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).
regards, Francois
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Received on Sun Feb 26 2006 - 06:10:05 PST
