Francesco Pietra wrote:
Does the atom2cg_v2.1.awk require the indication of the subunit (A, B,
C, etc) in the pdb file of a multimeric protein?
From
ATOM 1 N LEU 1 153.242 64.673 95.851 0.00 0.00 N
ATOM 2 CA LEU 1 154.534 64.963 95.169 0.00 0.00 C
ATOM 3 CB LEU 1 155.257 66.191 95.767 0.00 0.00 C
ATOM 4 CG LEU 1 156.589 66.550 95.065 0.00 0.00 C
ATOM 5 CD1 LEU 1 156.406 66.834 93.574 0.00 0.00 C
ATOM 6 CD2 LEU 1 157.222 67.770 95.727 0.00 0.00 C
ATOM 7 C LEU 1 155.425 63.717 95.081 0.00 0.00 C
ATOM 8 O LEU 1 155.371 63.026 94.063 0.00 0.00 O
ATOM 9 N SER 2 156.233 63.409 96.105 0.00 0.00 N
I get
ATOM 2 BN0 LEU 154.534 64.963 95.169 0.000 0.00 0.00
ATOM 4 SC1 LEU 156.589 66.550 95.065 0.000 0.00 0.00
ATOM 10 BN0 SER 157.124 62.235 96.094 0.000 0.00 0.00
i.e., weird residue numbers.
The awk script simply copies the information from one line to the new file,
using the old atom numbers. You can use genconf -renumber to fix this. The
reason why the residue number isn't being written is because there is a problem
with the atom2cg script that I have posted here a number of times. For example,
you need to fix each line of the script:
OLD LINE
if($1=="ATOM" && $4=="ARG" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2, "BN0",
$4, $6, $7, $8, $9,$10,$11);
FIXED LINE
if($1=="ATOM" && $4=="ARG" && $3=="CA")
printf("%4s %5i %4s %3s %4i %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2, "BN0",
$4, $5, $6, $7, $8, $9,$10,$11);
In another case (coming from AMBER, where the subunit indication is
omitted) with the subunit indicated, the residue numbers in the cg
file are correct. I don't see any other difference between the two
starting files. Or should I look for a different cause.
Then that's simply a matter of luck :) The print statements in the original awk
script do not expect chain identifiers, so the printing worked due to the extra
field.
-Justin
thanks
francesco pietra
.......
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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