On Aug 27, 2009, at 2:51 PM, sunny mishra wrote:
Dear all,
I was earlier facing problem regarding the mismatch of atoms in .top
and .gro file and then after useful discussion here I figured out
that some atoms were missing in my cg.pdb file and that problem is
because of the OLDER atom2cg.awk script which MARTINI folks have in
their website. When I was using the earlier version of atom2cg.awk
script I had 776 atoms in my .gro file and 804 atoms in .itp file
and thats why .top and .gro were not matching but again the same
problem raised even after using the new atom2cg.awk script which
they sent me but it included some ILE residues and now I have 784
atoms in .gro file and 804 atoms in .itp file
I pretty much now know how to fix the script but I am confused in
some of the things like:
Could you explain what was wrong and how you've fixed it.
Who gave you the new file?
1) In the cleaned.pdb file of my protein the ARG residue in the
atom2cg.awk script takes only CA, CG and NE with BN0, SC1, and SC2.
If I want to include other atoms as well like NH1, NH2, CZ, CD etc
what should I print for these atoms (either BN0, SC1, or SC2). As a
matter of fact I don't know what do SC1, BN0, SC2 mean?
I am not sure what you actually intent to do but adding atoms to use
on the CG level does not sound
like something you'll want to do.
SC1/SC2 are the names for the side chains beads and BN0 is for the
backbone bead with the
type N0.
So, i don't know while adding other atoms for ARG residue what
should I print for them and I searched in the martini website but
could not find anything. Please let me know if you got my problem.
Thanks,
Sunny
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