VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 09 2013 - 16:32:44 CDT

Hi,
  I checked with my colleagues and the existing version of the cg builder
won't work with AMBER-specific input files, to our knowledge. If you could
convert the AMBER files and atom types to CHARMM, then converting the actual
files to PSF etc is merely mechanical. Probably the atom type conversion is
the major issue there.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jul 01, 2013 at 03:21:14PM -0600, Nathaniel Eagan wrote:
> Hello everyone,
>
> I have created fully-atomistic simulations of a fatty acid in AMBER and
> would like to perform a shape-based coarse graining of the molecule
> using the built-in CG-builder, but have run into a few snags. I cannot
> tell which one is limiting me most, if this application of SBCG is even
> possible. Any insight would be appreciated.
>
> I currently have:
> AMBER topology files (.top), coordinate files (.crd and original .pdb),
> trajectory files (mdcrd), and every other AMBER file associated with
> generating a full simulation.
>
> Issues:
> -The CG-builder requires a .psf if I want to keep my generated point charges
> -The .psf generator appears only to work with CHARMM .top or
> X-PLOR/NAMD .psf
> -I can find no way to convert AMBER .top to these file types
> -Trying to ignore this and run .psf generator with my .pdb and .top
> presents the error that my entire molecule (labeled with a single
> residue name) is an unparametrized component---it may just not
> understand my topology file format
> -The CG-builder seems like it might only be applicable to proteins or
> nucleic acids, so a fatty acid may not even work as far as I know
>
> If anyone has any input about how to help or to just flat out tell me
> that this will not work, I would greatly appreciate it.
>
> Thank you for your time,
> Nathaniel 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/