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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Received on Thu Apr 22 2004 - 10:53:00 PDT
