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

From: <gtg549i.mail.gatech.edu>
Date: Mon, 30 May 2005 11:56:09 -0400

Attachment are the files of pdb. mol1.pdb is the first molecule, mol2.pdb is
the second molecule, complex.pdb is the initial structure of complex of
molecule1 and molecule2. I didn't notice anything unusal about atom C1 or its
environment. thanks!

Shuting



Quoting "David A. Case" <case.scripps.edu>:

> On Fri, May 27, 2005, gtg549i.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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Received on Mon May 30 2005 - 17:53:00 PDT
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