AMBER Archive (2009)

Subject: Re: [Barracuda SPAM] Re: [AMBER] Atom Type List

From: Javier Klett (jklett_at_cbm.uam.es)
Date: Mon Jun 22 2009 - 11:34:43 CDT

Thanks very much, and does anybody know from an open-code which assigns
amber atom types to the atoms in my pdb, in order to integrate it into
my code?

case escribió:
> On Mon, Jun 22, 2009, Javier Klett wrote:
>
>> I need to classify the atom types of a set of pdb files into the
>> amber atom type list. For that i used tleab obtaining the "top" and
>> "crd" files, and afterwards I used "ambpdb" to reconvert them into pdb
>> files with the "supposedly" amber atom types.
>>
>
> PDB files don't contain atom types, just atom names. The atom types are in
> the prmtop file. If the molecules aren't too big, you could save them as mol2
> format in antechamber -- that format also has atom types in it.
>
> ...dac
>
>
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