[gmx-users] OPLS-AA topologies for ATP
Thomas Piggot
t.piggot at soton.ac.uk
Wed Jun 23 11:48:27 CEST 2010
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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--
Dr Thomas Piggot
University of Southampton, UK.
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