No intrusion, but I have forwarded this to the GROMACS mailing list as
all correspondence is best kept there. It gives you have a much greater
chance of getting (better) help.
The information needed for the parameters is best obtained from the
supporting information given with the Carlson paper. The first thing to
do is to add an appropriate entry to the .rtp file. For the O3 atom you
need to give a new atom type (for example I have it as amber99_68). You
then need to add this new amber atom type to the nb.itp and .atp files.
The non-bonded parameters of the new O3 atom type are the same as O2, so
to add this new atom type to the nb.itp file is trivial, and the same is
true for the .atp file.
For the bonded parameters you need to edit the bon.itp file. Firstly you
need to add an entry into the [bondtypes] section for the O3 P bond.
Then you need to add entries into the [angletypes] for the O3 P O3 and
O3 P OS angles. Like the non-bonded parameters these are trivial as they
are by analogy to the O2 atom type interactions. For the [angletypes]
you also need to change the default P OS P values to those given in the
supplementary info of the Carlson paper. This could cause a problem if
you have another molecule in your system which uses this angle and you
don't want it to use the new angle parameters. I did not and so did not
worry about changing this value. If you do use this angle in another
molecule (and the default values of some of the P dihedrals which will
be changed next) then it would be easier to make an .itp file (where you
can just override the defualt values by having the new values in the
.itp), or introduce a new atom type for the P atom and use this in all
the bonds/angles/dihedrals/non-bonded interactions. Finally you need to
add in the new proper dihedrals from the supplementary info into the
[dihedraltpyes] section. To turn these parameters given into the correct
RB format you need to use the equations in the GROMACS manual (4.63 of
the GROMACS 3 manual/4.64 GROMACS 4 manual). As with the [angletypes]
you need to alter the default CT OS P OS dihedral to the new value from
the paper.
Hope this all makes sense and is all correct (I did this quite a while
ago!).
Cheers
Tom
Alice Chang wrote:
Dear Tom,
I hope this is not an intrusion, but I saw your answer on the gmx-users
mailing list about finding ATP parameters for use in GROMACS. I am
trying to solve the same problem, but without his luck! I've examined
the PREP and FRCMOD files, as well as the relevant Carlson paper and
ffamber files. I've been comparing the amber .itp, .atp, and .rtp files,
but I'm not sure what to use for the radius and epsilon values, or how
to parametrize the P-OS-P bond. I was wondering, if you don't mind,
could you point me in the right direction?
Thanks very much,
Alice Chang
Liao Research Group
Columbia University
--
Thomas Piggot
University of Bristol, UK.
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