[gmx-users] converting all-atom pdb to cg.pdb

[Justin A. Lemkul]

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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