sunny mishra wrote:
Yeah I agree wiht you but I tested another protein as well 1BL8 to check
if there was a problem specifically in 1K4C. Even after testing 1BL8 it
gives me the same error. What do you think?
1BL8 has a huge amount of atoms missing in the crystal structure, too. Be aware
of REMARK 470 lines in .pdb files that list missing atoms.
-Justin
On Thu, Aug 27, 2009 at 4:11 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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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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