[gmx-users] OPLS-AA topologies for ATP/ADP.
TJ Piggot
t.piggot at bristol.ac.uk
Thu Feb 26 23:16:00 CET 2009
Sorry realised I posted the amber ATP link wrong, it is without the ) at
the end:
http://www.pharmacy.manchester.ac.uk/bryce/amber
Tom
--On Thursday, February 26, 2009 17:15:22 +0000 TJ Piggot
<t.piggot at bristol.ac.uk> wrote:
> Some of these charges look a bit suspect to me (eg the charge on the
> gamma phosphate). If you do not need to use OPLS then there is ATP
> included in the (united atom) gromos forcefields (see the top folder) and
> also ATP parameters available for the (all atom) Amber forcefields (see
> http://www.pharmacy.manchester.ac.uk/bryce/amber), all you have to do is
> convert them into a gromacs format
>
> Tom
>
> --On Thursday, February 26, 2009 08:33:06 -0800 "Bruce D. Ray"
> <brucedray at yahoo.com> wrote:
>
>>
>> On Wednesday, February 25, 2009 12:06:20 AM, Lucio Ricardo Montero
>> Valenzuela
>>
>> <lucioric at ibt.unam.mx> wrote:
>>
>>> Does anybody have the topology files for ATP and/or ADP for the OPLS-AA
>>> forcefield?. If not, how can I parameterize this molecules?.
>>> Best regards.
>>> Lucio Montero.
>>>
>>> Lucio Ricardo Montero Valenzuela
>>> Instituto de Biotecnologia, UNAM
>>> Departamento de Biologia Molecular de Plantas
>>> Av. Universidad 2001, Col. Chamilpa
>>> Cuernavaca 62210
>>> Mexico
>>
>> I've not tested this at all, but from my attempts to add OPLS-AA to
>> topolbuild, I get the following that might be suitable for insertion in
>> the oplsaa rtp:
>>
>> [ ATP ]
>> [ atoms ]
>> O9P opls_441 -0.635 0 ;O2
>> O8P opls_441 -0.635 1 ;O2
>> O7P opls_441 -0.635 2 ;O2
>> PG opls_445 0.072 3 ;P
>> O6P opls_442 -0.286 4 ;OS
>> O5P opls_441 -0.516 5 ;O2
>> O4P opls_441 -0.516 6 ;O2
>> PB opls_440 0.280 7 ;P
>> O3P opls_442 -0.250 8 ;OS
>> O2P opls_441 -0.516 9 ;O2
>> O1P opls_441 -0.516 10 ;O2
>> PA opls_440 0.276 11 ;P
>> O5* opls_442 -0.315 12 ;OS
>> C5* opls_443 0.085 13 ;CT
>> H5*1 opls_444 0.059 14 ;HC
>> H5*2 opls_444 0.059 15 ;HC
>> C4* opls_174 0.113 16 ;CT
>> H4* opls_176 0.065 17 ;HC
>> O4* opls_186 -0.348 18 ;OS
>> C1* opls_193 0.160 19 ;CO
>> H1* opls_194 0.084 20 ;HC
>> N9 opls_354B -0.245 21 ;NA
>> C8 opls_353 0.092 22 ;CK
>> H8 opls_359 0.100 23 ;H5
>> N7 opls_352 -0.233 24 ;NB
>> C5 opls_350 0.145 25 ;CB
>> C6 opls_351 0.147 26 ;CA
>> N6 opls_356 -0.341 27 ;N2
>> H61 opls_357 0.144 28 ;H
>> H62 opls_358 0.144 29 ;H
>> N1 opls_346 -0.219 30 ;NC
>> C2 opls_347 0.120 31 ;CQ
>> H2 opls_355 0.066 32 ;H5
>> N3 opls_348 -0.218 33 ;NC
>> C4 opls_349 0.159 34 ;CB
>> C2* opls_174 0.127 35 ;CT
>> H2* opls_176 0.100 36 ;HC
>> O2' opls_171 -0.385 37 ;OH
>> H2' opls_172 0.210 38 ;HO
>> C3* opls_174 0.113 39 ;CT
>> H3* opls_176 0.065 40 ;HC
>> O3' opls_171 -0.386 41 ;OH
>> H3' opls_172 0.210 42 ;HO
>> [ bonds ]
>> PG O9P
>> PG O8P
>> PG O7P
>> O6P PG
>> PB O6P
>> PB O5P
>> PB O4P
>> O3P PB
>> PA O3P
>> PA O2P
>> PA O1P
>> PA O5*
>> O5* C5*
>> C5* C4*
>> C5* H5*1
>> C5* H5*2
>> C4* O4*
>> C4* H4*
>> C4* C3*
>> O4* C1*
>> C1* N9
>> C1* H1*
>> C1* C2*
>> N9 C8
>> C8 H8
>> C8 N7
>> N7 C5
>> C5 C6
>> C5 C4
>> C6 N6
>> N6 H61
>> N6 H62
>> C6 N1
>> N1 C2
>> C2 H2
>> C2 N3
>> N3 C4
>> C4 N9
>> C2* C3*
>> C2* H2*
>> C2* O2'
>> O2' H2'
>> C3* H3*
>> C3* O3'
>> O3' H3'
>>
>>
>> Please let me know if this actually works for computations.
>> Charges were derived from the .mol2 file generated by Sybyl.
>>
>>
>> Sincerely,
>>
>>
>> --
>> Bruce D. Ray, Ph.D.
>> Associate Scientist
>> IUPUI
>> Physics Dept.
>> 402 N. Blackford St.
>> Indianapolis, IN 46202-3273
>>
>>
>>
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>
>
>
> ----------------------
> TJ Piggot
> t.piggot at bristol.ac.uk
> University of Bristol, UK.
>
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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.
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