Hi,
when leap in AMBER 7 reads the following PDB snippet (residue with an
insertion code) it will insert an C-terminus and N-terminus into the
sequence although the residues 105 and 105A are bonded to each other.
The leap output for the 'loadpdb' and 'describe' commands are attached.
This problem does occur for both our AMBER7 SGI and Linux installations,
while for AMBER6 the program behaves correctly. Has anyone already
encountered this problem or knows a fix for it?
Thanks in advance!
Bernd
--------------PDB snippet t.pdb-----------------
ATOM 579 CA ASN 105 -8.232 -27.207 4.422 1.00 43.07
ATOM 580 C ASN 105 -7.747 -27.611 5.761 1.00 43.07
ATOM 581 O ASN 105 -8.515 -27.540 6.732 1.00 36.51
ATOM 582 CB ASN 105 -9.263 -28.273 3.953 1.00 36.51
ATOM 583 CG ASN 105 -9.490 -28.105 2.436 1.00 36.51
ATOM 584 OD1 ASN 105 -10.525 -27.649 1.923 1.00 36.51
ATOM 585 ND2 ASN 105 -8.502 -28.447 1.601 1.00 36.51
ATOM 586 N ILE 105A -6.511 -28.054 5.881 1.00 35.26
ATOM 587 CA ILE 105A -6.065 -28.361 7.220 1.00 35.26
ATOM 588 C ILE 105A -5.728 -26.999 7.863 1.00 35.26
ATOM 589 O ILE 105A -4.552 -26.550 7.813 1.00 50.38
ATOM 590 CB ILE 105A -4.849 -29.305 7.060 1.00 50.38
ATOM 591 CG1 ILE 105A -5.311 -30.628 6.345 1.00 50.38
ATOM 592 CG2 ILE 105A -4.155 -29.428 8.455 1.00 50.38
ATOM 593 CD1 ILE 105A -4.312 -31.843 6.304 1.00 50.38
ATOM 594 N PRO 106 -6.680 -26.265 8.485 1.00 51.20
ATOM 595 CA PRO 106 -6.505 -24.798 8.733 1.00 51.20
ATOM 596 C PRO 106 -5.206 -24.519 9.567 1.00 51.20
ATOM 597 O PRO 106 -4.407 -23.684 9.165 1.00 25.73
ATOM 598 CB PRO 106 -7.844 -24.355 9.417 1.00 25.73
ATOM 599 CG PRO 106 -8.735 -25.595 9.329 1.00 25.73
ATOM 600 CD PRO 106 -7.723 -26.779 9.384 1.00 25.73
---------------------------------------------------
-----------------tleap output------------------
> CCC=loadpdb t.pdb
Loading PDB file: ./t.pdb
(starting new molecule for chain (starting new molecule for chain )
-- residue 106: duplicate [] atoms (total 8)
ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
(same-name atoms are reduced to a single atom)
Unknown residue: number: 1 type: Terminal/last
...relaxing end constraints to try for a dbase match
-no luck
Added missing heavy atom: .R<CASN 105>.A<OXT 15>
Added missing heavy atom: .R<CASN 105>.A<N 1>
Creating new UNIT for residue: sequence: 106
Created a new atom named: within residue: .R< 106>
Added missing heavy atom: .R<CPRO 107>.A<OXT 15>
total atoms in file: 22
Leap added 16 missing atoms according to residue templates:
3 Heavy
13 H / lone pairs
The file contained 1 atoms not in residue templates
> describe CCC
UNIT name:
Head atom: null
Tail atom: null
Contents:
R<CASN 105>
R< 106>
R<CPRO 107>
>
-------------------------------
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Received on Mon Jul 05 2004 - 15:53:00 PDT
