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
As I recall, the root problem was that the original .pdb file from the RCSB had
missing atoms that you had not properly modeled back in.
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?
Hence the point of CG. You don't account for every single atom that was in the
atomistic structure. BN0 = backbone particle, SC1 and SC2 are side chain
particles that will be given specific attributes in the topology.
You should probably refer to the MARTINI publications for a more clear
understanding of how the force field was conceived and how it should be used.
-Justin
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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