[gmx-users] OPLS-AA topologies for ATP/ADP.
TJ Piggot
t.piggot at bristol.ac.uk
Thu Feb 26 18:15:22 CET 2009
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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