[AMBER] on antechamber of AMBER

From: Brett <brettliu123.163.com>
Date: Mon, 2 May 2016 21:02:48 +0800 (CST)

Dear All,

When I read the AMBER on-line tutorial on antechamber (the Sustiva example), I find the antechamber will determine the value of the charge of the ligand. But for some ligand, for example ADP (adenosine phosphate), if the H has been added by pdbtools (phenix), it will contain -3 charges. But if the H has been added by chimera, it will contain -2 charges. For antechamber, do I nee to add the H before I get the mol2 file by antechamber? And how many charges antechamber will give for ADP?

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Received on Mon May 02 2016 - 06:30:04 PDT
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