Amber Archive Oct 2015 by thread
- [AMBER] /share/apps/amber/amber14/bin/sander.MPI: error while loading shared libraries: libmpi_cxx.so.1: cannot open shared object file: No such file or directory Atila Petrosian (Thu Oct 01 2015 - 01:34:23 PDT)
- [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE in AMBER 12 using the new set 3ob-3-1 Emilio Lence (Thu Oct 01 2015 - 05:47:07 PDT)
- [AMBER] Parameters for trigonal bi-pyramid and square bi-pyramid Fe(II) Francesco Pietra (Thu Oct 01 2015 - 08:17:33 PDT)
- [AMBER] Units of the dipole moment? Ucisik, Melek Nihan (Thu Oct 01 2015 - 10:02:23 PDT)
- Re: [AMBER] Updates for PBSA energy calculations Christina Berti (Thu Oct 01 2015 - 12:29:03 PDT)
- [AMBER] Building a structure of levansucrase (1PT2) with a fructosyl residue attached to Asp86 Surasak Chunsrivirot (Thu Oct 01 2015 - 21:28:12 PDT)
- [AMBER] Problem with VDW energy Brent Krueger (Fri Oct 02 2015 - 10:54:07 PDT)
- [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15 Emilio Lence (Fri Oct 02 2015 - 11:11:03 PDT)
- [AMBER] problem with randomizing velocities Kalenkiewicz, Andrew (NIH/NICHD) [F] (Fri Oct 02 2015 - 13:58:55 PDT)
- [AMBER] TIP3 water not recognized Chitrak Gupta (Fri Oct 02 2015 - 16:03:35 PDT)
- [AMBER] mixing rules for various water models in AMBER conor parks (Sat Oct 03 2015 - 21:14:26 PDT)
- [AMBER] QM/MM performance Sofia Vasilakaki (Sun Oct 04 2015 - 04:23:02 PDT)
- Re: [AMBER] AMBER Digest, Vol 1361, Issue 1 Chitrak Gupta (Sun Oct 04 2015 - 11:00:49 PDT)
- [AMBER] CpHMD for non protein residues Rahul Ramesh (Sun Oct 04 2015 - 14:42:42 PDT)
- [AMBER] Question about mask in cpptraj Mohd Farid Ismail (Sun Oct 04 2015 - 20:42:58 PDT)
- Re: [AMBER] Leap : problem with copying and combining DNA items Jérémie Knoops (Mon Oct 05 2015 - 05:34:14 PDT)
- [AMBER] SC15 Call for abstracts - "Producing High-Performance and Sustainable Software for Molecular Simulation" Ross Walker (Mon Oct 05 2015 - 11:10:41 PDT)
- [AMBER] Atom 1512 was assigned a lower molecule # than previous atom Osman, Roman (Mon Oct 05 2015 - 11:51:19 PDT)
- [AMBER] Info: Bond types are assigned for valence state 5 with penalty of 1 Atila Petrosian (Mon Oct 05 2015 - 13:57:53 PDT)
- [AMBER] Pairwise energy decomposition Sara Omar (Mon Oct 05 2015 - 22:28:09 PDT)
- [AMBER] cpin file Arjun Sharma (Tue Oct 06 2015 - 07:16:33 PDT)
- [AMBER] How to do a QMMM calculation with a dynamic QM region 崔克新 (Wed Oct 07 2015 - 02:18:00 PDT)
- [AMBER] SIGSEGV: Segmentation Fault Steven Cole Mercer (Wed Oct 07 2015 - 16:46:12 PDT)
- [AMBER] hydrogen bond cpptraj Lara rajam (Wed Oct 07 2015 - 18:18:51 PDT)
- [AMBER] Dihedral/improper coefficient in AMBER + rmin vs sigma for lennard jones conor parks (Wed Oct 07 2015 - 21:33:05 PDT)
- [AMBER] Controlling size of the box Nicholus Bhattacharjee (Thu Oct 08 2015 - 08:48:31 PDT)
- [AMBER] "Vlimit exceeded for step..." error Vu Truong (Thu Oct 08 2015 - 13:21:47 PDT)
- [AMBER] Cytochrome P450 with heme simulation Abelak, Kavin (Fri Oct 09 2015 - 03:47:47 PDT)
- [AMBER] AIB parameter Elisa Frezza (Fri Oct 09 2015 - 04:56:06 PDT)
- [AMBER] http://q4md-forcefieldtools.org/ unavailable Jérémie Knoops (Fri Oct 09 2015 - 04:59:54 PDT)
- [AMBER] Restraints Wong Li Zhe (Fri Oct 09 2015 - 05:23:53 PDT)
- Re: [AMBER] AMBER Digest, Vol 1364, Issue 1 Arjun Sharma (Fri Oct 09 2015 - 07:02:14 PDT)
- [AMBER] resp input format 16I5 stecue.gmail.com (Fri Oct 09 2015 - 07:30:54 PDT)
- [AMBER] h-bond calculation - tokenise error Sidhu, Khushwant (Dr.) (Fri Oct 09 2015 - 07:57:40 PDT)
- [AMBER] non-standard residue (DNA-protein crosslink) Jackle, Chasen (Fri Oct 09 2015 - 09:35:14 PDT)
- [AMBER] Making Parameter and Topology Files for Protein-Ligand Complex Jim Wu (Fri Oct 09 2015 - 16:14:09 PDT)
- Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal (Sun Oct 11 2015 - 07:23:49 PDT)
- [AMBER] Prepgen difficulty Robert Molt (Sun Oct 11 2015 - 08:41:48 PDT)
- [AMBER] query about Bromide ion forcefield parameter jagannath mondal (Mon Oct 12 2015 - 04:01:09 PDT)
- [AMBER] A question about MMPBSA calculation anu chandra (Mon Oct 12 2015 - 09:14:08 PDT)
- [AMBER] How do you place two molecules in one water box? David Eugene Jones (Mon Oct 12 2015 - 11:28:54 PDT)
- [AMBER] Temperature fluctuations in stage heating Anitha Jagadesh (Mon Oct 12 2015 - 22:06:26 PDT)
- [AMBER] many atoms, same name Hadeer ELHabashy (Tue Oct 13 2015 - 11:08:08 PDT)
- [AMBER] cpptraj density Björn Karlsson (Tue Oct 13 2015 - 11:10:54 PDT)
- [AMBER] AmberTools14 configuration problem Ivanov, Maxim (Tue Oct 13 2015 - 14:25:14 PDT)
- [AMBER] Real-time hydrogen bond formation using VMD Abhipriya K (Tue Oct 13 2015 - 23:21:52 PDT)
- [AMBER] EVB related query bijyalaxmi athokpam (Wed Oct 14 2015 - 01:54:26 PDT)
- Re: [AMBER] [SPAM] AMBER Digest, Vol 1365, Issue 1 崔克新 (Wed Oct 14 2015 - 02:10:05 PDT)
- [AMBER] Minimization Wong Li Zhe (Wed Oct 14 2015 - 02:17:34 PDT)
- [AMBER] difficulties in generate .prmtop and .inpcrd file for complex using Guassian calculated ligand charges Jin Zhang (Wed Oct 14 2015 - 02:20:36 PDT)
- [AMBER] error with line 165 of cpinutil.py Hadeer ELHabashy (Wed Oct 14 2015 - 03:34:04 PDT)
- [AMBER] Is it possible to simulate a periodic crystal ? Hadeer ELHabashy (Wed Oct 14 2015 - 06:51:37 PDT)
- Re: [AMBER] RESP charge fitting Xing (Wed Oct 14 2015 - 08:03:40 PDT)
- [AMBER] RESP charge calculation li he (Wed Oct 14 2015 - 11:17:45 PDT)
- [AMBER] Ho Atom Inclusion in PDB from Leap Robert Molt (Wed Oct 14 2015 - 11:31:00 PDT)
- [AMBER] tinker_to_amber does not work Sun (Wed Oct 14 2015 - 14:52:10 PDT)
- [AMBER] cutoff problem with a periodic crystal box Hadeer ELHabashy (Thu Oct 15 2015 - 00:26:43 PDT)
- [AMBER] difficulties in generate .prmtop and .inpcrd file for complex using Guassian calculated ligand charges MarcZhang (Thu Oct 15 2015 - 01:23:01 PDT)
- [AMBER] No Internet Access Shahryar Alavi (Thu Oct 15 2015 - 01:27:00 PDT)
- [AMBER] What is the formula for calculating EPtot? Yip Yew Mun (Thu Oct 15 2015 - 02:26:29 PDT)
- [AMBER] Correctly deriving force constants for Amber Nash, Anthony (Thu Oct 15 2015 - 05:07:22 PDT)
- [AMBER] System gets unwrap while iwrap=1 in ti Khabiri, Morteza (Thu Oct 15 2015 - 06:18:17 PDT)
- [AMBER] Not atom type for Bromine atom in amber GAFF force field? MarcZhang (Thu Oct 15 2015 - 09:42:08 PDT)
- [AMBER] FW: System gets unwrap while iwrap=1 in ti Khabiri, Morteza (Thu Oct 15 2015 - 11:46:48 PDT)
- Re: [AMBER] difficulties in generate .prmtop and .inpcrd file MarcZhang (Thu Oct 15 2015 - 13:07:10 PDT)
- Re: [AMBER] Not atom type for Bromine atom in amber GAFF MarcZhang (Thu Oct 15 2015 - 13:29:07 PDT)
- Re: [AMBER] compare two trajectories Xing (Thu Oct 15 2015 - 19:29:08 PDT)
- [AMBER] CpHMD for non protein residues Rahul Ramesh (Thu Oct 15 2015 - 20:43:18 PDT)
- [AMBER] Documentation on Prepin File Format Robert Molt (Fri Oct 16 2015 - 05:00:19 PDT)
- [AMBER] CPPTRAJ : different RMSD calculation in a single run anu chandra (Fri Oct 16 2015 - 05:02:10 PDT)
- [AMBER] Random Number Generator Flag Ig Guqin Shi (Fri Oct 16 2015 - 09:13:35 PDT)
- [AMBER] Random Number Generator Flag Ig Guqin Shi (Fri Oct 16 2015 - 09:17:34 PDT)
- [AMBER] sander missing from AmberTools15? Novosielski, Ryan (Fri Oct 16 2015 - 12:44:38 PDT)
- [AMBER] Help Balajee Ramachandran (Fri Oct 16 2015 - 12:55:26 PDT)
- [AMBER] Leap PDB Input Error Robert Molt (Fri Oct 16 2015 - 16:13:31 PDT)
- [AMBER] donor and acceptor masks Hadeer ELHabashy (Sat Oct 17 2015 - 07:06:27 PDT)
- [AMBER] Membrane protein imagining problems Romero, Raquel (Sun Oct 18 2015 - 15:33:09 PDT)
- [AMBER] R.E.D. server down or out? Tan Yaw Sing (Sun Oct 18 2015 - 19:43:19 PDT)
- [AMBER] CPPTRAJ Wong Li Zhe (Sun Oct 18 2015 - 21:06:48 PDT)
- [AMBER] RED-tools Repic Matej (Mon Oct 19 2015 - 00:21:41 PDT)
- [AMBER] Why is water box getting bigger? Karolina Markowska (Mon Oct 19 2015 - 04:57:20 PDT)
- [AMBER] MMPBSA tutorial A3.2 Fabian gmail (Mon Oct 19 2015 - 07:17:02 PDT)
- [AMBER] Differences on MMPBSA calculation results MarcZhang (Mon Oct 19 2015 - 07:58:57 PDT)
- [AMBER] Differences on MMPBSA calculation results MarcZhang (Mon Oct 19 2015 - 08:00:18 PDT)
- [AMBER] [cpptraj] Changes in RMSF functionality? Juan Eiros Zamora (Mon Oct 19 2015 - 09:30:48 PDT)
- [AMBER] 1-4 nonbonded interactions does not cancel in MMPBSA calculation Renato Freitas (Mon Oct 19 2015 - 14:22:51 PDT)
- [AMBER] Lennard-Jones parameter for Sp, Sp2 and Sp3 Nitrogen Ebert Maximilian (Mon Oct 19 2015 - 14:37:43 PDT)
- [AMBER] Problems with the installation of ambertools15. Jinfeng Huang (Mon Oct 19 2015 - 20:33:15 PDT)
- [AMBER] The formulas of per-residue and pairwise-residue free energy decomposition in mm_pbsa wliu (Mon Oct 19 2015 - 23:33:20 PDT)
- [AMBER] Tutorial 3 section 1 Abelak, Kavin (Tue Oct 20 2015 - 04:54:58 PDT)
- [AMBER] gromacs to amber file format neha chaudhary (Tue Oct 20 2015 - 05:07:03 PDT)
- [AMBER] Measuring distance between protein and graphene surface Krantzman, Kristin D (Tue Oct 20 2015 - 11:01:37 PDT)
- Re: [AMBER] Measuring minimum distance between protein and graphene surface Krantzman, Kristin D (Tue Oct 20 2015 - 11:20:15 PDT)
- [AMBER] SGLDg Jérémie Knoops (Tue Oct 20 2015 - 22:45:23 PDT)
- [AMBER] The magnitude and the direction of the electric field Hadeer ELHabashy (Wed Oct 21 2015 - 05:54:48 PDT)
- [AMBER] MMPBSA: multiple trajectory approach usage George Tzotzos (Wed Oct 21 2015 - 08:19:44 PDT)
- [AMBER] pmemd.cuda.MPI on Comet- MPI dying Kenneth Huang (Wed Oct 21 2015 - 09:30:41 PDT)
- [AMBER] Problem configuring amber14 Mochena, Mogus D. (Wed Oct 21 2015 - 11:11:21 PDT)
- [AMBER] ff12SB vs ff14SB for protein-ligand MD simulations? yunshi11 . (Wed Oct 21 2015 - 18:10:07 PDT)
- [AMBER] MMPBSA for peptides interaction Fabian gmail (Thu Oct 22 2015 - 06:16:22 PDT)
- [AMBER] How can amber differentiate between terminal Oxygens Hadeer ELHabashy (Thu Oct 22 2015 - 07:00:59 PDT)
- [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Marcelo Andrade Chagas (Thu Oct 22 2015 - 07:34:51 PDT)
- [AMBER] Time correlation function of an atom Hadeer ELHabashy (Thu Oct 22 2015 - 08:54:24 PDT)
- [AMBER] Polardecomp in 3D-RISM fails Josep Maria Campanera Alsina (Thu Oct 22 2015 - 12:33:43 PDT)
- [AMBER] Atom match error in MMPBSA calculation Progress Zhang (Thu Oct 22 2015 - 14:31:52 PDT)
- [AMBER] Metal Ion Model Carlos Modenutti (Thu Oct 22 2015 - 15:42:05 PDT)
- [AMBER] If it's possible to add restraint on the steered MD ? 崔克新 (Fri Oct 23 2015 - 02:06:55 PDT)
- [AMBER] Steps after: AMBER annealing with restraints in vacuum.? towards improving the quality of structure with out RDC, Dihedrals V. Kumar (Fri Oct 23 2015 - 02:22:05 PDT)
- [AMBER] Steps after: AMBER annealing with restraints in vacuum.? towards improving the quality of structure with out RDC, Dihedrals V. Kumar (Fri Oct 23 2015 - 02:41:36 PDT)
- [AMBER] QM/MM Umbrella Mahmood Jasim (Fri Oct 23 2015 - 04:56:31 PDT)
- [AMBER] Stopping sander in production phase. Why? Atila Petrosian (Fri Oct 23 2015 - 06:40:41 PDT)
- [AMBER] Best suitable 'igb' value for MMPBSA.py calculation anu chandra (Fri Oct 23 2015 - 07:02:25 PDT)
- [AMBER] aMD: Bad data for namelist object ethreshp Claire Coderch Boué (Fri Oct 23 2015 - 09:29:56 PDT)
- [AMBER] compatibility of targeted MD with GPU amber vs. sander Naomi Rose Latorraca (Fri Oct 23 2015 - 15:13:46 PDT)
- Re: [AMBER] Query about adding hydrogens David Case (Sat Oct 24 2015 - 07:31:03 PDT)
- [AMBER] ALA but must be GLY MM-PBSA bharat lakhani (Sun Oct 25 2015 - 08:46:42 PDT)
- [AMBER] how to convert mdcrd to NetCDF trajectory file? shahab shariati (Sun Oct 25 2015 - 10:16:42 PDT)
- [AMBER] Constant pH MD Hadeer ELHabashy (Mon Oct 26 2015 - 01:07:05 PDT)
- [AMBER] atomiccorr Hadeer ELHabashy (Mon Oct 26 2015 - 04:43:47 PDT)
- Re: [AMBER] Oxygen parameters for AMBER99SB-ILDN Ebert Maximilian (Mon Oct 26 2015 - 07:05:52 PDT)
- [AMBER] paramfit multiple dihedrals combination CHAMI F. (Mon Oct 26 2015 - 10:53:57 PDT)
- [AMBER] paramfit multiple dihedral commbination CHAMI F. (Mon Oct 26 2015 - 11:47:17 PDT)
- [AMBER] cpptraj - bridging water Lara rajam (Mon Oct 26 2015 - 11:56:39 PDT)
- [AMBER] ante-MMPBSA question Mohammad Salem (Mon Oct 26 2015 - 15:18:25 PDT)
- [AMBER] AmberTools 15, Mac El Captain and Fink Alan (Mon Oct 26 2015 - 16:03:33 PDT)
- [AMBER] parameters for Boron jixiaofeng (Tue Oct 27 2015 - 00:36:09 PDT)
- [AMBER] (too) high absolute values for charges using resp and gaussian Jérémie Knoops (Tue Oct 27 2015 - 01:38:47 PDT)
- [AMBER] coordination number Hadeer ELHabashy (Tue Oct 27 2015 - 03:57:02 PDT)
- [AMBER] Help - buy the Amber software Adam Winiarski (Tue Oct 27 2015 - 04:01:13 PDT)
- [AMBER] unusual structure_after equilibration Andrew Bostick (Tue Oct 27 2015 - 05:44:43 PDT)
- [AMBER] Resulting cutoff is too small for your lower limit jfliu (Tue Oct 27 2015 - 05:58:22 PDT)
- [AMBER] N- and C- terminals constant PH simulation Hadeer ELHabashy (Tue Oct 27 2015 - 06:32:56 PDT)
- [AMBER] small energy jump when restoring a simulation production Fabian gmail (Tue Oct 27 2015 - 06:36:05 PDT)
- [AMBER] QMMM with inorganic molecules Robert Arbon (Tue Oct 27 2015 - 10:09:42 PDT)
- [AMBER] missingdisulfide Abelak, Kavin (Tue Oct 27 2015 - 11:51:43 PDT)
- [AMBER] Replica exchange temperature distribution maryam azimzadehirani (Tue Oct 27 2015 - 18:54:33 PDT)
- [AMBER] Charmm to Amber (where’s chamber?) Alan (Wed Oct 28 2015 - 02:32:32 PDT)
- [AMBER] cpptraj uses huge memory space while doing molsurf calculation anu chandra (Wed Oct 28 2015 - 05:48:40 PDT)
- [AMBER] Different Parameters for Nonbonded Interactions Batuhan Kav (Wed Oct 28 2015 - 08:02:08 PDT)
- [AMBER] Guanine base pair planarity in G-guadruplex V. Kumar (Wed Oct 28 2015 - 09:02:10 PDT)
- [AMBER] how to generate a model beta-sheet structure Jagannath Mondal (Wed Oct 28 2015 - 10:13:18 PDT)
- [AMBER] applying restraints using tinker Christina Berti (Wed Oct 28 2015 - 10:51:16 PDT)
- Re: [AMBER] Halogen bond force field in AMBER psu4.uic.edu (Wed Oct 28 2015 - 23:03:39 PDT)
- [AMBER] Tutorial 22 - aMD - how long should it last on Titan Black? Karolina Markowska (Thu Oct 29 2015 - 02:35:40 PDT)
- [AMBER] Guanine base pair planarity in G-guadruplex V. Kumar (Thu Oct 29 2015 - 04:26:47 PDT)
- [AMBER] [AMEBR] Amino acid side-chain carbonyl C=O(ASP, GLU) and side-cahin -HN (LYS, ARG) close proximity V. Kumar (Thu Oct 29 2015 - 05:05:20 PDT)
- [AMBER] MMPBSA for multiple mutants Fabian gmail (Thu Oct 29 2015 - 08:27:58 PDT)
- [AMBER] Glycam force field parameters for derivatives? yunshi11 . (Thu Oct 29 2015 - 21:51:36 PDT)
- [AMBER] How to prevent the water molecules entering into the binding pocket during the MD simulation ? fjliu (Thu Oct 29 2015 - 23:20:57 PDT)
- [AMBER] Why PBSA decomposition takes so long time? MarcZhang (Fri Oct 30 2015 - 03:52:40 PDT)
- [AMBER] ions cannot be viewed in gaussview Martina Devi (Fri Oct 30 2015 - 07:18:37 PDT)
- [AMBER] AMBER14 testing error Mahmoud A. A. Ibrahim (Fri Oct 30 2015 - 11:40:41 PDT)
- [AMBER] Elementary VMD Problem with Amber Trajectory Robert Molt (Fri Oct 30 2015 - 14:24:31 PDT)
- [AMBER] mmpbsa.py error Mohammad Salem (Fri Oct 30 2015 - 17:08:21 PDT)
- [AMBER] &rst + distance + coordinate restraint Gerald Monard (Sat Oct 31 2015 - 10:02:00 PDT)
- [AMBER] Can't install AMBER14: MissingProgram...Install patch from your package manager Jose Borreguero (Sat Oct 31 2015 - 15:54:06 PDT)
- Last message date: Sat Oct 31 2015 - 17:00:02 PDT
- Archived on: Fri Dec 20 2024 - 05:55:16 PST
