[gmx-users] Error in PDB2GMX

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 7 01:39:32 CEST 2009

sunny mishra wrote:
> Hi Justin,
> Thanks for the expedient reply. I referred MARTINI but after
> converting 1A8G.pdb to 1A8G_CG.pdb i.e. CG structure of protein I dnt
> know how to make the topol.top and conf.gro files for that and also I
> am not able to generate the posre.itp file with this CG structure
> because it says the fatal error : Incomplete ring of HIS 69. So I
> don't know how to proceed now and do my simulations.


See the "Peptides and Proteins" section.  There are several scripts - a Perl 
script that writes your topology based on sequence and secondary structure 
information, and an awk script that converts the structure from atomistic to CG.

Note that the awk script is incorrect; each printf line needs to contain $5 
between $4 and $6.


> 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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