Pdb models generated on Haddock 2.4 server

HADDOCK
1

Just a short observation:
I submitted an NMR ensemble that was split during the Haddock run. I just noticed that the first pdb structure (protein1.pdb) has a larger file size and some weird additional protons in each amino acid. This does not happen when I split the models using the pdb toolbox.

Comparison of the last amino acids from protein1.pdb and protein1_2.pdb:
ATOM 2651 N ASN A 125 11.103 13.351 0.652 1.00 1.09 N
ATOM 2652 CA ASN A 125 9.927 14.177 0.387 1.00 1.26 C
ATOM 2653 C ASN A 125 9.684 14.329 -1.109 1.00 1.21 C
ATOM 2654 O ASN A 125 9.496 15.438 -1.615 1.00 1.45 O
ATOM 2655 CB ASN A 125 10.047 15.553 1.052 1.00 1.53 C
ATOM 2656 CG ASN A 125 9.996 15.479 2.567 1.00 2.04 C
ATOM 2657 ND2 ASN A 125 11.159 15.456 3.200 1.00 2.41 N
ATOM 2658 OD1 ASN A 125 8.919 15.464 3.163 1.00 2.79 O
ATOM 2659 O01 ASN A 125 9.674 13.166 -1.941 1.00 1.21 O
ATOM 2660 HN ASN A 125 10.984 12.505 1.136 1.00 1.24 H
ATOM 2661 HA ASN A 125 9.163 13.717 0.770 1.00 1.35 H
ATOM 2662 HB1 ASN A 125 9.237 16.182 0.713 1.00 1.91 H
ATOM 2663 HB2 ASN A 125 10.891 15.955 0.795 1.00 1.68 H
ATOM 2664 HD21 ASN A 125 11.878 15.484 2.729 1.00 2.46 H
ATOM 2665 HD22 ASN A 125 11.154 15.411 4.059 1.00 3.02 H
ATOM 2666 H ASN A 125 10.928 12.632 1.091 1.00 1.09 H
ATOM 2667 1HB ASN A 125 10.881 15.968 0.780 1.00 1.53 H
ATOM 2668 2HB ASN A 125 9.330 16.124 0.736 1.00 1.53 H
TER
END

ATOM 1990 N ASN A 125 10.190 13.200 0.090 1.00 1.09 A N
ATOM 1991 CA ASN A 125 8.966 13.923 -0.246 1.00 1.26 A C
ATOM 1992 C ASN A 125 8.789 14.020 -1.762 1.00 1.21 A C
ATOM 1993 O ASN A 125 8.721 15.111 -2.333 1.00 1.45 A O
ATOM 1994 CB ASN A 125 8.965 15.318 0.397 1.00 1.53 A C
ATOM 1995 CG ASN A 125 7.647 16.052 0.215 1.00 2.04 A C
ATOM 1996 ND2 ASN A 125 7.707 17.374 0.166 1.00 2.41 A N
ATOM 1997 OD1 ASN A 125 6.583 15.438 0.131 1.00 2.79 A O
ATOM 1998 O01 ASN A 125 8.700 12.820 -2.534 1.00 1.21 A O1-
ATOM 1999 HN ASN A 125 10.115 12.366 0.599 1.00 1.24 A H
ATOM 2000 HA ASN A 125 8.141 13.353 0.156 1.00 1.35 A H
ATOM 2001 HB1 ASN A 125 9.751 15.910 -0.049 1.00 1.91 A H
ATOM 2002 HB2 ASN A 125 9.153 15.219 1.454 1.00 1.68 A H
ATOM 2003 HD21 ASN A 125 8.585 17.804 0.251 1.00 2.46 A H
ATOM 2004 HD22 ASN A 125 6.870 17.872 0.035 1.00 3.02 A H
END

In the original pdb file, the first model looks like this:
ATOM 1990 N ASN 125 11.103 13.351 0.652 1.00 1.09 A N
ATOM 1991 CA ASN 125 9.927 14.177 0.387 1.00 1.26 A C
ATOM 1992 C ASN 125 9.684 14.329 -1.109 1.00 1.21 A C
ATOM 1993 O ASN 125 9.496 15.438 -1.615 1.00 1.45 A O
ATOM 1994 CB ASN 125 10.047 15.553 1.052 1.00 1.53 A C
ATOM 1995 CG ASN 125 9.996 15.479 2.567 1.00 2.04 A C
ATOM 1996 ND2 ASN 125 11.159 15.456 3.200 1.00 2.41 A N
ATOM 1997 OD1 ASN 125 8.919 15.464 3.163 1.00 2.79 A O
ATOM 1998 O01 ASN 125 9.674 13.166 -1.941 1.00 1.21 A O1-
ATOM 1999 HN ASN 125 10.984 12.505 1.136 1.00 1.24 A H
ATOM 2000 HA ASN 125 9.077 13.665 0.813 1.00 1.35 A H
ATOM 2001 HB1 ASN 125 9.237 16.182 0.713 1.00 1.91 A H
ATOM 2002 HB2 ASN 125 10.985 16.000 0.766 1.00 1.68 A H
ATOM 2003 HD21 ASN 125 11.979 15.488 2.663 1.00 2.46 A H
ATOM 2004 HD22 ASN 125 11.153 15.405 4.178 1.00 3.02 A H
ENDMDL

Beate

2

In which directory are you looking? Under data/ensemble?

The relevant files for the docking are the ones in the begin dir where missing atoms have been rebuilt.
I would not expect you will find those weird additional protons there.

They could be the result of the processing done on the first model with molprobity.
But they will be discarded since not following the naming convention of the force field used by HADDOCK.

3

Right, it was in the input directory (from the input tgz). The files in the begin directory are fine !

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