I’m trying to dock a short polymer (~1.2 kDa) to a protein based on NMR data (chemical shift perturbations). From the documentation it seemed quite straightforward, but I keep running into problems when submitting my polymer structure.
HADDOCK interface: HADDOCK 2.4, easy interface
The protein PDB file:
The protein file is a .pdb I’ve downloaded from PDB. The original file contains two protein molecules defined as chain A and B. I simply removed one of the chains to get a file with only one protein structure. This file seems to be accepted by HADDOCK.
The polymer PDB file:
The polymer comprises 13 identical subunits made of a hydrocarbon backbone with carboxylic acid side chains. Each negative side group has a sodium ion as counter-ion. The structure was made in Avogadro and saved as .pdb. The structure looks fine in PyMOL.
When uploading the structure to HADDOCK I get the following error:
"Error in PDB file. Your PDB contains multiple residues with number 1 in chain or duplicated atom names.
HETATM 2 C UNL 1 -3.110 -42.084 -0.234 1.00 0.00 C (Offending Line) <–
ATOM 32 N ARG 3 11.281 86.699 94.383 0.50 35.88 N (Example Valid Line)"
As I understand it from reading other threads, this is caused by Avogadro not separating the different subunits into “residues”, but listing them as all belonging to the same “residue”. I can probably fix this, but I was wondering, do you have any extensive documentation on what the expected input file should look like and what “flags” are accepted? E.g. is the “UNL” flag accepted?
I’m asking because I’m a bit worried that something else is wrong with my file. I was trying out your pdb-tools web interface after seeing this thread; Error in load pdb file for HADDOCK, but when I preview my submitted file the preview shows the atoms of one subunit, but no bonds or any of the other subunits. Is this because of the above all-residues-are-numbered-the-same problem?
Then I just have another question: Can HADDOCK take surrounding ions, i.e. my Na+ ions, into consideration when performing the docking - or would it be better to remove them?
I’m thankful for any help I can get on the matter. Also, if anyone has any software that they think is better than Avogadro for building small molecules, I would appreciate any and all recommendations. Avogadro seems to randomly crash for me on Mojave. (I used to use Chemdraw, but they seem to have removed their 3D tools for OS X.)