This is part of my recent research. To make it simple, I am going to build a TIP3P water box with one PEG polymer (5 units).
CHARMM force field for ethers has been well testified in a the following paper with experimental data. So I have to say it the best force field for PEG by now.
Lee, Hwankyu, Richard M. Venable, Alexander D. MacKerell, and Richard W. Pastor. “Molecular Dynamics Studies of Polyethylene Oxide and Polyethylene Glycol: Hydrodynamic Radius and Shape Anisotropy.” Biophysical Journal 95, no. 4 (August 15, 2008): 1590–99. doi:10.1529/biophysj.108.133025.
You’d better know something about MD simulation or CHARMM. What you need to do is:
1. Download force field files.
2. Construct PEG in vacuum.
3. Build a water box.
Is it easy? This cost my four days to figure out how to do that. Dr. Justin Lemkul
gave me a lot of help.
The first part, force field files.
It is unbelievable that the published version for ethers missed some important termini for PEG. And you need to modify the par_all35_ethers-oh.prm file, because there are some duplicate terms. I choose to comment lines 157 to 166, which are old parameters. If you don’t do that. You will find that CHARMM will give error about these three dihedrals.
The second part, build PEG.
I knew nothing about CHARMM scripts. So I tried to figure out how CHARMMing.org and CHARMM-gui work. These online tools are really awesome! And I used the scripts got from them to do this step. The script is below.
* make a PDB file out of a sequence
read rtf card name top_all35_ethers-oh.rtf
read param card name par_all35_ethers-oh.prm
read sequ card
PEGM PEGM PEGM PEGM
gene a setup first GCL0 last GCL3
ic seed 1 C1 1 O1 1 C2
write coor pdb name peg5vac.pdb
* PDB file of custom sequence.
write psf card name peg5vac.psf
The third part, water box.
At the beginning, I tried to use scripts from CHARMMing and CHARMM-gui, but even I uploaded the ethers rtf and prm files, there would be errors. After trying hundreds of modification of these scripts, I gave it up.
Unintentionally, I found VMD can do that in a very easy way.
I am using iMac. So load the files in VMD by following commands using files got from the second part.
vmd peg5vac.psf peg5vac.pdb
Open tcl/tk console and input the following commands. New psf and pdb files will be generated. The size and center of box can be used in the simulation.
package require solvate
solvate peg5vac.psf peg5vac.pdb -t 15 -o peg5wat
set everyone [atomselect top all]
measure minmax $everyone
measure center $everyone
Commands are cited from http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node7.html.
Now you have peg5wat.psf and peg5wat.pdb. You can run your simulation!