AMBER Archive (2004)

Subject: Re: AMBER: Problem in loading a PDB file in Leap - Please help me

From: Mike (amber_list_at_speedpost.net)
Date: Sat Apr 17 2004 - 00:19:02 CDT

Hi,

Thanks for the reply...I got fixed all the errors except for magnesium
ion.

I am still getting the error

FATAL: Atom .R<MG 295>.A<MG 1> does not have a type.

Can you please let me know how should i go about this?

I would greatly appreciate your help.

Thanks
Mike

On Thu, 15 Apr 2004 07:53:41 +0200, "tim" <tim_at_mmb.pcb.ub.es> said:
> > FATAL: Atom .R<DA5 1>.A<P 31> does not have a type.
> > FATAL: Atom .R<DA5 1>.A<O1P 32> does not have a type.
> > FATAL: Atom .R<DA5 1>.A<O2P 33> does not have a type.
>
> the problem is the xleap DA5 unit terminates in a 'OH group while your
> structure terminates with a phosphate. should be fine if you delete the
> phosphate group and let xleap add the appropriate atoms
>
> > FATAL: Atom .R< 295>.A<MG M 1> does not have a type.
>
> your MG line in .pdb seems to be shiftet
>
> tail -4 Ch_100.pdb
> ATOM 9348 O3' THY B 147 46.246 7.648 1.090 1.00 0.00
> ATOM 9349 MG MG 148 2.451 26.592 -0.651 1.00 14.63
> TER
>
> fixing that should be enough
>
> tim
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