Hi,
I'm trying to generate input files (prmtop and inpcrd) of a protein that is
bound in its N-terminal to a Myristoyl group which is essentialy a 14
carbon fatty acid chain.
I followed all steps to define the Myristoyl group (MYR) in xleap, which
included adding charges, atom types and defining bonds.
it seems ok up to this point..
Then, I loaded into xleap a PDB file that contains the Myristoyl group as
the first residue (MYR), added bond between the first carbon of the Myr to
the N atom of the first Residue in the protein.
I saved the pdb and it seems that the bond was created (I can see it in
pymol)
However, when trying to generate *.prmtop and *inpcrd files I get the
following message:
*Could not find angle parameters: O2-C-N*
and the files failed to be saved
I browsed the mailing lists and tutorial quit extensively, and I tried a
*.frcmod file can fix that problem:
*# Definitions for protein-MYR linkage
MASS
BOND
ANGLE
O -C -N 50.000 121.000 # calculated from the pdb 1HCD_MYR_tit.prmtop
DIHE
IMPROPER
NONBON*
and when load it to xleap I get an error massage: *Unknown
keyword:
in parameter file*
my questions are:
1) where is the mistake in my *frcmod file?
2) can these errors be bypassed somehow with incorporation of some default
values?
3) Is generating a *.prepin file with antechamber and then creating a
frcmod file the correct way?
Thanks,
Amir
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Received on Tue Jan 24 2012 - 13:30:02 PST
