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
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Received on Mon Mar 11 2013 - 06:30:05 PDT
