[gmx-users] segmentation fault

rams rams rams.crux at gmail.com
Tue Jul 1 16:40:54 CEST 2008

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.

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