[gmx-users] error in ATOM2CG.awk script

sunny mishra mishra.sunny at gmail.com
Thu Aug 27 20:51:13 CEST 2009

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:

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?

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.


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