Amber Archive Apr 2016 by thread
- [AMBER] mmpbsa_py_energy failed with prmtop lig_tleap.prm sunita gupta (Thu Mar 31 2016 - 23:22:59 PDT)
- [AMBER] Problems running MD simulation using residual dipolar couplings as restraints Francisco Corzana López (Thu Mar 31 2016 - 23:31:35 PDT)
- [AMBER] aMD ruins membrane structure Michael Shokhen (Fri Apr 01 2016 - 01:03:06 PDT)
- Re: [AMBER] Periodicity box Eiros Zamora, Juan (Fri Apr 01 2016 - 02:21:15 PDT)
- [AMBER] Introducing the exciting next step in MD software development Jason Swails (Fri Apr 01 2016 - 03:32:51 PDT)
- [AMBER] Problems with periodic boundaries Luke Presson (Fri Apr 01 2016 - 06:24:53 PDT)
- Re: [AMBER] Relation between binding affinity and free enegy Carlos Simmerling (Fri Apr 01 2016 - 07:15:45 PDT)
- [AMBER] hoogsteen base pair Martina Devi (Fri Apr 01 2016 - 08:23:48 PDT)
- [AMBER] QM calculation mohammad r (Fri Apr 01 2016 - 22:54:34 PDT)
- Re: [AMBER] Hydrophobic solution environment ??? Mijiddorj Batsaikhan (Sat Apr 02 2016 - 01:50:43 PDT)
- [AMBER] Run Stage 2 of the RESP fit yhzahsc (Sun Apr 03 2016 - 00:17:13 PDT)
- [AMBER] How to use tiMerge properly in pmemd TI calculation jfliu.itcs.ecnu.edu.cn (Sun Apr 03 2016 - 06:29:11 PDT)
- [AMBER] how to prepare a pdb file of a protein being phosphorylated at specific residues 欧阳艳华 (Sun Apr 03 2016 - 20:15:03 PDT)
- [AMBER] how to run a MD of a phosphorylated protein using amber 欧阳艳华 (Sun Apr 03 2016 - 20:21:43 PDT)
- [AMBER] General question Sreemol G (Sun Apr 03 2016 - 23:04:28 PDT)
- [AMBER] build a phosphorylated protein structure pdb file YanhuaOuyang (Mon Apr 04 2016 - 00:21:29 PDT)
- [AMBER] turning of non-bonded interactions with addExclusions Batuhan Kav (Mon Apr 04 2016 - 02:42:30 PDT)
- [AMBER] MD simulations of deprotonated tyrosine residue with AMBER ABEL Stephane 175950 (Mon Apr 04 2016 - 06:22:41 PDT)
- [AMBER] spherical restraint flatwell potentials Kenneth McGuinness (Mon Apr 04 2016 - 11:03:05 PDT)
- [AMBER] sander number of atoms limit TERREUX RAPHAEL (Tue Apr 05 2016 - 01:59:59 PDT)
- [AMBER] The question about SMD wjli (Tue Apr 05 2016 - 06:56:05 PDT)
- [AMBER] cpptraj: reading in previously created covariance matrix Vlad Cojocaru (Tue Apr 05 2016 - 12:52:57 PDT)
- [AMBER] 回复： The question about SMD wjli (Tue Apr 05 2016 - 18:08:36 PDT)
- [AMBER] cpptraj: reading in previously created covariance matrix Vlad Cojocaru (Wed Apr 06 2016 - 01:09:16 PDT)
- [AMBER] Amber: .rst file not created ABHIJEET CHOWDHURY (Wed Apr 06 2016 - 05:08:56 PDT)
- Re: [AMBER] Convergence problem with the SCC-DFTB example. Gustavo Seabra (Wed Apr 06 2016 - 07:21:29 PDT)
- [AMBER] Amber14/AmberTools15 compliation error Kris Feher (Wed Apr 06 2016 - 07:34:04 PDT)
- [AMBER] Any issues if I make PMEMD understand bonds span imaging? David Cerutti (Wed Apr 06 2016 - 13:49:28 PDT)
- [AMBER] General Type Improper Dihedrals vs. Specifics Robert Molt (Wed Apr 06 2016 - 14:20:15 PDT)
- [AMBER] running charmm force field in amber Neha Gandhi (Wed Apr 06 2016 - 17:37:56 PDT)
- [AMBER] test: not getting emails from the list Vlad Cojocaru (Thu Apr 07 2016 - 01:24:04 PDT)
- [AMBER] Hbond command use with non-hydrogen bonds Krantzman, Kristin D (Thu Apr 07 2016 - 07:49:56 PDT)
- [AMBER] PCA Sofia Vasilakaki (Thu Apr 07 2016 - 11:59:38 PDT)
- [AMBER] MMPBSA : Calculation when keeping explicit water molecules 楊承翰 (Thu Apr 07 2016 - 21:14:59 PDT)
- [AMBER] on the MD of protein-ligand Brett (Thu Apr 07 2016 - 22:48:53 PDT)
- [AMBER] RMSD graph for protein-RNA complex Sreemol G (Fri Apr 08 2016 - 01:15:07 PDT)
- [AMBER] CpHMD 赵聪 (Fri Apr 08 2016 - 01:17:00 PDT)
- [AMBER] Regarding MM-PBSA calculation Sivanandam M (Fri Apr 08 2016 - 03:44:33 PDT)
- [AMBER] Regarding MM-PBSA free energy calculation Sivanandam M (Fri Apr 08 2016 - 03:51:05 PDT)
- [AMBER] Metal geometry Vasantha Kumar (Fri Apr 08 2016 - 06:13:15 PDT)
- [AMBER] Problem with MCPB.py Surya Prakash Tiwari (Fri Apr 08 2016 - 11:09:32 PDT)
- [AMBER] Error -per residue Energy Decomposition Arati Paudyal (Fri Apr 08 2016 - 12:12:41 PDT)
- [AMBER] How to prepare files cyclodextrin to use witch glycam04 CRISTIAN ROSSI PERARO (Fri Apr 08 2016 - 19:35:28 PDT)
- [AMBER] query regarding dssp plot cpptraj. Saman Yousuf ali (Sat Apr 09 2016 - 08:20:18 PDT)
- [AMBER] Amber script to delete all hydrogen atoms from protein? Michael Shokhen (Sun Apr 10 2016 - 02:11:18 PDT)
- [AMBER] PMF calculation via tunnel (SMD) wjli (Sun Apr 10 2016 - 05:03:23 PDT)
- [AMBER] mm_pbsa.pl, that I'm doing this right? CRISTIAN ROSSI PERARO (Sun Apr 10 2016 - 11:17:32 PDT)
- [AMBER] Is it possible to run TI with pmemd using the AMOEBA force field? Sumsamber Lee (Sun Apr 10 2016 - 15:07:03 PDT)
- [AMBER] query regarding -refc ABHIJEET CHOWDHURY (Sun Apr 10 2016 - 21:11:07 PDT)
- [AMBER] Refinement in explicit solvent Vasantha Kumar (Mon Apr 11 2016 - 01:13:19 PDT)
- [AMBER] MD tutorial workflows James Starlight (Mon Apr 11 2016 - 01:36:35 PDT)
- [AMBER] Could not find angle parameter Jesmita Dhar (Mon Apr 11 2016 - 02:32:32 PDT)
- [AMBER] geometric center with cpptraj Batuhan Kav (Mon Apr 11 2016 - 03:00:52 PDT)
- [AMBER] Box dimensions 達南杰 (Mon Apr 11 2016 - 04:28:21 PDT)
- [AMBER] ff12SB force field wjli (Mon Apr 11 2016 - 06:47:05 PDT)
- [AMBER] Multiple restraints for minimization Stevens, David Ryan (Mon Apr 11 2016 - 09:03:08 PDT)
- [AMBER] CHAMBER and CMAP error using new c36 FF Jun Feng (Mon Apr 11 2016 - 10:18:17 PDT)
- [AMBER] Implicit Solvent simulation - membrane proteins Balaji Selvam (Mon Apr 11 2016 - 10:51:35 PDT)
- [AMBER] Alanine Scanning ERROR!!! Jag Silwal (Mon Apr 11 2016 - 19:11:17 PDT)
- [AMBER] error while running MMPBSA script Harmeet Kaur (Mon Apr 11 2016 - 21:52:12 PDT)
- [AMBER] CHAMBER and CMAP error using new c36 FF Jun Feng (Tue Apr 12 2016 - 07:22:49 PDT)
- [AMBER] CHAMBER error for the updated CHARMM36 force fields Chitrak Gupta (Tue Apr 12 2016 - 08:23:46 PDT)
- [AMBER] Protein-DNA docking Lara rajam (Tue Apr 12 2016 - 13:38:40 PDT)
- [AMBER] Antechamber Problem Beale, John (Wed Apr 13 2016 - 00:18:07 PDT)
- [AMBER] Quasi-harmonic calculation Amika Sood (Wed Apr 13 2016 - 06:15:06 PDT)
- [AMBER] Both positional and distance restraints Damiano Spadoni (Wed Apr 13 2016 - 06:59:06 PDT)
- [AMBER] Natural bond orbital analysis Kenneth McGuinness (Wed Apr 13 2016 - 07:31:40 PDT)
- [AMBER] MMGBSA and dielectric constants Cortopassi, Wilian (Wed Apr 13 2016 - 09:37:34 PDT)
- [AMBER] Amber custom hardware setup Leonardo Lazzaro (Wed Apr 13 2016 - 17:39:55 PDT)
- [AMBER] Regarding Input file preparation in AMBER Sivanandam M (Thu Apr 14 2016 - 00:01:41 PDT)
- [AMBER] mm_pbsa.pl ERROR yhzahsc (Thu Apr 14 2016 - 00:42:02 PDT)
- [AMBER] LEAP RUN FAILED Neal Broomhead (Thu Apr 14 2016 - 02:38:06 PDT)
- [AMBER] how to embed amber14 Ayesha Kanwal (Thu Apr 14 2016 - 03:34:57 PDT)
- [AMBER] Modelling of proteins Aishani Prem (Thu Apr 14 2016 - 14:30:00 PDT)
- [AMBER] How can I extract PDB files from a molecular dynamics simulation Luis Esteban (Thu Apr 14 2016 - 19:02:03 PDT)
- [AMBER] hbond analysis of phosphotyrosine Wu Xu (Thu Apr 14 2016 - 19:55:56 PDT)
- [AMBER] Fortran Modernisation Workshop - Numerical Algorithms Group NAG CHAMI F. (Fri Apr 15 2016 - 03:23:45 PDT)
- [AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file Shreeramesh (Fri Apr 15 2016 - 04:27:48 PDT)
- [AMBER] Conversion of CHARMM-GUI generated file into Lipid14 readable file Shreeramesh (Fri Apr 15 2016 - 05:01:04 PDT)
- [AMBER] TI Calculation doubt Mary Varughese (Fri Apr 15 2016 - 23:34:02 PDT)
- [AMBER] facing problems simulating in implicit solvent Avik Bhattacharjee (Sat Apr 16 2016 - 09:43:42 PDT)
- [AMBER] Change PBRadii after simulation Jag Silwal (Sat Apr 16 2016 - 20:30:27 PDT)
- [AMBER] cpptraj SolventAcc and ligand distance plotting Saman Yousuf ali (Sat Apr 16 2016 - 23:59:11 PDT)
- [AMBER] error in MCPB.py 3b jixiaofeng (Sun Apr 17 2016 - 19:43:18 PDT)
- [AMBER] was the MCPB.py compiled correctly？ jixiaofeng (Sun Apr 17 2016 - 19:59:35 PDT)
- [AMBER] Error in 3DRISM calculation ATUL KUMAR (Sun Apr 17 2016 - 22:46:49 PDT)
- [AMBER] on antechamber Brett (Sun Apr 17 2016 - 23:38:26 PDT)
- [AMBER] on antechamber Brett (Mon Apr 18 2016 - 02:28:10 PDT)
- [AMBER] clustering waleed zalloum (Mon Apr 18 2016 - 11:14:33 PDT)
- [AMBER] mpi problems Gard Nelson (Mon Apr 18 2016 - 11:46:06 PDT)
- [AMBER] Early bird extended! ISQBP2016 meeting - Bergen Norway Vlad Cojocaru (Mon Apr 18 2016 - 12:34:15 PDT)
- [AMBER] amber v16 Arjun Sharma (Mon Apr 18 2016 - 12:38:01 PDT)
- [AMBER] glycam O-glycosylation at Ser Neha Gandhi (Mon Apr 18 2016 - 22:17:43 PDT)
- [AMBER] want to ask you about MMPBSA.py .mdcrd file Ayesha Kanwal (Tue Apr 19 2016 - 00:55:36 PDT)
- [AMBER] HEME group in a protein Anna Cebrian Prats (Tue Apr 19 2016 - 04:14:45 PDT)
- [AMBER] query about .mdcrd file Ayesha Kanwal (Tue Apr 19 2016 - 04:23:44 PDT)
- [AMBER] [cpptraj] Automating pcmin/pcmax selection of modes command Eiros Zamora, Juan (Tue Apr 19 2016 - 04:52:01 PDT)
- [AMBER] Approach for transmembrane protein Elisa Pieri (Tue Apr 19 2016 - 05:03:53 PDT)
- [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj peter.schmidtke.discngine.servier.com (Tue Apr 19 2016 - 05:41:14 PDT)
- [AMBER] building DNA with extruded base giulia palermo (Tue Apr 19 2016 - 10:17:46 PDT)
- [AMBER] interactive MD applied to AI Bill Ross (Tue Apr 19 2016 - 12:19:05 PDT)
- [AMBER] Electrostatic Energies - MMPBSA Cortopassi, Wilian (Tue Apr 19 2016 - 13:55:24 PDT)
- [AMBER] Regarding atom types Elvis Martis (Tue Apr 19 2016 - 21:56:47 PDT)
- [AMBER] error while putting the whole path into python script Ayesha Kanwal (Wed Apr 20 2016 - 00:37:51 PDT)
- [AMBER] XLeap didn't save the parameter file Nikolay N. Kuzmich (Wed Apr 20 2016 - 01:27:17 PDT)
- [AMBER] problem in 3DRISM convergence ATUL KUMAR (Wed Apr 20 2016 - 03:29:41 PDT)
- [AMBER] questions about energy terms of amber MD yuandandan (Wed Apr 20 2016 - 06:57:38 PDT)
- [AMBER] warning message for antechamber by acpype Brett (Wed Apr 20 2016 - 07:41:28 PDT)
- [AMBER] Force field parameters for glycerophophate anu chandra (Wed Apr 20 2016 - 15:24:47 PDT)
- [AMBER] Error in the conversion of CHARMM-GUI generated file into lipid14 readable format Shreeramesh (Thu Apr 21 2016 - 00:52:48 PDT)
- [AMBER] How to read mdinfo file without crashing the simulation? Karolina Markowska (Thu Apr 21 2016 - 02:01:03 PDT)
- [AMBER] qmmm mmpbsa spin multiplicity problem Ayesha Fatima (Thu Apr 21 2016 - 08:32:28 PDT)
- [AMBER] GeForce GTX 960 ? Marek Maly (Thu Apr 21 2016 - 08:51:43 PDT)
- [AMBER] mmpbsa complex McElheny, Dan (Thu Apr 21 2016 - 12:42:52 PDT)
- [AMBER] Building Cyclic Peptide in xleap Maral Aminpour (Thu Apr 21 2016 - 13:55:19 PDT)
- [AMBER] How to deal with monoatomic ion, such as ILs cation Takuya Uto (Thu Apr 21 2016 - 18:29:56 PDT)
- [AMBER] How to deal with monoatomic ion, such as ILs anion Takuya Uto (Thu Apr 21 2016 - 18:45:45 PDT)
- [AMBER] atom does not have a type jixiaofeng (Thu Apr 21 2016 - 19:23:53 PDT)
- [AMBER] CUDA and restraint Domenico Marson (Fri Apr 22 2016 - 02:21:43 PDT)
- [AMBER] System size limitations for Amber 14 pmemd.cuda? Kasprzak, Wojciech (NIH/NCI) [C] (Fri Apr 22 2016 - 05:48:38 PDT)
- [AMBER] Decomposition energy after mutation! Jag Silwal (Fri Apr 22 2016 - 09:52:14 PDT)
- [AMBER] Hydroxyproline Mijiddorj Batsaikhan (Sat Apr 23 2016 - 05:00:41 PDT)
- [AMBER] No torsion terms for CB-N*-CR-H5 Prayagraj Fandilolu (Sun Apr 24 2016 - 00:12:13 PDT)
- [AMBER] Read/visualize volmap output (opendx) Jean-Patrick Francoia (Mon Apr 25 2016 - 01:44:54 PDT)
- [AMBER] Energies in QM/MM MD 王美婷 (Mon Apr 25 2016 - 01:46:48 PDT)
- [AMBER] How to rebuild pH-based trajectory files from CpHMD restarted simulations Elisa Pieri (Mon Apr 25 2016 - 02:39:46 PDT)
- [AMBER] Error while converting CHARMM-GUI generated file Shreeramesh (Mon Apr 25 2016 - 05:17:08 PDT)
- [AMBER] protein complex dissociation during md Brett (Mon Apr 25 2016 - 06:54:34 PDT)
- [AMBER] rotation angle around an axes giulia palermo (Mon Apr 25 2016 - 10:55:54 PDT)
- [AMBER] Problem Running MMPBSA.py Martin Floor (Mon Apr 25 2016 - 15:29:23 PDT)
- [AMBER] Using PBSA to Calculate Solvation Free Energy Jiaqi Jin (Mon Apr 25 2016 - 15:31:48 PDT)
- [AMBER] parmed.py Sanjib Paul (Tue Apr 26 2016 - 07:44:15 PDT)
- Re: [AMBER] AMBER Project Niharikav Veeresh (Tue Apr 26 2016 - 11:52:30 PDT)
- [AMBER] MD of 1:1 mixture compound Saman Yousuf ali (Tue Apr 26 2016 - 22:10:56 PDT)
- [AMBER] debug issue Zhenyu Meng (Tue Apr 26 2016 - 23:53:13 PDT)
- [AMBER] tleap parametrization of metalo-binding proteins James Starlight (Wed Apr 27 2016 - 02:25:23 PDT)
- [AMBER] Question about RESP with iodine Lorenzo Gontrani (Wed Apr 27 2016 - 03:55:29 PDT)
- [AMBER] Problem in calculating auto time correlation function with ptraj Saheb Dutta (Wed Apr 27 2016 - 08:32:55 PDT)
- [AMBER] How can I use FF14SB in DOCK6 calculation? Mijiddorj Batsaikhan (Thu Apr 28 2016 - 03:20:40 PDT)
- [AMBER] CUDA and restraint Domenico Marson (Thu Apr 28 2016 - 03:31:34 PDT)
- [AMBER] tleap - protein + ligand + heme group Anna Cebrian Prats (Thu Apr 28 2016 - 08:52:13 PDT)
- [AMBER] Targeted MD error Shukla, Saurabh (Thu Apr 28 2016 - 09:46:03 PDT)
- [AMBER] Cpptraj LipidOrder error: mask groups are not the same length Amy Rice (Thu Apr 28 2016 - 11:30:14 PDT)
- [AMBER] Calculate Percentage of Hydrogen Occurrence Jag Silwal (Fri Apr 29 2016 - 06:27:54 PDT)
- [AMBER] ambpdb error Arati Paudyal (Fri Apr 29 2016 - 06:41:40 PDT)
- [AMBER] accelerated MD on set of dihedrals Giuseppina La Sala (Fri Apr 29 2016 - 09:56:00 PDT)
- [AMBER] on antechamber Brett (Sat Apr 30 2016 - 02:00:14 PDT)
- [AMBER] Release of Amber16 and AmberTools16 David A Case (Sat Apr 30 2016 - 09:27:51 PDT)
- Re: [AMBER] help identifying dihedral parameters for paracetemol using Antechamber Andrew Schaub (Sat Apr 30 2016 - 22:01:04 PDT)
- Last message date: Sat Apr 30 2016 - 22:30:03 PDT
- Archived on: Sun Dec 22 2024 - 05:55:20 PST
