[AMBER] -regarding failure in addition of Na+ ions in tleap

From: Patil Pranita Uttamrao <bo19resch01001.iith.ac.in>
Date: Wed, 24 Jul 2019 19:56:22 +0530

Respected sir,
I am trying to do MD simulationof whole translation complex. I have
started the sample preparation but after removing water moleculaes and
adding hydrogens using pdb4amber and using this output file for tleap
giving atoms not bonded error.
So i tried removing all hydrogens which didn't give that error and
successfully ran in tleap. The main problem is occurring while addition of
Na+ ions as i have to add more than 3000 Na+ ions to neutralize the whole
complex and its not giving any output , it's getting stuck there.
So sir can you please suggest me to solve this problem and dealing with
macromolecule like ribosomes ?

Thanks and regards,
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Received on Wed Jul 24 2019 - 07:30:01 PDT
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