Dear Brandon,
- Concerning the "F-90" R.E.DD.B. project you can also find a frcmod file.
See
http://q4md-forcefieldtools.org/REDDB/projects/F-90/script3.ff
script3.ff is automatically loaded by the LEaP script:
http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff
You can obviously on the top of these FF parameters add your own set:
parm99 = loadamberparams parm99.dat
frcmod99SB = loadamberparams frcmod.ff99SB
FRCMOD = loadamberparams script3.ff
# your own set of FF parameters
FRCMD2 = loadamberparams own-set-of-ffparm.ff
- Concerning analogs of GTP or more generally analogs to of XYP (X =
nucleobase; Y = integer) a similar query was made in the q4md-fft
mailing list:
See
http://lists.q4md-forcefieldtools.org/wws/arc/q4md-fft/2012-06/msg00005.html
and related messages...
An answer is the building block approach : an example is presented in
this F-90 project; in the abstract of this project it is written:
"The building block approach presents the following advantages over
the whole molecule approach: (i) the cpu time required for geometry
optimization and molecular electrostatic potential (MEP) computation
is drastically decreased, (ii) the optimized geometry of the
conformation(s) of each building block is fully defined and
controlled, (iii) conformations not suited for charge derivation,
presenting non-bonded interactions only observed in gas phase geometry
optimization are discarded, (iv) cofactors and their analogs are
simultaneously involved in a single and highly homogenous approach,
and finally (v) by generating averaged charge values for connecting
groups, additional and highly compatible charge derivation procedures
can be performed for an infinity of new cofactor analogs constituting
"add-ons" to the present R.E.DD.B. project."
In your case, you only need to generate new fragments for your
multiple phosphate group analogs...
regards, Francois
> On a similar note, has anyone had success modeling GCP
> (or phosphomethylphosphonic acid guanylate ester
> )? It is the nonhydrolizable analogue of GTP - replace the oxygen bridging
> the phosphate groups with a carbon.
>
> Structure can be found http://xray.bmc.uu.se/hicup/GCP/index.html
>
> What approach would you suggest, as those parameters are not available
> (although those for GTP are)?
>
> Thanks,
> Brandon
>
>
> On Tue, Jun 19, 2012 at 4:24 AM, David A. Case
> <case.biomaps.rutgers.edu>wrote:
>
>> On Mon, Jun 18, 2012, Brandon Sim wrote:
>> >
>> > This is incorrect: the GDP files at the website above should have
>> everything
>> > > you need.
>> > >
>> >
>> > There is an .frcmod file there - could you or anyone else outline briefly
>> > how to use just the parameter file to create a unit to load to create a
>> > library file such that minimisation can occur?
>>
>> There is a "guide to usage", a frcmod file and a prep file. After reading
>> the
>> "guide to usage", you basically use loadAmberPrep to load the prep file,
>> loadAmberParams to load the frcmod file, and loadPdb to load a pdb file.
>> If
>> you have other components (e.g. a protein) you would also need to source an
>> appropriate leaprc file, such as leaprc.ff12SB.
>>
>> ...good luck....dac
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Received on Wed Jun 20 2012 - 01:00:02 PDT
