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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Received on Sat Sep 08 2012 - 00:30:02 PDT
