AMBER Archive (2003)

Subject: Re: protonate problem

From: David A. Case (case_at_scripps.edu)
Date: Wed May 14 2003 - 13:36:04 CDT

On Wed, May 14, 2003, Venkata S Koppuravuri wrote:
>
>
> 2. the second molecule that i am trying on is 1FGU. with this molecule i
> have taken only subunit B and deleted the subunits A and C.
> Protonate did work fine with this but when i try to get prmtop and prmcrd
> files using leap i got the following error message
>
> ------------------------
> FATAL: Atom .R<CCYS 289>.A<HG 13> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> -----------------------
>

Since forever (as far as I can tell), the name of the proton attached to S in
N- and C-terminal residues has been "HSG" rather than (correct) "HG".

This only matters if you start from a pdb residue with that proton there,
called "HG".

The simplest solution to both of your problems is just to remove the "HG"
atom from the CYS residue before loading into LEaP. LEaP will then build
it back on with the name it wants it to have.

Note that you almost certainly had error messages in LEaP before the one
you cite above, probably "added missing atom". Get in the habit of studying
the LEaP output carefully, especially when you have problems.

You should also consider upgrading to a newer version of the codes.

..hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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