AMBER Archive (2007)

Subject: Re: AMBER: problems in adding ACE and NME group

From: David A. Case (case_at_scripps.edu)
Date: Wed Jun 27 2007 - 11:19:51 CDT

On Wed, Jun 27, 2007, backy wrote:

> REMARK
> ATOM 1 N ALA 1 70.146 65.827 40.009
> ATOM 2 H1 ALA 1 69.336 66.290 40.398
> ATOM 3 C ACE 1 70.907 65.903 40.670
> ATOM 4 H3 ALA 1 69.929 64.849 39.886
> ATOM 5 CA ALA 1 70.526 66.443 38.710
> ATOM 6 HA ALA 1 71.550 66.812 38.798
> ATOM 7 CB ALA 1 70.498 65.414 37.563

There is no "H3" atom in the alanine residue. Also, you have seven atoms
in residue 1: six have the ALA name, and one has the ACE name. This is only
going to confuse LEaP. I don't think even a human would really be able to
discern your intent here, and certainly not a program trying to follow strict
rules.

> FATAL: Atom .R<ALA 3>.A<H3 11> does not have a type.

Confirms my comment above.

I feel I should repeat my earlier question: are you *sure* you need capping
groups on a protein? One reason this is somewhat hard is because almost no
one else ever feels the need to do it.

...dac
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