Re: AMBER: Drug bound to the protein

From: Guillermo Mulliert Carlín <>
Date: Wed, 17 Jan 2007 16:27:45 +0100 (CET)


On Wed, 17 Jan 2007, Sophie Barbe wrote:

|> 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.

        I think it will be better if you build your residue SERINE-DEP with
the covalent bond in another program (for exambple insight or sybyl), and then
calculate the charges as indicated in the manual with antechamber.

        If you want to have both DEP and SEH in separated residues, my guess is
that you have to define wich atom is head and/or tail in each one.

                                        Hope this help,

                                        Guillermo Mulliert

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Received on Sun Jan 21 2007 - 06:07:07 PST
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