AMBER Archive (2005)

Subject: Re: AMBER: question about loadiing pdb file of a molecule complex

From: David A. Case (case_at_scripps.edu)
Date: Sun May 29 2005 - 00:29:53 CDT

On Fri, May 27, 2005, gtg549i_at_mail.gatech.edu wrote:

> 3. Open the modified pdb files in ViewLite and bring them to proximity for
> H-bond interaction, save the file as "complex.pdb",the two molecules were
> named as "BE2" and "MAA". here is the file looks like:
>
> ATOM 1 C7 BE2 1 0.035 1.199 -0.000 1.00 0.00
> ATOM 2 C10 BE2 1 0.872 2.543 -0.032 1.00 0.00
> ...
> ATOM 44 H86 BE2 1 -6.124 -2.328 -0.042 1.00 0.00
> TER
> ENDMDL
> TER
> ATOM 1 C3 MAA 2 3.776 7.634 0.370 1.00 0.00
> ATOM 2 H12 MAA 2 4.741 7.876 0.262 1.00 0.00
> ...
> ATOM 12 O5 MAA 2 1.280 6.280 0.431 1.00 0.00
> TER
> ENDMDL
>
> 4.When i try to load it into xleap, the following messages come out:
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 142
> !FATAL: Message: Atom named C1 from MAA did not match !
> !
> !ABORTING.
>

I think we will need to see the pdb file to be of much help here. Is there
anything unusal about atom C1 or its environment?

...dac

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