AMBER Archive (2009)
Subject: Re: [AMBER] how can i include ANP residue
From: David Watson (dewatson_at_olemiss.edu)
Date: Mon Dec 14 2009 - 16:44:30 CST
On Dec 14, 2009, at 4:00 PM, Bradley Dickson wrote:
> oh yeah. sorry.
> i have ANP in a pdb file and i cannot create a set of AMBER input files. in xleap, the residue ANP is unknown. i need to find how to include it.
Why not strip out everything but the ANP residue from the pdb file.
Then follow the sustiva tutorial using GAFF and antechamber to provide a mol2 file from your modified pdb, and generate parameters so that tleap can deal with your small molecule.
>> Dear Bradley,
>>> does any one have a way to correctly include ANP
>>> (phosphoaminophosphonic acid...)? i was able to use the contributed
>>> parameters database to include PTR, thanks to the archived messages,
>>> but i have no direction here.
>> Do you mean something like:
>> You want to include phosphoaminophosphonic acid in what ?
>> regards, Francois
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