[gmx-users] OPLS-AA topologies for ATP
Thomas Piggot
t.piggot at soton.ac.uk
Wed Jun 23 18:36:56 CEST 2010
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
>>>> --
>>>> gmx-users mailing list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before
>>>> posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface or send it to gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org
>>>>> .
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> --
>> Dr Thomas Piggot
>> University of Southampton, UK.
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Dr Thomas Piggot
University of Southampton, UK.
More information about the gromacs.org_gmx-users
mailing list