AMBER Archive (2002)

Subject: prmtop file question.

From: Carlos Andres Ramirez-Mondragon (cramirez_at_andrew.cmu.edu)
Date: Wed Jul 17 2002 - 16:15:59 CDT

I have a question regarding a 'BLA' character that appears in the FLAG
TREE_CHAIN_CLASSIFICATION section of my prmtop file. These appear at the
very beginning of the section, and correspond exactly to the atoms of the
N-terminal residue. As well, this BLA statement appears at the very end of
the section corresponding to the atoms of the C-terminal residue. I made
sure to have the NMET defined at the beginning of my pdb file, and TER
CGLN at the end. I went ahead and opened xleap with the leaprc.ff02 and
immediately (no solvent) created my inpcrd and prmtop files. However, I
still get these BLA characters in the FLAG_TREE_CHAIN_CLASSIFICATIOn
section of the prmtop file. Is this normal? Is this an error on the pdb
file? When I open xleap and load the .pdb it states:

Added missing heavy atom: .R<CGLN 355>.A<OXT 18>
total atoms in file: 2825
Leap added 2706 missing atoms according to residue templates:
1 Heavy
2705 H /lone pairs

When using saveAmberparm I get:

Building topology.
Building atom parameters.
Building bond angles.
Building proper torsion parameters.
Building improper torsion parameters.
 total 1161 improper torsions applied
Building H-Bond parameters.
Marking per-residue atom chain types
 (Residues lacking connect0/connect1 -
  these don't have chain types marked:

        res total affected

        CGLN 1
        NMET 1
)
(no restraints)

Thank you so very much for your attention. Any input would be appreciated.
As well, I am inquiring on what M,S,B,3,E mean exactly under tree name
(JTREE(I))?

Carlos Andres