Hi,
I am trying to dock heparin against my protein using NMR derived AIRs. I have tried to do this on the HADDOCK2.4 webserver but heparin blows apart. I have installed cns1.3 and HADDOCK2.4 on my local machine and they appear to be working correctly. I have defined heparin as 3 units (a disaccharide unit for the reducing end, a repeating disaccharide unit for the polymer length and an oxidising end disaccharide unit). I have used PRODRG to create topology and parameter files and have merged these. I created the following link file as with the .top and .param, placed these in the HADDOCK toppar dir:
link GL14 head - * tail + * end
With this link file it runs but then in the output dock, the heparin disaccharide units have again blown apart. However, if I instead run it without the wildcards:
link GL14 head - NHO tail + CHO end
link GL14 head - CHO tail + CHO end
link GL14 head - CHO tail + THO end
I get the following error message below. So I am sure this is to do with my files but not quite sure what. Any advice will be very gratefully received - and I can post/send topology/param/pdb files as well if requested
thanks
J
PDB_FILE1 /Users/jimmy-imac/Desktop/haddock/hep/md1_A.pdb
AMBIG_TBL /Users/jimmy-imac/Desktop/haddock/hep/site1/site1_air.tbl
PROJECT_DIR /Users/jimmy-imac/Desktop/haddock/hep/site1
PDB_FILE2 /Users/jimmy-imac/Desktop/haddock/hep/heparin10_B.pdb
looking for existing files
waiting for /Users/jimmy-imac/Desktop/haddock/hep/site1/run1/begin/heparin10_B.pdb…
waiting for /Users/jimmy-imac/Desktop/haddock/hep/site1/run1/begin/heparin10_B.psf…
waterdock false
waiting for /Users/jimmy-imac/Desktop/haddock/hep/site1/run1/begin/heparin10_B.pdb…
waiting for /Users/jimmy-imac/Desktop/haddock/hep/site1/run1/begin/heparin10_B.psf…
waiting for the psf files…
…
waiting for /Users/jimmy-imac/Desktop/haddock/hep/site1/run1/begin/heparin10_B.pdb…
waiting for /Users/jimmy-imac/Desktop/haddock/hep/site1/run1/begin/heparin10_B.psf…
Error in the topology generation: prot_psf_mol2 could not be created
=> HADDOCK stopped