[gmx-users] segmentation fault

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 1 16:46:24 CEST 2008

The whole story continues to emerge... :-)

You're probably experiencing this problem because you're trying to 
process two separate proteins with one pdb2gmx command.  You will need 
to separate (i.e., using a text editor) chain A (whatever protein) from 
B&C (insulin).  Process them separately with pdb2gmx, using -merge with 
the insulin portion.  What you'll have to do is then concatenate the 
output structure files (again, text editor or Unix 'cat' command), and 
include the insulin topology within the topol.top from Protein A.  See 
Chapter 5 of the manual for more details on this, but it is essentially 
analogous to including a ligand topology (.itp) within a system topology 


rams rams wrote:
> Dear users,
> Thanks a lot to Justin and a few others who really helped me in 
> successfully running insulin. Now, I am trying to setup  the input 
> file for insulin with other enzyme and I am trying to merge the two 
> chains of insulin. I am using the following command:
> pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb -inter -merge -ignh
> it is asking whether to merge (A &B, B&C). I allowed it to merge B&C 
> they are insulin chains and A is the rest of the enzyme. With the 
> above command after adding all the protons to LYS etc.., it complains 
> the folling:
> Segmentation fault: pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb 
> -inter -merge -ignh
> It says like its creating the pdb and top files but nothing it could.
> The same command works fine if I remove -merge and its also worked 
> well with insulin chains.
> I have enough space to run this too.
> Please let me know the suggestions.
> Ram.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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