Hi Jason,
Sorry for my late replay, it took me some time to implement you offer, but
it seems to work like charm.
Thanks again,
Itamar
On 12 March 2013 00:21, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Mar 11, 2013 at 6:34 AM, Itamar Kass (Med)
> <itamar.kass.monash.edu>wrote:
>
> > Hi,
> >
> > In the last few years I have used GROMAC in my research. Recently I moved
> > to work with amber (amber12).
> >
> > Currently, I am trying to study cyclic peptides, in which the backbone
> > amino group of the first residue has a peptide-bond with the carboxyl
> > backbone group of the last residue. My question is how to do this in
> tleap.
> > I tried to use 'crosslink' and 'bond' but the FF missed parameters. for
> > this new bond, I guess because tleap translate the residues to N-ter and
> > C-ter. Is there anyway to overcome it without tinkering the topology
> file?
> >
>
> Huh, neat. My suggestion: copy the leaprc.ff12SB file
> ($AMBERHOME/dat/leap/cmd/) into your current directory as just "leaprc".
> Then, get rid of the residue mapping that defines terminal residues as the
> N- or C-terminal variants of those residues. It will look something like
> this:
>
> addPdbResMap {
> { 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" }
> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
> { 0 "HID" "NHID" } { 1 "HID" "CHID" }
> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
> { 0 "MET" "NMET" } { 1 "MET" "CMET" }
> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
> ...
>
> Then, manually draw the bond from the C-terminal carbon to the N-terminal
> nitrogen.
>
> While I think the above should work, I've never actually tried it.
>
> Good luck!
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
===========================================
| Itamar Kass, Ph.D.
| Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass.monash.edu
============================================
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Mar 24 2013 - 04:00:03 PDT
