AMBER Archive (2006)

Subject: AMBER: Ligand charge

From: bybaker_at_itsa.ucsf.edu
Date: Wed Jan 04 2006 - 12:51:57 CST

('binary' encoding is not supported, stored as-is) Dear Ilyas and Pawel:

Thank you very much for your helps.

>Then use antechamber to create the .prep file. Here, it is important what
>kind of a charge method you are using. As an example;

>antechamber -i chol3_new.pdb -fi pdb -o chol3_new.prepi -fo prepi -c bcc
>-nc 0 -at gaff

>will use the bcc charge method, and the gaff atom types. If you have the
>charges for each atom in the 'chol' molecule in a file, u can give that
>file explicitely, too, using antechamber.

The ligand, a cholesterol here, has 0 net-charge according to 'xleap'. I
am not sure if I need to work out the partial atomic charge for the
lignad. I only want to subject the system (protein and ligand) to
minimization and a short MD. So I can have rough idea on how the
cholesterol located inside the protein. In this case, how necessary to
care about the ligand charge statue?

Thank you for any advices.

All the best

Bo

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