AMBER Archive (2006)

Subject: Re: AMBER: instructions for making a library file for an unusual residue?

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Feb 21 2006 - 00:28:49 CST

Dear Kenley,

The procedure of creating a lib file for an unusual residue is a little
bit complex, but let me try to describe it step by step:

1. What kind of a residue is this? Is there any similar structure in the
amber force field? If yes, that particular structure will be very useful
to get the atom types for your unusual residue.

2. U need to have the RESP charges for your new residue. Again, what kind
of a structure is it? Is it a residue which is part of a protein or RNA,
or is it a structure which bounds itself to RNA or protein? If its the
second case, it is a little bit easy. If not, then its a little bit
tricky. Why? If your residue is part of a protein or RNA, then it has
JOINT points with the other residues. In this case u have to use the
program RESP to do multimolecular fitting. This means the following: U
have to create your own residue libraries in order to have a complete
force field (in that sense).

This part can be made simple if u assume that the backbone atoms of your
NEW residue has the same atom charges. If u use this argument, what u need
to do is to use an ab initio program, and get the ESP data points for
your NEW residue. Then, u need to use the 'resp' program supplied in AMBER
8. While creating the input file for this 'resp' program, u need to tell
that the backbone atoms of your NEW structure has specific charges. This
will restrain those atoms with the given charges, and will resp fit the
rest of the atoms. And u will end up with the RESP charges of your new
residue.

For more on this, I would strongly suggest to read Cornell et al 95
paper. It describes how they did the multimolecular RESP fitting for
nucleic acids and aminoacids.

3. After getting the charges, u have to specify what the atom types of
your new residue's atoms are. The easiest way is to find a similar
structure in AMBER, and then make comparison between your new residue and
the similar residue. In order xleap to recognize this new residue, u need
to supply the necessary force field parameters. U will probably have some
missing force field parameters, and therefore u will make a modified force
field file which includes those missing parameters. After all this, xleap
will recognize your new structure, and u will be able to create the
prmtop/inpcrd files.

The whole procedure is complicated and the info I gave above assumes that
u have enough knowledge on ab initio calculations, resp protocol, and
AMBER. If you have some specific question, let me know about that. Good
luck.

Best,

On Mon, 20 Feb 2006, Kenley Barrett wrote:

> Francois,
>
> Thank you very much for your reply. I'm afraid that I'm still confused about
> what I need to do. Can R.E.D or R.E.D. II match the Duan et al. 2003 force
> field, or do I need R.E.D. III to match the 2003 force field? If I need
> R.E.D. III, is it available for downloading yet? Does it have a manual
> online? I was only able to find information on your website relating to
> R.E.D. and R.E.D. II.
>
> You mentioned that you had discussed the making of library files in a former
> e-mail--I'm afraid I wasn't able to find this e-mail. If I'm asking
> questions that you have already answered, could you please refer me to the
> date of that e-mail? I apologize if I'm wasting your time asking questions
> that have already been answered.
>
> Please let me know any clarification that you can offer regarding my
> questions. Thank you very much for your help.
>
> Kenley
>
>
>
> On 2/19/06, FyD <fyd_at_u-picardie.fr> wrote:
> >
> > Quoting Kenley Barrett <kenley.barrett_at_gmail.com>:
> >
> > > I need to make a library file for a methylated histidine that fits the
> > 2003
> > > force field. I have read the Duan et al. article, but I am inexperienced
> > > with making library files (and with ab initio calculations in general)
> > and I
> > > am not sure how to go about things. Are there step-by-step instructions
> > > anywhere for how to make a library file for an unusual residue?
> >
> > As I just said in my former email, a tutorial about RESP ESP charge
> > derivation
> > using R.E.D. III/R.E.DD.B. should be available very soon now.
> >
> > In R.E.D. III, you just have to change a line of code to generate residues
> > (molecule fragment) for Duan et al FF.
> >
> > Here is the general strategy followed in the tutorial using R.E.D.
> > (http://www.u-picardie.fr/labo/lbpd/RED/) output:
> > Initial PDB file -- R.E.D. II --> Tripos mol2 "whole molecule"
> > or
> > Initial PDB file -- R.E.D. III --> Tripos mol2 "whole molecule" or
> > Tripos mol2 "molecule fragment"
> >
> > The Tripos mol2 file
> > (
> > http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0
> > )
> > is used as a _precursor_ of OFF library file in LEaP (or to generate
> > CHARMM psf
> > files). This OFF file is used to generate the prmtop/prmcrd files.
> >
> > In LEaP:
> > YOUR-UNIT = loadmol2 YOUR-FILE.mol2
> > You define the head & tail of your residue
> > You define the FF atom types
> > saveoff YOUR-UNIT YOUR-UNI.off
> > saveamberparm YOUR-MOLECULE your-molecule.prmtop your-molecule.prmcrd
> > quit
> >
> > See the leaprc-mol2tooff.ff file of the project F-60 for a quite complex
> > example
> > of LEaP script in R.E.DD.B.:
> >
> > http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-60/leaprc-mol2tooff.ff
> >
> > You should be able to find soon more simple examples in the R.E.DD.B.
> > database
> > for the AIB (dimethylalanine) residue:
> > 1) Central fragment:
> >
> > http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-1/leaprc-mol2tooff.ff
> >
> > http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-2/leaprc-mol2tooff.ff
> >
> > http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-3/leaprc-mol2tooff.ff
> > 2) (+)NH3-terminal fragment:
> >
> > http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-7/leaprc-mol2tooff.ff
> > 3) (-)OOC-terminal fragment:
> >
> > http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-11/leaprc-mol2tooff.ff
> >
> > I will put the corresponding AIB, NAIB & CAIB leaprc-mol2tooff.ff scripts
> > in
> > R.E.DD.B. (should be available in one hour or so from the links provided
> > above).
> >
> > regards, Francois
> >
> >
> >
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> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
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  - http://www.pas.rochester.edu/~yildirim/			-
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