I have been reading this paper Soft Matter, 2017, 13, 1904 and in this paper, they simulate benzene in GROMACS using CHARMM.
They mention that they performed simulations of benzene using the CHARMM force field, in GROMACS-4.6. However, I have been trying to find the parameters for benzene from the CHARMM force field, but I am not able to find them. CHARMM-GUI seems to work best for complex structures available on RCSB, CGenFF is not yielding results, and I also tried swissparam.ch, but even that did not provide an ITP file I can use for GROMACS.
My question is: where can I find parameters for benzene so I can can create my own .itp file and .pdb file, so I can run simulations on GROMACS? Once I have those files, I believe I can write a quick topol.top file to run my simulation.
Dear Satyen Dhamankar ,
Which error did swissparam return?
I was able to get the .itp and .pdb converting a .xyz coordinate file to a .mol2 file using openbabel and then submitting this latter to swissparam.
(I tried with a .mol2 file generated by molden, but its format was strange and swissparam did not recognize it).
Best,
Felippe
One can always do things by hand. Phenylalanine (RESI PHE in the CHARMM basic topology file) has a convenient benzene ring. In your favorite text editor, delete everything but the phenyl group and CB. Rename CB to HG and set its type to be HP. Adjust the charges and fix the bonding table and voila: you have benzene.
Personally, I think it educational to occasionally get one's hands dirty. Poking around in the parameter files lets one understand what is truly happening inside the black boxes. There generally isn't any magic.
You can try this "http://www.charmm-gui.org/?doc=input/ligandrm" You can simply draw benzene and generate its topology and parameters files.
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