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.
I got new tasks from my dear advisor. Two PEGs in one TIP3P water box. In AMBER, this is pretty simple, I just need to prepare a PDB files contains two PEG and add TER between the two molecules. Never mind, my story in this blog is using CHARMM ether force field for PEG. By the way, PEG with GAFF seemed not that rational compared with that using CHARMM ether force field.
As a beginner of CHARMM, the learning process is really painful. I got help from CHARMMing.org. I used a multiple chains protein in PDB as input files, and look into the input scripts. 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.
Based on the script from the website, I tried several times and got the answer. The following procedure is what I used for the system.
- I got the PDB files of one PEG from my previous simulation.
- Use VMD to prepare two PEG PDB files with proper coordinates.
- Save the two PEG PDB files separately as 1.pdb and 2.pdb.
- Use the following 1.inp to generate 1.psf, and change 1 to 2 and generate 2.psf.
- Use combine.inp to generate two PEG vacuum PSF file.
- Use VMD to generate PSF and PDB of the water box.