AMBER Archive (2004)

Subject: AMBER: Ligand from CCDC.

From: Osman Gani (osman.gani_at_fagmed.uit.no)
Date: Thu May 06 2004 - 10:38:16 CDT

Hello,
I was wondering about a ligand. I have built a small molecule (Isobutyramide)in Xleap to be docked in a protein. Then I went for MD for calculeting binding energy. The energy seems to be 7-8 kcal/mol higher then the experimental value. I used the LIE method for energy determination.

The X-ray structure for Iso butyramide is also available in CCDC.I sent an e-mail to them to get the sructure.But the file seems to strange looking.

My questions are:
1.Can I get relatively better interaction energy with CCDC structure?
2. How can I convert the CCDC structure to an AMBER readable format?

I will appreciate your answere.

Regards,
Osman
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