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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