I agree with Anselm -- you should look at the Manchester Parm database and
see if what you need is there, there is no point reinventing the wheel.
However, I'll address the issue you are having, as well, in case you need to
come back to it.
The error you're receiving is indicative of the residue not having a head or
tail atom defined (basically, leap doesn't know which atoms to connect to
the previous and next residues, so it chokes). What you should do is define
these. I'm going to assume you have some kind of amber prep file that you
got from amber (although mol2 works just as well, just substitute the prep
for mol2 in the commands I suggest). First what you should do is create an
OFF library of your residues. You can do this in a separate leap session,
and there is no need to source another leaprc to load a force field (since
all you're doing is saving a library).
RES = loadamberprep your_prep_file.prep
set RES head RES.1.ATOM
set RES tail RES.1.ATOM2
saveoff RES RES.lib
Where ATOM and ATOM2 are the atoms that connect to the residue before and
after, respectively. And now you can use the RES.lib (via loadoff) when you
load your library.
Hope this helps,
Jason
On Fri, Dec 10, 2010 at 10:04 AM, Anselm Horn <
Anselm.Horn.biochem.uni-erlangen.de> wrote:
> Hi Baljinder,
>
> > I am working on protein with three phophorylated residues. Parameters for
> > these residues was generated using ANTECHAMBER and was uploaded and it
> > seemed working . But finally while uploading the protein tleap gave this
> > message:
> > *> apoprotein= loadpdb apoprotein.pdb
> > Loading PDB file: ./apoprotein.pdb
> > One sided connection. Residue: Displayed missing connect0 atom.
> > One sided connection. Residue: missing connect1 atom.
> > One sided connection. Residue: Displayed missing connect0 atom.
> > One sided connection. Residue: missing connect1 atom.
> > One sided connection. Residue: Displayed missing connect0 atom.
> > One sided connection. Residue: missing connect1 atom.
> > total atoms in file: 2717
> > Leap added 2660 missing atoms according to residue templates:
> > 2660 H / lone pairs*
> > I am working on AMBER 10.
>
> it seems that you have issues with the definition of the backbone
> connection atoms within your new residues.
>
> Maybe the parameters you need are readily available from
>
> http://www.pharmacy.manchester.ac.uk/bryce/amber
>
> so that you don't have to reinvent the wheel but can rely on already
> published work.
>
> Regards,
>
> Anselm
>
> Bioinformatik
> Institut für Biochemie
> Friedrich-Alexander-Universität Erlangen-Nürnberg
> Germany
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 10 2010 - 08:00:02 PST
