AMBER Archive (2006)

Subject: AMBER: Problem with "impose" in leap

From: Osmar Norberto de Souza (osmarns_at_inf.pucrs.br)
Date: Mon May 15 2006 - 06:27:13 CDT

Dear AMBER Users,

     I am trying to generate a specific 3D structure for a polypeptide starting from the sequence and a
pair of phi-psi angles using the leap module of AMBER7. The angles are imposed using the "impose"
command in leap. However, whilst the psi angle of residue "i" is placed correctly, the phi angle of
residue "i" is being assigned to residue "i+1", generating therefore a distorted structure.
     Is this a known problem with leap? Is there a solution to it? Any help is welcome.

     Its follows below an example of the leap input for the Trp_cage polypeptide I am using. The
"impose" command is shown only for the first three residues.

------leap.in------------------------------
source leaprc.ff94
TRP_cage = sequence { NASN LEU TYR ILE GLN TRP LEU LYS ASP GLY
                          GLY PRO SER SER GLY ARG PRO PRO PRO CSER }
impose TRP_cage { 1 } {
{ C N CA C -45.00 }
{ N CA C N -56.14 }
}
impose TRP_cage { 2 } {
{ C N CA C -43.98 }
{ N CA C N -51.31 }
}
impose TRP_cage { 3 } {
{ C N CA C -66.47 }
{ N CA C N -30.90 }
}
          .
          .
          .
savePdb TRP_cage TRP_cage_teste.pdb
------end of leap.in------------------------

     Thank you very much for your attention,

     Osmar

Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas - LABIO
----------------------------------------------------------------------------
Osmar NORBERTO DE SOUZA, PhD |
LABIO | Tel: +55-51-3320-3611 r.24
PPGCC, PPGBCM & IPB - PUCRS | Fax: +55-51-3320-3621
Av. Ipiranga, 6681 |
Prédio 16 - Sala 106 |
90619-900 - Bairro Partenon | E-mail:
Porto Alegre - RS | osmarns_at_inf.pucrs.br
Brasil |
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