Re: [modeller_usage] (no subject)

[Modeller Caretaker <modeller-care@ucsf.edu>]

On Fri, Jul 16, 2004 at 12:21:40PM -0700, karl schweighofer wrote:
> I am trying to protonate at ADP molecule with modeller6. THe ADP
> residue is specified in the library, but I keep getting this error:
> 
> gener___479E> Must not use patching residues here.
>               Residue type index, residue type:       33  #
> recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

You need to edit modlib/restyp.lib and change the 1-letter code for ADP
(by default '#') to something unique - I used '!'. Otherwise Modeller
gets confused when generating the topology - it tests the '#' to see if
it's a patching residue, and since there are multiple residues defined
with that code, it just matches the first one, which is GLP, the glycine
N-terminus patch. It subsequently thinks you're trying to build a model
with patching residues (which you can't do, of course) and dies. This is
of course a bug, but the workaround is straightforward for now.

> RENAME_SEGMENTS SEGMENT_IDS = 'A'

I'm not sure why you do this, but you should either comment it out or
move it to the end of the file. Modeller rereads adp.pdb during
GENERATE_TOPOLOGY, and dies if the segment IDs don't match (which they
won't any more, since you renamed them).

	Ben Webb, Modeller Caretaker
-- 
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