AMBER Archive (2006)

Subject: AMBER: I'm very sorry, please disregard previous e-mail--problem seems to be fixed

From: Kenley Barrett (kenley.barrett_at_gmail.com)
Date: Wed May 10 2006 - 15:04:16 CDT

I'm sorry, this just gets stranger and stranger--I became suspicious that
changing the first line was really fixing the problem, so I tried recreating
the library file from the old prep file, without altering the prep file at
all. For some reason, this time, it created a library file without the
missing residue name.

I'm sorry for the unnecessary e-mail. Hopefully the problem is fixed and
things will go smoothly from here. Thank you very much for all of your help.

Kenley

On 5/10/06, Kenley Barrett <kenley.barrett_at_gmail.com> wrote:
>
> Thank you very much for your reply--I really appreciate you taking the
> time to give me your advice. As you suggested, I looked at differences
> between my prep file and the prep files of all_amino03.in. I found a
> difference that seems to be the culprit: as the first line of
> all_amino03.in, it has the sequence: "1 1 2". The first line of my
> prep file had the sequence "0 0 2". When I changed it to "1 1 2",
> the prep file was then able to create a library file that didn't have the
> missing residue name.
>
> I have no idea what the sequence "1 1 2" refers to, so I don't know
> why this fixed the problem. I want to make sure that I know what's going on
> here--I don't want to manually fix this and move on if there's the
> possibility that my prep file could be otherwise flawed.
>
> Does anyone understand what "1 1 2" refers to, and does anyone have
> any advice on the appropriate way to proceed from here? I would be very
> grateful for any input.
>
> Kenley
>
>
> On 5/9/06, David A. Case <case_at_scripps.edu> wrote:
> >
> > 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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>
>

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