AMBER Archive (2007)

Subject: AMBER: Drug bound to the protein

From: Sophie Barbe (sbarbe_at_insa-toulouse.fr)
Date: Wed Jan 17 2007 - 02:56:21 CST

Hi,

I want to simulate a molecular dynamic with a drug bound to a SERINE residu of
the protein.
I made several prep files :
- one for the drug, called DEP : this file was made by antechamber.
- one for SEH which is the SERINE without the Hydrogen terminal (because the
Oxygen of the alcool function must be bind to the drug).
In the pdb file, DEP and the protein residus are separated by TER.
With xleap, I loaded the prep files and the pdb file. Then, I wanted to bound
the P1 atom od DEP to the O atom of SEH. For this purpose, I made :
bond x.1300.OG x4609.P1
But this is not correct.

Morever, I think that I have also a problem with the SEH prep.

Could you help me, please?

Thank you very much

Sophie

PS: I use amber 9

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