Re: [AMBER] problem with type of pdb output.

From: Ben Roberts <ben.roberts.geek.nz>
Date: Tue, 12 Jul 2011 14:51:50 -0400

Hi Lawrence,

On 12/7/2011, at 2:07 p.m., lawrence awadetsi wrote:

> i did this with nab.
> *molecule m;
> m = bdna("tatatatatatatatatatatatatatatatata");
> *
> *putpdb("ta_34.pdb", m);*
>
>
>
> the output:
>
> ATOM 1 HO5' DT5 A 1 -0.443 -8.367 -1.903 1.00 0.00
>
> ATOM 2 O5' DT5 A 1 0.401 -8.012 -1.614 1.00 0.00
>
> ATOM 3 C5' DT5 A 1 1.429 -7.769 -2.593 1.00 0.00 ......
>
> i had wanted the form of pdb file to contain "EIC" instead of "DT5, etc" in
> the corresponding column. how do i do that cos i want to use the output file
> in "antechamber" to do something like this:
>
>
> *antechamber -i eic_clean1.pdb -fi pdb -o eic_clean1.mol2 -fo mol2 -c bcc -s
> 2
> *
> *parmchk -i eic_clean1.mol2 -f mol2 -o eic_clean1.frcmod*

I'm sure what you're wanting could be done by means of judicious searching and
replacing in a text editor. But why not keep the residues intact and use a
nucleic acid force field?

Regards,
Ben
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Received on Tue Jul 12 2011 - 12:00:04 PDT
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