On Wednesday, February 25, 2009 12:06:20 AM, Lucio Ricardo Montero Valenzuela
<[email protected]> 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 _______________________________________________ gmx-users mailing list [email protected] http://www.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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
