Dear prof Bovin et al,
I’m having some problems performing MD simulations with the dimer I obtained from HADDOCK.
I used Haddock to dock two proteins and to obtain a dimer. I tried to prepare the dimer for a MD simulation with Amber, but I’m obtaining 300 errors like the following:
check dimer
Checking ‘dimer’…
Warning: The unperturbed charge of the unit (-10.000000) is not zero.
FATAL: Atom .R<NALA 1>.A<HN 13> does not have a type.
FATAL: Atom .R<THR 2>.A<HN 15> does not have a type.
FATAL: Atom .R<LYS 3>.A<HN 23> does not have a type.
FATAL: Atom .R<ALA 4>.A<HN 11> does not have a type.
FATAL: Atom .R<VAL 5>.A<HN 17> does not have a type.
FATAL: Atom .R<GLY 302>.A<HN 8> does not have a type.
FATAL: Atom .R<VAL 303>.A<HN 17> does not have a type.
FATAL: Atom .R<ILE 304>.A<HN 20> does not have a type.
FATAL: Atom .R<GLY 305>.A<HN 8> does not have a type.
FATAL: Atom .R<ILE 306>.A<HN 20> does not have a type.
FATAL: Atom .R<ALA 307>.A<HN 11> does not have a type.
FATAL: Atom .R<CGLN 308>.A<HN 19> does not have a type.
FATAL: Atom .R<ZN2 309>.A<ZN+2 1> does not have a type.
FATAL: Atom .R<CU2 310>.A<CU+2 1> does not have a type.
The PDB file of the dimer is here loaded:
wt_wt_holo.pdb (217.6 KB)
Note that the monomer worked fine and it was loaded correctly.
So for the dimer I tried with a python script to change atom types: HN into H, ZN+2 into ZN, , CU+2 into CU and residues type: ZN2 into ZN and CU2 into CU, it seems Amber it doesn’t like them.
The new PDB file with those corrections is:
wt_wt_holo_new.pdb (218.1 KB)
Comparing the two PDB files, it seems that che code was effective.
However I got two more errors now when I try to load the new PDB in Amber:
check dimer
Checking ‘dimer’…
Warning: The unperturbed charge of the unit (-2.000000) is not zero.
FATAL: Atom .R<NALA 1>.A<H 13> does not have a type.
FATAL: Atom .R<NALA 156>.A<H 13> does not have a type.
It seems that the fact that I renamed HN into H, had no effect on residue 1 and 156.
I forgot to mention that before loading each PDB file in amber, I used the following instruction:
pdb4amber -i <dimer.pdb> -o <dimer_for_amber.pdb>
After those corrections, also the charge changed (from -10 to -2) but I can’t find the reason for that.
Sorry for the long question, I hope I can have some guidelines to make this work, thank you very much in advance.
Have a nice day
Marco