Memory Down

Bugs? The newly released amber14sb made modifications for protein, DNA and RNA. This force field could be ported into gromacs as I already introduced previous. However, there are some small bugs in the improper dihedral angles of HID, HIE and HIP. So when generating tpr file, errors would be prompted. When run grompp -f npt.mdp -p topol.top -c protein.gro -o product.tpr -n index, errors occur: ERROR 1 [file topolff14sb_Protein_chain_B.itp, line 208041]:   No default Improper Dih. types The reason is that the parameters for some dihedral angles are missing. So we need to fix this. How to fix? Add the following two lines in the ffbonded.itp after the 730th lines: NA  CW  CC  CT       4      180.00     4.60240     2     ;;; HID force field added NA  CV  CC  CT       4      180.00     4.60240     2     ;;; HID force fie...

Amber force fields are popular for protein, DNA, RNA and lipid simulations. Recently updated amberff12, amberff14 and amberff15 were reported to perform better than amber99sb and amber99sb-ildn. Gromacs is a commonly used simulation software, which using OpenMM to enable GPU acceleration. Gromacs is fast and easy to use. A lot of people use amberff in Gromacs. So to use the newly release amberff12 and amber14sb in gromacs, we need to some work. Step 1. Install Gromacs 4.6.x or Gromacs 5.0.x or Gromacs 5.1.x Installation instructions could be find here: For 4.6.x http://www.gromacs.org/Documentation/Installation_Instructions_4.6 For 5.0.x and 5.1.x http://www.gromacs.org/Documentation/Installation_Instructions_5.0 Suppose you are user john, you installed a gromacs 4.6.7 in /home/john/applications/. After installation, you should source the GMXRC by: source  /home/john/applications/gromacs.4.6.7/GMXRC And add topology files to environments by: export GMXLIB=/home/joh...

AmberTools 16 together with Ipython notebook Amber (starting from 16) supports Ipython notebook (also known as jupyther notebook), which is useful for trajectories visulization and analysis and is very powerful tool to record your commands.  Besides the amber mdcrd trajectories, you may also use it to analyze your gromacs trajectories.  The strength of IPython notebook is that it is flexible and extendable and very user-friendly.  In case you'd like to try IPython notebook together with MD trajectory analysis, you could first read few pages about Jupyter notebook and AMBER pytraj. http://jupyter.org/ http://ambermd.org/tutorials/analysis/tutorial_notebooks/nglview_notebook/ http://ambermd.org/tutorials/analysis/ If you'd like to use it, these are useful step-by-step instructions for Pytraj with Ipython here : You need to install conda or anaconda first. See this link   https://docs.continuum.io/anaconda/install 1. login to ...

There are some bugs when running GOLD 5.4 in parallel with PVM (parallel virtual machine). In the "intcor", there is not value reported in the final docking result file "bestranking.lst". Run-1: In parallel with PVM using 8 cpus (parallel_gold_li*) ============================== ====================== #     Fitness  S(hb_ext) S(vdw_ext)  S(hb_int)    S(int)      intcor      time                               File name                Ligand name        46.25       9.00       27.86              0.00      -1.06       ----         15.870    './ligands_ m1_2.mol2'    'ligand_001' ============================== ====================== If running...

Well, I am a Gromacs user, I am thinking about installing gromacs in windows, thus I could do some simple analysis more easily since my daliy work is all in Win 7 and SSH shell. So I did some research online, and found some websites talking about this topic. But I didnit find a very clear way to do so. Then I tried to install Gromacs 4.5.5 by myself in my HP Prodesk, which has Win 7 64-bit OS with Cygwin. Firstly, I tried to install FFTW 3.3.4, and things went quick well. $ tar zxvf fftw-3.3.4.tar.gz $ cd fftw-3.3.4 $ ./configure --prefix=/cygdrive/c/cygwin64/home/user/software/fftw-3.3.4 --enable-float --enable-shared $ make $ make install So far, everything was okay. Then, I downloaded Gromacs-4.5.5.tar.gz and copy to installation folder. And I unzip it and configure it, following by  "make -j 4", which gave me errors. Thus I added some commands in ./configure step. Later, I tried the following commands and still some error massage. $./configure --disable-...