VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Thu Oct 15 2020 - 01:05:34 CDT

What I would do is generate "template" parameters with paramchem, split the
.str file into the respective .rtf and .prm files for the topology and
parameters, respectively. And then copy paste the associated fragment
parameters into these files.

When dealing with overlaps, you could compare the overlapping portions of
both and see if there's good agreement, and then decide which ones you'll
paste into the whole molecule.

The CGenFF menu in the BuildPar tab of FFTK can generate PSF/PDB files from
your .str file

*Daniel Fellner BSc(Hons)*
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326

On Thu, Oct 15, 2020 at 6:52 PM Emma Wu <ewu20_at_illinois.edu> wrote:

> Hi all,
> I have a molecule that I have fragmented and parameterized each fragment
> using ffTK. I am now trying to combine the fragments but I am unsure how I
> should proceed. I have overlapping fragments that include the linker
> portion.
>
> Here are the things I am confused about:
> 1. Since I have the linker portions optimized through overlapping
> fragments, how would I combine that information into the pdb, psf, and par?
>
> 2. How would I get a new pdb of the full molecule from fragments pdbs that
> I have optimize?
>
> Thank you so much for all and any suggestions!
>
> Best,
> Emma
>