On 07/04/15 12:54, Vaibhav Dixit wrote:
> Loading parameters: ./HEM_HS.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
> Unknown keyword:
> in parameter file. Perhaps a format error?
1) You (as attached anyway) have stray carriage return characters in
some of your parameter files. Run:
dos2unix HEM_HS.frcmod
dos2unix HEM_pentacoordinateHS.mol2
to fix this.
2) As Dave mentions, I would let leap build the topology as a function
the (correct) PDB residue names, i.e. remove all hydrogens, and CONECT
records before loading into leap. This is a fragile example that will
probably work:
grep -v " H " 1W0E_prepared.pdb.orig > a
grep -v "CONECT" a > b
3) I would also indicate the HEM linked CYS residue by renaming it to
match the resname in the CYP.mol file (CYP-IC6) of the SI of
http://dx.doi.org/10.1002/jcc.21922
sed s/CYX/CYS/g b > 1W0E_prepared.pdb
and then ensure you have these extra bits in your leap script:
CYP = loadMol2 CYP.mol2
# Needed because mol2 does not contain head/tail info
set CYP head CYP.1.N
set CYP tail CYP.1.C
desc CYP
You will also need an extra "bond" command here in leap to link it with
the iron atom in the HEM residue, since this was removed with the
stripping of the CONECT records above.
Regards,
Mark
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Received on Tue Apr 07 2015 - 07:30:05 PDT
