Amber Archive Sep 2016 by thread
- Re: [AMBER] change the atom charge in a restart simulations windy (Wed Aug 31 2016 - 18:53:55 PDT)
- Re: [AMBER] Regarding the use of sed command to replace water MOHD HOMAIDUR RAHMAN (Wed Aug 31 2016 - 21:29:51 PDT)
- [AMBER] Fwd: MD stop at different time period without giving any error Garima Singh (Thu Sep 01 2016 - 01:39:30 PDT)
- Re: [AMBER] changing atom type Jacopo Sgrignani (Thu Sep 01 2016 - 01:43:19 PDT)
- [AMBER] error in sander minimization Prayagraj Fandilolu (Thu Sep 01 2016 - 04:45:13 PDT)
- [AMBER] how to center a polipeptide inside a solvent box Elisa Pieri (Thu Sep 01 2016 - 05:27:59 PDT)
- [AMBER] Unable to find mopac charges in mopac.out Sneha Rai (Thu Sep 01 2016 - 05:29:18 PDT)
- Re: [AMBER] autocorr of hydrogen bonds Osman, Roman (Thu Sep 01 2016 - 09:06:44 PDT)
- [AMBER] noshakemask and qmshake Fabrício Bracht (Thu Sep 01 2016 - 11:34:47 PDT)
- [AMBER] radial distribution function from 1drism calculation Jingyi Yan (Thu Sep 01 2016 - 12:21:32 PDT)
- [AMBER] Any idea about this Amber compile bug? David Cerutti (Thu Sep 01 2016 - 13:45:35 PDT)
- [AMBER] accelerated MD Neha Gandhi (Thu Sep 01 2016 - 14:55:27 PDT)
- [AMBER] QMMM simulation with user-specified basis set in amber zycz138.126.com (Thu Sep 01 2016 - 20:31:59 PDT)
- [AMBER] Fwd: File redirection commands with targeted MD Sonia Ziada (Fri Sep 02 2016 - 00:03:35 PDT)
- [AMBER] query regaridng unrestarint minimization step Saman Yousuf ali (Fri Sep 02 2016 - 00:29:56 PDT)
- [AMBER] Which is the best thermostat for cMD? Dd H (Fri Sep 02 2016 - 01:15:21 PDT)
- Re: [AMBER] Question about QM/MM Anna Cebrian Prats (Fri Sep 02 2016 - 02:01:06 PDT)
- [AMBER] RMS-fit during PCA Anasuya Dighe (Fri Sep 02 2016 - 02:38:31 PDT)
- [AMBER] Trajectory analysis Anna Cebrian Prats (Fri Sep 02 2016 - 08:05:39 PDT)
- [AMBER] lig.frcmod file is not formed Vishal Nemaysh (Sat Sep 03 2016 - 07:37:58 PDT)
- [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 sunyeping (Sun Sep 04 2016 - 01:35:20 PDT)
- [AMBER] Hydrophobic interactions in MM-GBSA Atila Petrosian (Sun Sep 04 2016 - 13:37:01 PDT)
- [AMBER] Parmed.py, deleteBond and setBond Aronica, Pietro (Sun Sep 04 2016 - 21:18:05 PDT)
- [AMBER] Select a snapshot Anna Cebrian Prats (Mon Sep 05 2016 - 02:42:24 PDT)
- [AMBER] Temperature connected to the dipole convergence in the output BLEY Michael (Mon Sep 05 2016 - 07:39:57 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety Mark Abraham (Mon Sep 05 2016 - 08:19:19 PDT)
- [AMBER] historical changes to LYN charges in amber03 Mark Abraham (Mon Sep 05 2016 - 08:40:38 PDT)
- [AMBER] How to fixed residues in amber? windy (Mon Sep 05 2016 - 19:32:36 PDT)
- [AMBER] resp charges in LIPID14 jojartb.jgypk.u-szeged.hu (Tue Sep 06 2016 - 04:55:21 PDT)
- Re: [AMBER] Checking AmberTools16 installation Bence Hégely (Tue Sep 06 2016 - 05:24:34 PDT)
- [AMBER] about print_res in MMPBSA.py Thomas Evangelidis (Tue Sep 06 2016 - 08:37:34 PDT)
- [AMBER] [Amber] Periodic Box Issue Chase Zagorec-Marks (Tue Sep 06 2016 - 09:04:41 PDT)
- [AMBER] query regarding radial distribution function plot. Saman Yousuf ali (Tue Sep 06 2016 - 14:08:46 PDT)
- [AMBER] MMPBSA analysis for a heme protein Smriti Sharma (Tue Sep 06 2016 - 22:07:34 PDT)
- [AMBER] How to assign frame range for cpptraj analysis? sunyeping (Wed Sep 07 2016 - 02:04:30 PDT)
- [AMBER] Problem with MCPB.py workflow after calculation of force constants. Abhi Acharya (Wed Sep 07 2016 - 02:15:49 PDT)
- [AMBER] changepot Xiaoliu Zhang (Wed Sep 07 2016 - 11:49:10 PDT)
- [AMBER] distance based mask Kris Feher (Wed Sep 07 2016 - 12:09:24 PDT)
- [AMBER] Switching from PM3-PDDG to SCC-DFT method Thakur, Abhishek (Wed Sep 07 2016 - 14:02:20 PDT)
- [AMBER] Upgrade AMBER 14 to 16 Anton Perera (Thu Sep 08 2016 - 01:44:52 PDT)
- [AMBER] On the simulation of phosphate ions in water solution Casalini Tommaso (Thu Sep 08 2016 - 01:49:56 PDT)
- [AMBER] question on the reference data of GIST Shunsuke Mizutani (Thu Sep 08 2016 - 01:54:31 PDT)
- [AMBER] Radial Distribution Function Fatema Al-Haddad [fy14fmah] (Thu Sep 08 2016 - 02:27:02 PDT)
- Re: [AMBER] autoimage bug? Filip Persson (Thu Sep 08 2016 - 05:32:36 PDT)
- [AMBER] Problem with CRD files dhanasekar.mbu.iisc.ernet.in (Thu Sep 08 2016 - 08:05:38 PDT)
- [AMBER] PME calculation for Vacuum? Mochena, Mogus D. (Fri Sep 09 2016 - 11:36:27 PDT)
- [AMBER] generating topology file for non-standard amino acid Chitrak Gupta (Fri Sep 09 2016 - 15:17:06 PDT)
- [AMBER] Calculations of dG for protein-ions James Starlight (Sat Sep 10 2016 - 13:57:36 PDT)
- [AMBER] lipid bilayer Sofia Vasilakaki (Sat Sep 10 2016 - 16:17:05 PDT)
- [AMBER] Add Molecule symmetry to sander tanfei777.sina.cn (Sat Sep 10 2016 - 17:58:28 PDT)
- [AMBER] Speed issue with Accelerated molecular dynamics. Abhilash J (Sun Sep 11 2016 - 00:35:47 PDT)
- [AMBER] PCA plotting waleed zalloum (Sun Sep 11 2016 - 04:00:32 PDT)
- [AMBER] 回复：Re: Add Molecule symmetry to sander tanfei777.sina.cn (Sun Sep 11 2016 - 06:53:00 PDT)
- [AMBER] 回复： Enforced Symmetry? tanfei777.sina.cn (Sun Sep 11 2016 - 18:02:50 PDT)
- [AMBER] Problems about creating ligand leap input files 康宁 (Sun Sep 11 2016 - 20:37:20 PDT)
- [AMBER] cpptraj Beale, John (Mon Sep 12 2016 - 02:16:14 PDT)
- [AMBER] MMPBSA with different external Dielectric Constant Elvis Martis (Mon Sep 12 2016 - 03:15:25 PDT)
- [AMBER] cpinutil.py describe flag Elisa Pieri (Mon Sep 12 2016 - 07:47:03 PDT)
- [AMBER] pmemd Segmentation fault on Tutorial A27 liu junjun (Mon Sep 12 2016 - 09:01:33 PDT)
- [AMBER] SCC-DFTB Thakur, Abhishek (Mon Sep 12 2016 - 09:04:01 PDT)
- [AMBER] NVIDIA GTX-970 Class Action Suit $30 settlement link Ross Walker (Mon Sep 12 2016 - 12:03:23 PDT)
- [AMBER] bad atom type: Mn Thomas Evangelidis (Mon Sep 12 2016 - 18:08:07 PDT)
- [AMBER] How by residue decomposition in MMPBSA.py is performed? Irina Ivanova (Mon Sep 12 2016 - 21:53:48 PDT)
- [AMBER] comparing pytraj vs. sander output Niel Henriksen (Mon Sep 12 2016 - 22:07:57 PDT)
- [AMBER] Error: cannot run "/share/apps/amber/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit shahab shariati (Tue Sep 13 2016 - 04:25:41 PDT)
- [AMBER] Fullerene RESP charges derivation Fabio Bologna (Tue Sep 13 2016 - 06:04:41 PDT)
- [AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type. Failed to generate parameters Parameter file was not saved. shahab shariati (Tue Sep 13 2016 - 22:29:57 PDT)
- [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations hari krishna (Tue Sep 13 2016 - 22:30:10 PDT)
- [AMBER] Fwd: query with amber Pooja Kesari (Tue Sep 13 2016 - 23:00:50 PDT)
- [AMBER] How to "not" strip an ion (say Mg) in MMPBSA Hirdesh Kumar (Wed Sep 14 2016 - 03:06:57 PDT)
- [AMBER] Force field ff14SB Anna Cebrian Prats (Wed Sep 14 2016 - 04:06:44 PDT)
- [AMBER] Parameters for GppNHp ligand. Dd H (Wed Sep 14 2016 - 07:31:29 PDT)
- [AMBER] Potential Energy in 3D-RISM Maksim Mišin (Wed Sep 14 2016 - 12:16:29 PDT)
- [AMBER] Problem with CRD files dhanasekar.mbu.iisc.ernet.in (Wed Sep 14 2016 - 23:24:10 PDT)
- [AMBER] Glaycam04 version for q4md-CD FF Helen Lvy (Thu Sep 15 2016 - 07:20:41 PDT)
- [AMBER] Continue a simulation run Pooja Kesari (Thu Sep 15 2016 - 08:18:47 PDT)
- [AMBER] WARNING: The unperturbed charge of the unit: -0.99 is not zero. shahab shariati (Thu Sep 15 2016 - 11:41:22 PDT)
- [AMBER] changeLJPair/pmemd.cuda Batuhan Kav (Thu Sep 15 2016 - 13:32:23 PDT)
- [AMBER] DNA residue atom names. Christian Schafmeister (Thu Sep 15 2016 - 17:57:41 PDT)
- [AMBER] hbond and autoimage Francesco Gentile (Thu Sep 15 2016 - 23:24:29 PDT)
- [AMBER] aromatic ring plane distorted Thomas Evangelidis (Fri Sep 16 2016 - 04:03:03 PDT)
- [AMBER] "ATTN, need revision" in frcmod file / Could not find bond parameter & Could not find angle parameter shahab shariati (Fri Sep 16 2016 - 11:25:50 PDT)
- [AMBER] How to get GppNHp parameters. Dd H (Fri Sep 16 2016 - 19:44:46 PDT)
- [AMBER] Simulation of protein complex with four protein chains Jag Silwal (Sat Sep 17 2016 - 12:30:01 PDT)
- [AMBER] AMBER installation help Huma Tahir (Sat Sep 17 2016 - 12:58:22 PDT)
- [AMBER] Installing amber tools on ubuntu neelam wafa (Sat Sep 17 2016 - 13:07:37 PDT)
- [AMBER] chamber in parmed (Amber16) Song-Ho Chong (Sun Sep 18 2016 - 09:21:18 PDT)
- [AMBER] delete residue in tleap Thomas Evangelidis (Sun Sep 18 2016 - 15:46:19 PDT)
- [AMBER] adaptive qm/mm NVT, number of quantum atoms outside the legal range Stregone (Mon Sep 19 2016 - 05:12:19 PDT)
- [AMBER] SCC-DFTB Thakur, Abhishek (Mon Sep 19 2016 - 07:44:03 PDT)
- [AMBER] Parmchk - missing nitro improper Miha Purg (Mon Sep 19 2016 - 11:50:37 PDT)
- Re: [AMBER] Problem with atommap function in cpptraj (v16) Daniel Roe (Tue Sep 20 2016 - 07:06:49 PDT)
- Re: [AMBER] Amber16: COM's in GPU version Carlos Simmerling (Tue Sep 20 2016 - 07:53:13 PDT)
- [AMBER] what is DFTB and SCC-DFTB Thakur, Abhishek (Tue Sep 20 2016 - 07:55:50 PDT)
- [AMBER] fixing concentration in implicit solvent simulation Chitrak Gupta (Tue Sep 20 2016 - 08:12:48 PDT)
- [AMBER] positive electrostatic energy MM-PBSA Trang Nguyen (Tue Sep 20 2016 - 22:03:34 PDT)
- [AMBER] Parmchk - missing improper parameter for nitro group Miha Purg (Wed Sep 21 2016 - 00:25:45 PDT)
- [AMBER] frame wise MMPBSA energy difference Hirdesh Kumar (Wed Sep 21 2016 - 02:15:07 PDT)
- [AMBER] DFTB and slater koster files Markus Kaukonen (Wed Sep 21 2016 - 02:30:58 PDT)
- [AMBER] A refresher on how non-bonding terms are represented in a topology file. Christian Schafmeister (Wed Sep 21 2016 - 10:10:42 PDT)
- [AMBER] setup time with pmemd.cuda Hannes Loeffler (Wed Sep 21 2016 - 11:06:34 PDT)
- [AMBER] Segmentation fault in tleap when using "sequence" command Lane Votapka (Wed Sep 21 2016 - 13:31:58 PDT)
- [AMBER] dihedral PCA amber Neha Gandhi (Wed Sep 21 2016 - 20:08:10 PDT)
- [AMBER] Plot activesite water vs time. Saman Yousuf ali (Wed Sep 21 2016 - 21:24:38 PDT)
- [AMBER] Implicit solvent with GPU AMBER and Pulling direction in SMD Ana Bergues (Thu Sep 22 2016 - 00:38:16 PDT)
- [AMBER] How to 2D-RDF in cpptraj. Saman Yousuf ali (Thu Sep 22 2016 - 01:05:25 PDT)
- [AMBER] Fw:car_to_files.py in AMBER16 is not available. Jinfeng Huang (Thu Sep 22 2016 - 02:23:43 PDT)
- [AMBER] Unstable SHAKE ABHIJEET CHOWDHURY (Thu Sep 22 2016 - 08:49:51 PDT)
- [AMBER] minimzation & MD in vacuo Thomas Evangelidis (Thu Sep 22 2016 - 09:54:48 PDT)
- [AMBER] cpptraj gist core dumped peter.schmidtke.discngine.servier.com (Thu Sep 22 2016 - 23:40:23 PDT)
- [AMBER] netcdf trajectory Andrew Bostick (Fri Sep 23 2016 - 01:28:50 PDT)
- [AMBER] MM-PBSA calculation in different temprature shahab shariati (Fri Sep 23 2016 - 05:07:04 PDT)
- [AMBER] strip waters using distance criteria Thomas Evangelidis (Fri Sep 23 2016 - 06:23:07 PDT)
- [AMBER] How aggressively should bond, angle, torsion parameters be coalesced? Christian Schafmeister (Sat Sep 24 2016 - 06:58:11 PDT)
- [AMBER] netcdf trajectory Andrew Bostick (Sat Sep 24 2016 - 13:39:38 PDT)
- [AMBER] netcdf trajectory Andrew Bostick (Sun Sep 25 2016 - 00:09:01 PDT)
- [AMBER] Signal: Segmentation fault (11) shahab shariati (Sun Sep 25 2016 - 02:10:03 PDT)
- [AMBER] Restrain in Umbrella Sampling ATUL KUMAR (Sun Sep 25 2016 - 07:12:10 PDT)
- [AMBER] 2 ns heating in constant pH tutorial inquiry Andrew Schaub (Sun Sep 25 2016 - 08:56:29 PDT)
- [AMBER] create a cubic box of 4.5 nm Jesmita Dhar (Mon Sep 26 2016 - 01:39:18 PDT)
- [AMBER] problem about Using ParmEd or xParmEd 杨金鹏 (Mon Sep 26 2016 - 04:06:02 PDT)
- [AMBER] PGI Fortran/C/C++ workstation Hector A. Baldoni (Mon Sep 26 2016 - 05:29:32 PDT)
- [AMBER] pmemd.cuda: multiple bonds illegal for SHAKEH Hannes Loeffler (Mon Sep 26 2016 - 07:57:31 PDT)
- [AMBER] RESP charge fitting error in MCPB.py zycz138.126.com (Mon Sep 26 2016 - 17:54:06 PDT)
- [AMBER] Issue regarding parametrization Mahrukh Imtiaz (Tue Sep 27 2016 - 04:22:41 PDT)
- [AMBER] tleap cannot solvate unit in amber16 windy (Tue Sep 27 2016 - 05:53:00 PDT)
- [AMBER] Tcl problem Elisa Pieri (Tue Sep 27 2016 - 06:59:02 PDT)
- [AMBER] Amber NaN error DIAO Jianxiong (Tue Sep 27 2016 - 15:53:13 PDT)
- [AMBER] Can amber handle carbon -- nitrogen double and single bond? Ming Tang (Wed Sep 28 2016 - 01:43:52 PDT)
- [AMBER] ACS COMP award deadline for Spring 2017 Carlos Simmerling (Wed Sep 28 2016 - 03:48:05 PDT)
- [AMBER] mdin for LIO interface Hector A. Baldoni (Wed Sep 28 2016 - 04:03:53 PDT)
- [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes. Pooja Kesari (Wed Sep 28 2016 - 04:38:28 PDT)
- [AMBER] MMPBSA.py error Your ligand residues must be sequential in your complex maryam azimzadehirani (Wed Sep 28 2016 - 06:06:42 PDT)
- [AMBER] scaling of mpi version of pmemd.mpi (AMBER14) and that of the MMPBSA.py.MPI Kris Feher (Wed Sep 28 2016 - 12:40:37 PDT)
- [AMBER] on periodic conditions and unspecified launch failure Elisa Pieri (Wed Sep 28 2016 - 13:46:26 PDT)
- [AMBER] FMN parameters ruqaiya khalil (Wed Sep 28 2016 - 22:46:13 PDT)
- [AMBER] Disparities in H-bond lifetimes calculated through different approaches Praneeth Bommisetti (Wed Sep 28 2016 - 23:03:25 PDT)
- [AMBER] Error in the second step using MCPB.py Tiffani Rovira (Thu Sep 29 2016 - 02:26:41 PDT)
- [AMBER] using boundary information from previous run Hirdesh Kumar (Thu Sep 29 2016 - 04:45:46 PDT)
- [AMBER] Pressure of the system during equilibration Debodyuti Dutta (Thu Sep 29 2016 - 06:01:20 PDT)
- [AMBER] Problem regarding sccdftb not converging amitosh gautam (Thu Sep 29 2016 - 22:36:34 PDT)
- Re: [AMBER] LEaP and PARMSETs David A Case (Fri Sep 30 2016 - 04:57:06 PDT)
- [AMBER] How to read prmtop file flag pointer section Xiaoyu Wang (Fri Sep 30 2016 - 11:43:05 PDT)
- [AMBER] Save the average structure from two pdb files Iqbal, Muhammad Sajid (Fri Sep 30 2016 - 15:22:11 PDT)
- Last message date: Fri Sep 30 2016 - 20:00:02 PDT
- Archived on: Fri Nov 15 2024 - 05:55:28 PST
