Use VMD to generate PSF and PDB of the water box.Use combine.inp to generate two PEG vacuum PSF file.Use the following 1.inp to generate 1.psf, and change 1 to 2 and generate 2.psf.Save the two PEG PDB files separately as 1.pdb and 2.pdb.Use VMD to prepare two PEG PDB files with proper coordinates.I got the PDB files of one PEG from my previous simulation.The following procedure is what I used for the system. I find the clue that CHARMM will generate multiple PSF files for each segments at the beginning, and then attached all PSF files together as a whole.īased on the script from the website, I tried several times and got the answer. I used a multiple chains protein in PDB as input files, and look into the input scripts.
By the way, PEG with GAFF seemed not that rational compared with that using CHARMM ether force field.Īs a beginner of CHARMM, the learning process is really painful.
Vmd movie rotate and trajectory Pc#
This tutorial has been prepared in an PC computer running the Linux Ubuntu operating system with VMD version 1.9.3. The topology file is vph.prmtop and the trajectory file is vph.nc. Never mind, my story in this blog is using CHARMM ether force field for PEG. For this tutorial we are going to use a trajectory of a protein receptor that has a bound ligand in the active site. In AMBER, this is pretty simple, I just need to prepare a PDB files contains two PEG and add TER between the two molecules. If you read through my blog, you will see I did post one blog about setting up PEG in a TIP3P water box with CHARMM ether force field. The third thing is to change the animation format. In line 67, change rockandroll to rotation. The second thing is to change the movement of molecules. And delete line 130 to 147, this part will find a working directory according to different system. The first thing I change is the working directory in Line 63, delete frames and write to your specific directory. The file is /Applications/VMD 1.9.3.app/Contents/vmd/plugins/noarch/tcl/vmdmovie1.9/vmdmovie.tcl If you need to generate tons of animation and sometimes VMD crashed, the repeatable setting will make me crazy. What I want is GIF, rotation along y axis and a specific working directory. The default movement of molecules is Rock and Roll. The default working directory is lkjadfljaslkfjlasdfjlsadfdd……. But the default setting is not proper for me. I use it every week to make gif animation and show them in the group meeting. #set sphere radius set probe 0.8 #set the box side-length, this is a cube set length 39.91 #the side-length is divided into N grid, 50 is enough to visualize set step [expr close $outfile mol new Si_close_index.xyz
#Change background color to white color Display Background white
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