Dear Francois,
Thank you for the valuable information.
Best regards
Sajeewa
On Sat, Oct 13, 2012 at 6:42 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Sajeewa Pemasinghe,
>
> the prep, off and mol2 file formats have the same role: they are used
> to handle FF libraries. prep is the old format designed with the
> 'plep' program; off was introduced with LEaP; then came the mol2 file
> format. We will use soon the mol3 file format in R.E.D.
> See http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
> http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
>
> Nowadays R.E.D. generates only mol2 files and no prep file:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1
>
> When one wants to create a FF library for a new amino-acid; one often
> need the corresponding fragment obtained from a dipeptide:
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
> Other fragments (terminal ones) can also be designed:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#16
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17
>
> The different fragments can be generated in a single step by now:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
> vs
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
>
> regards, Francois
>
>
>
> > As far as I know this goes as a non-standard residue. So you give your
> > modified amino acid a new three letter name in the pdb file. But as AMBER
> > tleap or xleap doesn't understand the new residue (coz it is not in the
> > standard list of residues in the force fields loaded) you have to create
> a
> > .frcmod file and a .prep file for the new residue. To create the .frcmod
> > you have to first build the structure of the modified amino acid using a
> > software like Gaussian, then optimize the structure and get the optimized
> > parameters. Using these parameters you can create a .frcmod file (Google
> to
> > check for the format of the .frcmod file, in some cases you can use
> > Antechamber to do this for you) for the new residue. To create the .prep
> > file you will need the charges for the new residue which you can obtain
> > using R.E.D.tools (http://q4md-forcefieldtools.org/RED/).
> >
> > Once you have the .frcmod and the .prep files
> >
> > 1) As usual you do tleap -s -f leaprc.ff99SB (whatever the force field
> you
> > wanna use)
> >
> > 2) loadamberparams xxx.frcmod (choose a name and replace xxx)
> >
> > 3) loadamberprep xxx.prep (choose a name and replace xxx)
> >
> > 4) a=loadpdb xxx.pdb (in this pdb you should have the new name for the
> > modified amino acid, you don't have to have the methyl group as tleap
> will
> > do it for you according to the parameters you specified in the .frcmod
> file)
> >
> > Hope this helps
> >
> > Sajeewa Dewage
> >
> > On Fri, Oct 12, 2012 at 10:17 PM, Changqing Yan <ycqchemical.gmail.com
> >wrote:
> >
> >> Hi all,
> >>
> >> If I want to methylated one amino acid in a peptide sequence, for
> example I
> >> want to methylate VAL residue in TSPNR(N-Methylated)VGDE. What should I
> do?
> >>
> >> Thanks in adavance.
> >> C.Q.
>
>
>
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>
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Received on Sat Oct 13 2012 - 06:00:02 PDT
