AMBER Archive (2006)

Subject: Re: AMBER: GLUTATHIONE

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Jan 11 2006 - 09:38:56 CST

Dear Joachim,

You dont need the double_a info in your .pdb file while using antechamber.
Extract the necessary ATOM lines to a file. The .pdb file u need to create
must have the right format. See more on .pdb format at the following
website:

http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/guide2.2_frame.html

What I would do is to use the following command first, and play with the
.pdb file to make the right .pdb file format.

grep "ATOM " aps.dat > deneme.pdb

check the deneme.pdb file and be sure that the file has the ATOM info.s in
it. Then use the awk script as follows:

more test.pdb | awk '{print $1" "$2" "$3" "$4" "$5" "$7"
"$8" "$9}' > deneme_format.pdb

Check out deneme_format.pdb file and play with it a little bit to bring it
to the right .pdb format. Now, u have a deneme_format.pdb which needs to
be protonated. There is a program in AMBER which does that (never used
that, but must not be hard to use). U can use that protonated file in
antechamber, and create your .prepi file.

Or, if u want to see what u are doing, use the deneme_format.pdb
(which is in right .pdb format) file in xleap. Load it, and connect the
atoms by hand (it is not a big structure, so must not be hard to do).

Good luck,

On Wed, 11 Jan 2006, Joachim Reichelt wrote:

> Dear all,
>
> I want to model a structure with GLUTATHIONE.
> I extracted the GTT-Lines from pdb1gsa.ent with grep an tried
> to run antechamber. But all I get is:
>
> Cannot successfully assign bond type for this molecule, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase MAXVASTATE in define.h and recompile bondtype.C
>
> I increase MAXVASTATE, but it did not help, so I set debug to 1.
> Now I see:
> ...
> double_a C1 0 0 0 0
> double_a O11 0 0 0 0
> double_a O12 0 0 0 0
> double_a CB1 0 0 0 0
> double_a CG1 0 0 0 0
> double_a CD1 0 0 0 0
> double_a OE1 0 0 0 0
> double_a N2 0 0 0 0
> double_a CA2 0 1 -4 -1
> double_a C2 1 2 0 3
> double_a O2 0 0 0 0
> double_a CB2 0 0 0 0
> double_a SG2 0 0 0 0
> double_a N3 1 1 0 0
> double_a CA3 0 0 0 0
> double_a C3 0 0 0 0
> double_a O31 0 0 0 0
> double_a O32 0 0 0 0
> double 11 CA2 C2 6
> Cannot assign bond types for the current valence state
>
> The current valence state (35) is listed as the following
> ...
>
> More see in ant.log
>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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