AMBER Archive (2006)

Subject: Re: AMBER: Pt containing complex: xleap

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Sun May 28 2006 - 23:00:08 CDT

As far as I can see, xleap does not recognize a residue called MOL. So, u
have to either create a library for this MOL residue, or change the
residue name MOL in your loaded .pdb file to something which leap will
recognize it.

Good luck,

On Mon, 29 May 2006, a a wrote:

> Dear Sir/Madam,
>
> I am trying to do an MD calculation for Pt containing inorganic complex. I
> tried to edit the pdb file as nuc.pdb in tutorial one. but when I tried to
> open the file with xleap, the following message occur
>
> "Unknown residue: MOL number: 0 type: terminal/last .. relaxing and
> constraints to try for a dbase match no luck
> Creating a new UNIT for residue: MOL sequence: 1
> Created a new atom named: PT1 within residue: R < MOl 1>
> Created a new atom named: N1 within residue: R< Mol1>
> ........
> total atoms in file: 39
> The file contained 39 atoms not in residue templates"
>
> When I type edit filename, I see all the atoms in the right positions but no
> connections between them in the picture. I think it is a wrong way of doing
> this calculations for Pt containing complexes.
>
> Could you please kindly give me a hand to teach me how to do it correctly?
>
> Best regards,
>
> aa
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
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