AMBER Archive (2006)

Subject: Re: AMBER: xleap not recognizing residue--I fixed it, but I'm not sure why

From: Kenley Barrett (kenley.barrett_at_gmail.com)
Date: Wed May 10 2006 - 14:54:46 CDT

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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