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.

> -b
>
>
>> 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:
>> http://www.drugbank.ca/cgi-bin/getCard.cgi?CARD=DB04395
>>
>> You want to include phosphoaminophosphonic acid in what ?
>>
>> regards, Francois
>>

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