AMBER Archive (2003)

Subject: Re: AMBER: mgbjsb radii in GBSA

From: Giulio Rastelli (rastelli.giulio_at_unimo.it)
Date: Mon Nov 10 2003 - 17:02:00 CST

Hi David, the prep file was generated using antechamber starting from a
pdb file:
antechamber -i lig.pdb -fi pdb -o lig.prep -fo prepi -c bcc -nc 1

As you noticed, the XYZ keyword is present in file.prep; however, the
file reports internal coordinates and not cartesian coordinates. Don't
know if the XYZ keyword is disturbing GBSA (I got no warning or error
message from Leap). I will remove it and run GBSA again.
Thanks
Giulio

David A. Case wrote:
> On Mon, Nov 10, 2003, Giulio Rastelli wrote:
>
>
>>>>I include a prep file of a molecule that did NOT work, as an example.
>>>>
>>>> 0 0 2
>>>>
>>>>This is a remark line
>>>>molecule.res
>>>><1> XYZ 0
>>>>CORRECT OMIT DU BEG
>>>> 0.0000
>>>> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
>>>> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
>>>> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
>>>> 4 O18 o M 3 2 1 1.540 111.208 180.000 -0.604
>>>> 5 C12 c M 4 3 2 1.219 123.332 167.874 0.131
>>>> 6 O19 o E 5 4 3 1.219 119.978 153.351 -0.604
>
>
> This looks like a bad prep file. Can you say what commands you used to
> create this? A prep file with the "XYZ" attribute (also known as "prepc"
> in antechamber) should not have dummy atoms. Try using the "prepi" rather
> than the prepc format, and see if that helps. (The prepc format used to
> be broken in other respects...I'm not sure if they got fixed or not.)
>
> ..good luck....dac
> 

-- 

Giulio Rastelli
Dipartimento di Scienze Farmaceutiche
Universita di Modena e Reggio Emilia
Via Campi 183
41100 Modena - ITALY
-------------------------------------
tel 0039-059-2055145
fax 0039-059-2055131
-------------------------------------

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