[gmx-users] How to modify the initial CG reduction structure to the usable one matching the .itp atom designation?

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 5 13:57:58 CET 2010

Aymeric Naômé wrote:
> Dear users,
> By what mean does one correct te CG structure file generated with the 
> atom2cg script to the final structure matching the .itp file atom types?
> I mean, how to convert the PDB-like format with generic atom types (BN0, 
> SC1, SC2, SC3) of atom2cg output file to the proper .gro structure file 
> with the corresponding atom types generated with seq2itp?
> Could someone help?

When you run the structure through grompp, it will complain about a lot of 
mismatching atom names.  It will then tell you that the names in the coordinate 
file will be ignored and those in the topology will be used.  For normal usage, 
mismatching is bad news, but for CG, it is the only appropriate way to get the 
coordinate and structure files synced up.  I believe this is explained in the 
MARTINI documentation and/or tutorials.


> Thanks in advance
> Aymeric


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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