Quoting Kenley Barrett <kenley.barrett.gmail.com>:
> 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.
YES
Modifying a single line of code in R.E.D. II or R.E.D. III.
Providing the theory level used by Duan et al in the MEP computation:
See for instance
http://amber.ch.ic.ac.uk/archive/200504/0152.html
to get information about the Gaussian route.
> 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.
Email ? No script yes
Scripts to convert mol2 files (library precursor) into LEaP OFF file (force
field library): mol2 to off files
You can now find these script 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
Regards, Francois
> On 2/19/06, FyD <fyd.u-picardie.fr> wrote:
> >
> > Quoting Kenley Barrett <kenley.barrett.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).
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Received on Sun Feb 26 2006 - 06:10:11 PST
