AMBER Archive (2004)

Subject: AMBER: Bond type in leap

From: anshul_at_imtech.res.in
Date: Thu Apr 22 2004 - 14:22:31 CDT

I have sketched some peptides using InsightII for use in amber for running
dynamics. when i load the saved pdb files in leap and use desc to get the
description, it shows that C and O atoms of the peptide bond are joined
with asingle bond instead of the double bond.

> desc x.1.C
ATOM
             Normal Perturbed
Name: C C
Type: C C
Charge: 0.612 0.000
Polarization: 0.000 0.000
Element: C (not affected by pert)
Atom flags: (decimal 131072 hex 0x20000)
        posfxd n posblt n posdrwn n selected n
        pert n notdisp n touched n posknwn Y
        internal n needsmin n needsbuild n
Atom position: 5.486000, 2.705000, 0.000000
Atom velocity: 0.000000, 0.000000, 0.000000
  Bonded to .R<NGLN 1>.A<CA 5> by a single bond.
  Bonded to .R<NGLN 1>.A<O 19> by a single bond.
  Bonded to .R<GLN 2>.A<N 1> by a single bond.

Do I need to add the double bonds in this case using the bond con=mmand or
what else should I do.

Initially when I loaded the peptide in leap it added 4 missing atoms:

> x = loadpdb glutamin.pdb
Loading PDB file: ./glutamin.pdb
Created a new atom named: H within residue: .R<NGLN 1>
  Added missing heavy atom: .R<CGLN 10>.A<OXT 18>
  total atoms in file: 170
  Leap added 4 missing atoms according to residue templates:
       1 Heavy
       3 H / lone pairs
  The file contained 1 atoms not in residue templates

When I edit the unit I see an additional hydrogen which is not bonded to
any of the atoms. Using bondbydistance command it gets attached to the N
of NH3 group. Should i delete this additional hydrogen or not. Otherwise
if the unit is checked it shows this Hydrogen to be without a type along
with a wrning of close contact.

check x
Checking 'x'....
FATAL: Atom .R<NGLN 1>.A<H 20> does not have a type.
Warning: Close contact of 1.554606 angstroms between .R<NGLN 1>.A<HG2 11> and .R<GLN 2

Any suggestions will be highly useful to me.
With regards,

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