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Generate residue-residue contact matrix for MD simulation trajectories Using residue-residue contact map to understand the distance and spatial relationship is important for protein dynamics and protein 3D conformation modeling. Here in this tutorial, I use mdtraj to demonstrate how to generate a contact map from a static single-frame PDB file and visualise it with matplotlib. Taken mini protein gHEEE_02 as an example, we first load the pdb file (generated from rosetta modeling). You could virtually take any protein containing PDB file as an example, such as 5W9F. # load mdtraj package  import mdtraj as mt # load the pdb file and transform it into a mdtraj.Trajectory object p = mt.load_pdb("5W9F.pdb") # now we could check some properties of the trajectory object p <mdtraj.Trajectory with 1 frames, 335 atoms, 41 residues, without unitcells at 0x820a38208> Therefore, we know that this protein contains 1 frame, 41 residues....

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...

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-...