Previous Thread
Next Thread
Print Thread
Starter - How to create a correct .psf file (carbon)
#38294 06/29/21 02:12 PM
Joined: Jun 2021
Posts: 2
F
Forum Member
OP Offline
Forum Member
F
Joined: Jun 2021
Posts: 2
Hello,

I am a recent starter regarding the CHARMM forcefield. I am trying to learn it the best I can, however my field of interest is carbonaceous materials (graphene / carbon nanotubes / fullerenes) and despite the number of tutorials I have watched or read, I am still encountering problems for generating the required .psf file.

Basically, I have created a model of a fluoride-functionalized fullerene in Avogadro 1.2, and exported the .pdb file. I am providing it as an attachment here.

All I need at the moment is to obtain an accurate .psf file. From what I have read on this forum and other sources, I understand that most of the time fullerenes are parameterized as the sp2 aromatic carbon. I have also read articles that provide some experimental values regarding C-C interactions specific to carbon nanotubes. From what I have read, manually building or changing existing .psf files is not recommended for beginners, due to the way they are supposed to be built following specific rules and orders according to the .rtf and .prm files.

One specific way I have tried is by using the VMD plugin called AutoPSF, but it always ends up with 1 unparameterized component, which I am not sure how to go about.

Can anyone provide me some ideas as to how generating a .psf file for a fullerene should be approached? Is it really so difficult (I have been stuck for at least 2 weeks now)? Can you recommend some good sources that can help me do this?

Let me know if I can provide you with any more details.

Attached Files
C240-F-1.txt (48.82 KB, 195 downloads)
SHA1: 91d29fb7bd63e11511795888ecefafba9ad9635d
Last edited by FlickerBeam; 06/29/21 02:12 PM.
Re: Starter - How to create a correct .psf file (carbon)
FlickerBeam #38295 06/29/21 03:35 PM
Joined: Sep 2003
Posts: 8,580
Likes: 11
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,580
Likes: 11
The CHARMM force field is designed for discrete small molecules, either as single residues, or polymers of small residues with a small number of well defined linkages. While fullerenes might be reasonable to attempt, large sheets like graphene or nanotubes with variable registration of the how the tube is sealed pose challenges for tools designed for residue based biological force fields. As it stands, you would first need to create a residue that defines the complete fullerene or nanotube, which can be used to create a PSF.

Since you've used Avogadro, one thing you might try is export the structure as a .mol2 file and then use the cgenff tool to create the residue and assign the atom parameter types and bond based parameters. As usual, no warranty expressed or implied.

There are some (older) discussions of nanotubes in the parameter forum.

The charmm-gui site has some facilities for building nanotubes.

Last edited by rmv; 06/29/21 08:32 PM. Reason: charmm-gui

Rick Venable
computational chemist

1 member likes this: FlickerBeam
Re: Starter - How to create a correct .psf file (carbon)
rmv #38332 09/01/21 02:58 PM
Joined: Jun 2021
Posts: 2
F
Forum Member
OP Offline
Forum Member
F
Joined: Jun 2021
Posts: 2
Thank you very much for your reply rmv.

I have looked into CGenFF tool and .mol2 files, as well as charmm-gui website. Took me a while, and I had a side project that intervened in the meantime, but I am back.

Being a beginner I have not managed to find a very good way of using these to attain the fullerene parameterization. However, I have used the Tk console to set the types of atoms to CG2R61, CG2R66 and FGA1. Although I have managed to successfully create .pdbs and .psfs files through the Tk console, I have yet to run the simulations so I am not sure if this will work to the end.

My system contains three such fullerenes in one single box.

I have not created residues for the structures, because I have not yet found a protocol. I hope it will work this way, I will post here again if I achieve any progress.

On the side, would anyone be able by chance to share a bit more guidance on how one would use the CGenFF tool to create a carbon-structure residue?


Moderated by  lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 7.3.31-1~deb10u1 Page Time: 0.008s Queries: 22 (0.005s) Memory: 0.7277 MB (Peak: 0.7877 MB) Data Comp: Off Server Time: 2021-12-01 00:01:47 UTC
Valid HTML 5 and Valid CSS