[gmx-users] error in ATOM2CG.awk script

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> 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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> 
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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

========================================