Sir,
Does it means i need to source only leaprc.ff99bsc0?
On Sat, Sep 8, 2012 at 12:40 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Mary,
>
> let's take an example:
>
> cd $AMBERHOME/dat/leap/cmd
> more leaprc.ff99SB
>
> you can find:
> # Load the main parameter set.
> #
> parm99 = loadamberparams parm99.dat
> frcmod99SB = loadamberparams frcmod.ff99SB
>
> # --> i.e. the FF parameters...
>
> and
>
> # Load DNA/RNA libraries
> #
> loadOff all_nucleic94.lib
> #
> # Load main chain and terminating
> # amino acid libraries (i.e. ff94 libs)
> #
> loadOff all_amino94.lib
> loadOff all_aminoct94.lib
> loadOff all_aminont94.lib
>
> # --> i.e. the FF libraries...
>
> then; you can read the leaprc.ff99bsc0 by comparison.
>
> > on sourcing leaprc.ff99bsc0 , parameters of aminoacids are also seems to
> > be loading.
> > Then should i load again by
> > source leaprc.ff99SB.
>
> do not do twice the same command.
>
> > Does sourcing leaprc.ff99bsc0 takes care of both nucleic acid and
> dipeptide.
>
> It looks like:
>
> parm99 = loadamberparams parm99.dat # -> peptide + nucleic acid (1995;
> 1999)
> frcmod99SB = loadamberparams frcmod.ff99SB #-> peptide (on the top*)
> frcmodbsc0 = loadamberparams frcmod.parmbsc0 #-> nucleic acid (on the top*)
> # * new FF parameters overwrite older ones available in parm99
>
> > Also on loading into leap the his-his dipeptide the second His residue
> gets
> > added OXT atom with the C=O bond. is it correct.?
>
> OXT means C-terminal residue; i.e. CHIS that ends by OXT
>
> compare NHIS, HIS and CHIS in
> loadOff all_amino94.lib -> HIS
> loadOff all_aminoct94.lib -> NHIS
> loadOff all_aminont94.lib -> CHIS
>
> See also NALA + ALA + CALA at:
> http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
>
> regards, Francois
>
>
> > On Tue, Sep 4, 2012 at 3:25 PM, FyD <fyd.q4md-forcefieldtools.org>
> wrote:
> >
> >> Dear Mary,
> >>
> >> > I have to do a simulation study on nucleic acid-dipeptide complex.
> Can i
> >> > use a combination ff99bsc0 and ff99SB. I thought as i am using
> standard
> >> > aminoacid dipeptide as the ligand i dont have to do any QM charge
> >> > derivation procedure. ff99SB would take care of it. Am Icorrect?
> >>
> >> ff99SB and ff99bsc0 handle regular amino-acid and nucleic acid residues.
> >> A regular aminoacid dipeptide should be handled by ff99SB...
> >>
> >> regards, Francois
>
>
>
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>
--
Mary Varughese
Research Scholar
School of Pure and Applied Physics
Mahatma Gandhi University
India
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Received on Sun Sep 09 2012 - 07:30:04 PDT
