Hello,
I couldn't find a similar topic in the archives list, so I wanted to
bring up the question. When neutralizing a protein (or protein-ligand
complex) using tleap, tleap has a weird propensity. If the charges
calculated for the ligand by antechamber make the system have a charge
like -15.001, tleap neutralizes the molecule with 15Na+ ions, realizing
that the charge is actually fifteen. However, when the system has a
charge of -14.999, instead of 15, tleap decides to titrate the molecule
with 14Na+, although it can recognize the system has a final charge of
-0.999. It causes particular hardship when I automatize my calculations
with a bash script, because I have to go back and change the charges
manually, use tleap again, etc. This was a problem I encountered with
Amber12, now I see the same thing happening with Amber14. I thought
someone should have mentioned it until now, not seeing any remark also
makes me think if I've been doing something wrong.
Any comments on this?
Thanks,
Alican
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Received on Sun Sep 14 2014 - 11:30:02 PDT
