[gmx-users] error in ATOM2CG.awk script

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 27 22:11:43 CEST 2009

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.


> 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


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