I chose the AMBER ATP for OPLS as I wanted to simulate my system with
two different all-atom forcefields and knew that I could use AMBER in
GROMACS with these published parameters (through use of the ffamber
ports). The only other all-atom forcefield in GROMACS at that time was
OPLS and rather than attempt a new parameterisation of ATP for OPLS I
first tried these parameters to see how they would perform.
For the testing then I am sure if you think about this then you can come
up with some idea's of what good tests would be. If not then look for
papers where people have done similar things in the past.
Again I must reiterate if you wish to simulate ATP with an all-atom
forcefield then I would suggest it is currently much easier to use the
AMBER forcefields than to use OPLS unless there is a specific reason to
use OPLS.
Cheers
Tom
BIN ZHANG wrote:
Dear Tom:
Thanks for your suggestion. You are absolutely right on doing more
testings. I simply haven't figure out what the appropriate test is
yet. Could you be more specific about "these parameters perform just
as well as"? What kind of test did you do?
Also, is there a reason why you choose Amber over Charmm? Is it more
"compatible" with OPLS?
Thanks,
Bin
On Jun 23, 2010, at 2:48 AM, Thomas Piggot wrote:
Well I would suggest you should do some very careful testing to
validate the combination of CHARMM charges and one dihedral with the
rest of the parameters from OPLS. It is not very common (or
generally wise) to mix and match parameters from different
forcefields, see:
http://www.gromacs.org/index.php?title=Documentation/How-tos/Parameterization
I would also say that you should also take care with the OPLS-AA DNA
parameters as these have not been substantially tested/used and so
you should double check the atom types for yourself.
On the specific topic of ATP for OPLS-AA/L I have performed
simulations using the AMBER ATP parameters in OPLS-AA/L (with no
changes for anything such as the different combination rules) and
have found these parameters perform just as well as with the AMBER
forcefields. There will be a section about this (showing the results
from some of the tests I performed) in a paper I am currently writing.
The AMBER ATP parameters can be found at:
http://www.pharmacy.manchester.ac.uk/bryce/amber#cof
However, I would also ask is there a specific reason you wish to use
OPLS-AA/L? If not then it is probably easier to use one of the AMBER
forcefields with these parameters as you do not need to do any
testing (or wait for me to publish my work!)
Cheers
Tom
BIN ZHANG wrote:
Hi, I recently made up a topology for ADP. You can probably modify
it to ATP easily. I used native OPLS atom types based on the DNA
parameters (http://rnp-group.genebee.msu.su/3d/ff.htm). The charges
are copied from CHARMM27. Also, there is one dihedral angle
missing, again, copied from CHARMM.
Please let me know if you have any question, suggestion, ....
Cheers,
Bin
===============================
In the ffoplsaa.rtp file, I added:
[ ADP ]
[ atoms ]
PB opls_440 1.100 0 ;P
O1B opls_441 -0.900 1 ;O
O2B opls_441 -0.900 2 ;O
O3B opls_441 -0.900 3 ;O
PA opls_440 1.500 4 ;P
O1A opls_441 -0.820 5 ;O2
O2A opls_441 -0.820 6 ;O2
O3A opls_442 -0.740 7 ;OS
O5' opls_442 -0.620 8 ;OS
C5' opls_443 -0.080 9 ;CT
H5'' opls_444 0.090 10 ;HC
H5' opls_444 0.090 11 ;HC
C4' opls_158 0.160 12 ;CT
H4' opls_156 0.090 13 ;HC
O4' opls_180 -0.500 14 ;OS
C1' opls_158 0.160 15 ;CT
H1' opls_156 0.090 16 ;HC
N9 opls_354 -0.050 17 ;NA
C8 opls_353 0.340 18 ;CK
H8 opls_359 0.120 19 ;H5
N7 opls_352 -0.710 20 ;NB
C5 opls_350 0.280 21 ;CB
C6 opls_351 0.460 22 ;CA
N6 opls_356 -0.770 23 ;N2
H61 opls_357 0.380 24 ;H
H62 opls_358 0.380 25 ;H
N1 opls_346 -0.740 26 ;NC
C2 opls_347 0.500 27 ;CQ
H2 opls_355 0.130 28 ;H5
N3 opls_348 -0.750 29 ;NC
C4 opls_349 0.430 30 ;CB
C2' opls_158 0.140 31 ;CT
H2'' opls_156 0.090 32 ;HC
O2' opls_171 -0.660 33 ;OH
H2' opls_172 0.430 34 ;HO
C3' opls_158 0.140 35 ;CT
H3' opls_156 0.090 36 ;HC
O3' opls_171 -0.660 37 ;OS
H3T opls_172 0.430 38
[ bonds ]
PB O3A
PB O1B
PB O2B
PB O3B
O3A PA
PA O1A
PA O2A
PA O5'
O3' H3T
O5' C5'
C5' C4'
C4' O4'
C4' C3'
O4' C1'
C1' N9
C1' C2'
N9 C4
N9 C8
C4 N3
C2 N1
C6 N6
N6 H61
N6 H62
C6 C5
C5 N7
C2' C3'
C2' O2'
O2' H2'
C3' O3'
C1' H1'
C2' H2''
C3' H3'
C4' H4'
C5' H5'
C5' H5''
C8 H8
C2 H2
N1 C6
N3 C2
C4 C5
N7 C8
===============================
===============================
In the ffoplsaabon.itp file, I added:
; copied from ffoplsaanr
[ angletypes ]
NA CT OS 1 109.500 418.680 ; DNA DCY
[ dihedraltypes ]
; these are again copied from ffoplsaanr
NA C CM CT 3 30.35430 0.00000 -30.35430
0.00000 0.00000 0.00000 ; aromatic ring DNA DTH
C CM CT HC 3 -0.77874 -2.33623 0.00000
3.11498 0.00000 0.00000 ; aromatic ring DNA DTH HC CT
CT NA 3 0.97134 2.91401 0.00000 -3.88535
0.00000 0.00000 ; RNA NA CT CT OH 3
16.74720 -16.74720 0.00000 0.00000 0.00000 0.00000 ; RNA
CM NA CT OS 3 -3.14010 -3.14010 6.28020
0.00000 0.00000 0.00000 ; DNA DCY
C NA CT OS 3 -3.14010 -3.14010 6.28020
0.00000 0.00000 0.00000 ; DNA DCY
CT OS CT NA 3 -5.23350 7.32690 6.28020
-8.37360 0.00000 0.00000 ; [ dihedraltypes ]
; copied from charmm
O2 P OS P 1 0.0 0.1255 3.0
O2 P OS P 1 0.0 0.4184 2.0
OS P OS P 1 0.0 0.1255 3.0
OS P OS P 1 0.0 0.1255 2.0
===============================
On Jun 22, 2010, at 5:07 AM, Efrat Noy wrote:
Hi,
Does anyone have OPLS-AA topologies for ATP?
Thanks, Efrat
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