Messages

1

General discussions (Q&As) / Re: haddock compatible pdb

« on: March 13, 2012, 01:39:17 am »

Thank you so much... as I intend to use 3DNA for a large number of samples, my job has been much simplified now that -three has been added directly to the fiber program... and it works alright with HADDOCK without the need for -connect.

2

General discussions (Q&As) / Re: haddock compatible pdb

« on: March 05, 2012, 02:48:05 am »

Hi!

Thank you Dr. Xiang-Jun for such a detailed reply. I used the x3dna2charmm_pdb script and modified it as follows:

...........................................................

#!/usr/bin/env perl
use strict;
use warnings;

## This is utility Perl script, intially written by Dr. Xiang-Jun for converting 3DNA generated PDB file
## to CHARMM acceptable format, has been modified for converting to that accepted by HADDOCK.

## Please note that this script may not be that sophisticated, since I
## know little about the specifications of the HADDOCK PDB format.
## Please let me know if you find any bug in it.

die "Usage: $0  3DNA_generated_PDB  converted_PDB\n" unless @ARGV == 2;
my $x3dna_pdb  = $ARGV[0];
my $charmm_pdb = $ARGV[1];

open( FH, "$x3dna_pdb" )   || die "Can't open <$x3dna_pdb> for reading: $!\n";
open( FO, ">$charmm_pdb" ) || die "Can't open <$charmm_pdb> for writing: $!\n";

while (<FH>) {
    if (/^ATOM/) {
        chomp;

        # expand this list as necessary ...
        my %one2three = (
                          '  A' => 'ADE',
                          '  C' => 'CYT',
                          '  G' => 'GUA',
                          '  T' => 'THY'
                        );
        my $residue = substr( $_, 17, 3 );
        substr( $_, 17, 3 ) = $one2three{$residue}
            if ( exists $one2three{$residue} );
        my $chainID = substr( $_, 21, 1 );
        substr( $_, 21, 1 )  = $chainID;
        substr( $_, 54, 18 ) = '  1.00  0.00      ';
        my $rc = substr( $_, 13, 1 );
   my $addspace = "     ";
   my $replace_copy = $addspace.$rc;
      substr( $_, 72, 1 )  = $replace_copy;
        print FO "$_\n";
    } else {
        print FO;
    }
}
close(FH);
close(FO);

=for example

Sample HADDOCK PDB file:
ATOM     27  H2'   ADE A    1      -3.643   6.134   3.867  1.00  0.00          H
ATOM     28  C3'   ADE A    1      -4.155   7.022   5.806  1.00  0.00          C
ATOM     29  H3'   ADE A    1      -5.203   7.382   5.738  1.00  0.00          H
ATOM     30  O3'   ADE A    1      -3.256   8.063   5.448  1.00  0.00          O
ATOM     31  P       THY A    2      -3.070   8.432   3.902  1.00  0.00          P
ATOM     32  O1P THY A    2      -4.195   7.871   3.120  1.00  0.00          O
ATOM     33  O2P THY A    2      -2.853   9.889   3.761  1.00  0.00          O
ATOM     34  O5'   THY A    2      -1.722   7.646   3.549  1.00  0.00          O

Sample CHARMM PDB file:
ATOM     27  H2'   ADE     1      -3.643   6.134   3.867  0.00  0.00      A
ATOM     28  C3'   ADE     1      -4.155   7.022   5.806  0.00  0.00      A
ATOM     29  H3'   ADE     1      -5.203   7.382   5.738  0.00  0.00      A
ATOM     30  O3'   ADE     1      -3.256   8.063   5.448  0.00  0.00      A
ATOM     31  P       THY     2      -3.070   8.432   3.902  0.00  0.00      A
ATOM     32  O1P THY     2      -4.195   7.871   3.120  0.00  0.00      A
ATOM     33  O2P THY     2      -2.853   9.889   3.761  0.00  0.00      A
ATOM     34  O5'   THY     2      -1.722   7.646   3.549  0.00  0.00      A

Sample 3DNA generated PDB file:
ATOM     50  O3'   C A   3      -7.224  -1.903   7.585
ATOM     51  C2'   C A   3      -6.408   0.308   8.023
ATOM     52  C1'   C A   3      -5.322   0.045   6.986
ATOM     53  N1    C A   3      -4.202   0.995   7.051



=cut

.........................................

This works perfectly fine. thank you!

Regards
Sumedha

3

General discussions (Q&As) / Re: haddock compatible pdb

« on: March 02, 2012, 04:55:06 am »

Well sorry, actually the pdb is almost ok except that haddock expects the new PDB format for nucleotides which has three letter notations like ADE, GUA, CYT, THY. 3DNA v2.1 stil returns single letters ATCG.

4

General discussions (Q&As) / Re: haddock compatible pdb

« on: March 02, 2012, 04:16:05 am »

Hi!

Thank you, it works perfectly!

Sumedha

5

General discussions (Q&As) / Re: haddock compatible pdb

« on: March 01, 2012, 07:52:17 am »

I have attached the two different versions - one that I got from fiber and second one is the Haddock compatible version (from 3D-DART).
I will be obliged if you could help.

Thank you!

6

General discussions (Q&As) / haddock compatible pdb

« on: February 29, 2012, 05:11:23 am »

Hello!

I am using fiber to generate B-DNA models but the resulting pdb file is not HADDOCK compatible. I know how to do that on the 3D-DART webserver but not on the standalone software. Pls help.

Regards
Sumedha