBER] Using AmberTools17 and Amber14 David Adrian Saez San Martin (Fri Apr 28 2017 - 20:40:38 PDT)
- [AMBER] Too many iterations in routine! in RMSD calculation kungking Hanpaibool (Sat Apr 29 2017 - 02:16:06 PDT)
- [AMBER] Restraint in Steered MD/Jarzynski method Ramin Salimi (Sat Apr 29 2017 - 04:02:01 PDT)
- [AMBER] Restraint in Steered MD/Jarzynski method Ramin Salimi (Sat Apr 29 2017 - 10:55:20 PDT)
- [AMBER] Dftb3 Jacopo Sgrignani (Sat Apr 29 2017 - 13:40:28 PDT)
- [AMBER] External electric fields on CUDA enabled PMEMD Neville Bethel (Sun Apr 30 2017 - 13:14:00 PDT)
- Last message date: Sun Apr 30 2017 - 17:30:03 PDT
- Archived on: Fri Apr 26 2024 - 05:55:35 PDT
