[gmx-users] error in ATOM2CG.awk script

XAvier Periole x.periole at rug.nl
Thu Aug 27 23:08:36 CEST 2009

On Aug 27, 2009, at 2:51 PM, 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
> I pretty much now know how to fix the script but I am confused in  
> some of the things like:
Could you explain what was wrong and how you've fixed it.
Who gave you the new file?
> 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?
I am not sure what you actually intent to do but adding atoms to use  
on the CG level does not sound
like something you'll want to do.
SC1/SC2 are the names for the side chains beads and BN0 is for the  
backbone bead with the
type N0.
> 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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