AMBER Archive (2006)

Subject: Re: AMBER: xleap not recognizing residue

From: David A. Case (case_at_scripps.edu)
Date: Tue May 09 2006 - 17:42:14 CDT

On Mon, May 08, 2006, Kenley Barrett wrote:

> Thanks very much for your reply. First, a question: When you say I need to
> replace the "first blank string" with my residue name, do you mean that it
> should look like this:
>
> >!entry.HMH.unit.residues table str name int seq int childseq int
> startatomx str restype int imagingx
> >"HMH" 1 27 1 "?" 0
>
> instead of like this?:
>
> >!entry.HMH.unit.residues table str name int seq int childseq int
> startatomx str restype int imagingx
> >"" 1 27 1 "?" 0
>

yes.

> I read Mhaa_New_h_edited.prep and Mhaa_New_h.frcmod into Xleap,
> erased the blocking groups on the residue, and saved it as HMH.lib.

Given the long history in getting to this point, it's hard to tell if
the Mhaa_New_h_edited.prep has a problem or not. Here's some things to
check:

1. Look at differences between your file, and example files, e.g. in
$AMBERHOME/test/antechamber or in $AMBERHOME/dat/leap/prep. See if you can
spot anything that would lead to blank residue name.

2. Try reading in a "good" prep file into LEaP, and then writing it out
as on off file. Make sure the residue name gets written correctly, and that
you can read back in the lib/off file.

...good luck...dac

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