AMBER Archive (2005)

Subject: AMBER: ambpdb TER problems

From: Sam (samuel.arey_at_epfl.ch)
Date: Fri Dec 23 2005 - 10:23:26 CST

Dear fellow AMBER users,

I created a solvated box of protein and DNA using xleap and
then used "check" to resolve issues with the structure, etc.
The ordering of components in the pdb file is: a protein,
DNA strand 1, DNA strand 2, cations, water.

After using saveamberparm to create prmtop and prmcrd files,
I re-generated a pdb file using:

ambpdb -aatm -p a.top < a.crd > a.pdb

and found several problems in the newly created pdb file:
(1) The terminal protein residue (CSER) is incorrectly
identified as nonterminal ("SER"). (2) No TER card is inserted
between this residue (SER) and the starting terminal residue
(DA5) of the first DNA strand. (3) A TER card is incorrectly
inserted partway into the DA5 residue. This causes problems
when the new pdb file is loaded into xleap, because it can't
correctly identify the terminals of these units.

Here is a relevant section of the ambpdb-generated pdb file:

ATOM 5622 HB3 SER 352 25.607 45.434 77.789
ATOM 5623 OG SER 352 23.867 45.867 78.819
ATOM 5624 HG SER 352 23.462 46.293 78.060
ATOM 5625 C SER 352 25.465 43.810 79.990
ATOM 5626 O SER 352 26.277 42.887 79.969
ATOM 5627 OXT SER 352 24.267 43.548 80.075
ATOM 5628 H5T DA5 353 54.943 35.236 36.371
ATOM 5629 O5' DA5 353 55.363 35.103 37.224
ATOM 5630 C5' DA5 353 56.662 34.493 37.273
ATOM 5631 H5'1 DA5 353 57.333 35.133 36.701
ATOM 5632 H5'2 DA5 353 56.613 33.509 36.807
ATOM 5633 C4' DA5 353 57.193 34.350 38.682
ATOM 5634 H4' DA5 353 58.156 33.840 38.651
ATOM 5635 O4' DA5 353 57.490 35.650 39.240
TER
ATOM 5636 C1' DA5 353 56.547 36.000 40.247
ATOM 5637 H1' DA5 353 56.936 36.141 41.255
ATOM 5638 N9 DA5 353 56.039 37.330 39.900
ATOM 5639 C8 DA5 353 55.263 37.694 38.823

I have inspected the prmtop file and it seems fine: the
sequence of both CSER and DA5 match those found in standard
1994 libraries. CSER ends with atom OXT and DA5 begins with
atom H5T. I am stumped. The relevant section of prmtop file:

CE3 HE3 CD2 C O N H CA HA CB HB1 HB2 HB3 C O N H CA HA CB
HB2 HB3 OG HG C O OXT H5T O5' C5' H5'1H5'2C4' H4' O4' C1' H1' N9 C8 H8
N7 C5 C6 N6 H61 H62 N1 C2 H2 N3 C4 C3' H3' C2' H2'1H2'2O3' P O1P O2P
...

Moreover, if I view the sequence of the saveamberparm-generated
off file, it appears to contain the correct terminal sequence
between the end of the protein (CSER) and the beginning of the
first DNA strand (DA5). Xleap exmination of these residues shows:

RESIDUE name: CSER
RESIDUE sequence number: 360
RESIDUE PDB sequence number: 352
Type: protein
Connection atoms:
 Connect atom 0: A<N 1>
... etc

RESIDUE name: DA5
RESIDUE sequence number: 361
RESIDUE PDB sequence number: 353
Type: nucleic
Connection atoms:
 Connect atom 0: A<H5T 1>
 Connect atom 1: A<O3' 30>
... etc

Thanks kindly for any insights you may be able to provide..
Sam

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