Re: [AMBER] antechamber

From: David A Case <>
Date: Thu, 21 Aug 2014 10:42:54 -0400

On Thu, Aug 21, 2014, Jason Swails wrote:
> >
> > I download a pdb named 1U13. It has the 'heme' cofactor. I have downloaded
> > its parameters from ''.

It's not clear exactly which files you downloaded. The ones you want are
"" and "frcmod.hemall", which are also available in
$AMBERHOME/dat/contrib/heme in the AmberTools distribution.

> > > loadamberparams hem.frcmod
> > > loadamberprep hem.prep
> > > loadamberprep hem.back.prep

It's not clear exactly what is in these files, or why you loaded two separate
prep files. These are pretty old files, and there could be problems with
them, but first make sure that you are loading the correct files (listed
above); there should only be one prep file neede.

> > WARNING: There is a bond of 16.983232 angstroms between:
> > ------- .R<GLY 84>.A<C 6> and .R<ARG 85>.A<N 1>
> > WARNING: There is a bond of 8.335559 angstroms between:
> > ------- .R<PRO 206>.A<C 13> and .R<ASP 207>.A<N 1>

You will have to fix the the problems above, which have nothing to do with the
HEM group.

> > For atom: .R<HEM 435>.A<NA 2> Could not find type: NP

These types are present in the frcmod.hemeall file, which is why I suspect
that somehow it did not get loaded correctly.

Jason's concerns (below) don't appear to be a problem here.
> You have to make sure that all atom names in your PDB file match the
> corresponding atom names in the HEM library file.
> If your HEM residue is topologically different than the HEM residue in
> the library file you downloaded, it won't work.


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Received on Thu Aug 21 2014 - 08:00:03 PDT
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