[gmx-users] New Molecule Topology

[Todor Antonijevic]

Hi,

I tried ATB but it has wrong database files. For example, Gromacs united
atom .itp file is missing Carbon 28,29 and 30. I hope I will get help from
them on this matter.

Thank you


On Fri, May 30, 2014 at 2:06 AM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:

> I think the Ausi ATB is a bit beter for initial topologies,but still needs
> some input afterwards.  They usually have less to change around needed, or
> beter charge sets, but tend to have problems with adding a hydrogen.  Only
> for 53a6 though.  Also, just loking at the ff topoloy you canput one
> together from scratch from what is already in gromacs, but painfull...there
> are a large amunt of MD's with all atom or berger lipids in a 53a6 which
> should work with a7 as well, and the ATB has a few constructed all or UA
> lipids, cholestorols on its site already done...
>
> My opinion,
>
> Stephan Watkins
>
> *Gesendet:* Donnerstag, 29. Mai 2014 um 16:55 Uhr
> *Von:* "Todor Antonijevic" <t_antoni at uncg.edu>
> *An:* gmx-users at gromacs.org
> *Betreff:* Re: [gmx-users] New Molecule Topology
> Hi Justin,
>
> Thank you for you answer.
> It sounds to me that using PRODRG server for the initial topology and then
> correcting atom types and other parameters according to Berger lipids is
> acceptable method.
>
> What about "constructing" cholesteryl oleate molecule by "gluing" together
> known cholesterol force field with oleate chain taken from POPC?
>
> Thank you in advance,
>
> Anton
>
>
> On Wed, May 28, 2014 at 8:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 5/28/14, 1:33 PM, Todor Antonijevic wrote:
> >
> >> Hi,
> >>
> >> I would like to create a topology file for cholesteryl oleate molecule.
> >> Is it a good practice to use PRODRG server to generate all connections,
> >> and
> >> then to change atom types and parameters according to the Berger force
> >> field?
> >>
> >> Is there a better approach?
> >>
> >>
> > No matter how you produce the initial topology (PRODRG, ATB, etc), you'll
> > likely end up gutting nearly the entire topology to replace the atom
> types,
> > charges, and bonded parameters.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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