[gmx-users] g77 error in martini

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 3 22:44:39 CEST 2009

sunny mishra wrote:
> Dear all,
> In the martini tutorial there is a approach of martini + ElneDYN . In 
> the tutorial they provided me a script which converts the cleaned pdb 
> structure to CG structure of protein. I compiled the script using g77 
> (as they recommended) and then I am trying to make the CG structure of 
> 1BL8 protein but it gives me a wierd error "Something wrong in the Arg 
> 5". I have no idea how to deal with this error. Do you guys have any 
> idea about this. Your reply for the same will be highly appreciable.

Have a look at the original .pdb file.  Search for MISSING entries, and you will 
see that 1BL8 has a substantial number of atoms missing from the structure.  One 
of these is Arg27, which, given the fact that the first 22 residues are missing, 
becomes Arg5.

The first step in any simulation is to understand the flaws in your initial 
model.  In 1BL8, you have to deal with a large amount of missing information. 
Before doing anything else, you have to model in the missing atoms using the 
appropriate modeling software.


> 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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