[gmx-users] Topology from semiempiricaly optimized structure

Erik Lindahl lindahl at csb.stanford.edu
Fri Jun 11 17:14:18 CEST 2004


The Gromacs program x2top can probably construct the connectivity 
automatically for you and create an rtp entry, but you will have to 
assign atomtypes and charges manually.

There are a couple of commercial programs on the market that claim to 
do parameter assignments completely automatically for any molecules, 
but if you check their results you'll be pretty scared...



On Jun 11, 2004, at 4:59 PM, Semen Esilevsky wrote:

> Hi all!
> I have a small molecule (a fluorescent probe), which
> is optimized on the semiempirical level, so I know the
> geometry. As far as I understand the only way to make
> a topology for it is to write it by hands using
> appropriate atom types and forcefield parameters.
> However it seems to be a week of work for ~80 atoms.
> Does the program (or script) exists for this routine
> task?
> Thank you in advance,
> Semen
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