For example, C* is used in ffbonded.itp, which can be looked up in ffnonbonded as opls_500, which atomtypes.atp reveals as a Trp gamma carbon.
Mark On Sat, Jun 1, 2013 at 2:27 AM, Broadbent, Richard < [email protected]> wrote: > The conversion is in ffnonbonded.itp. However, unless you plan to modify > the forcefield you shouldn't need this. > > Richard > > On 01/06/2013 00:57, "Hari Pandey" <[email protected]> wrote: > > >Dear Gromacs users, > > > >I am a new user and I have some questions > > I confused about indexing. in atomtypes.atp clearly we can know the > >index is for what kind of atom but in ffbondedtype.itp there is > >different kind of the indexing so I confused how do i pathch the force > >field . > >Some are obvious (OH, is oxygen bonden to hydrogen and HO is a hydrogen > >bonded to oxygen) > >but definitively I dont know what type of bond makes the carbon atoms like > >C_2, C_3 or C * > >Can somebody help me what represents in ffbonded.atp. > >for example : opls_083 means S in RSR , opls_091 means CH2 in RCH2SR > >but what type of atoms are C*, C_2, C_3 , CT, CM, CS, LP, CT_2, CT_3, > >CW, NB etc. > > > > > >could you please provide me idea or list for that if somebody have. > >Thanks > > > > > >In Oplsaa.ff the indexing is as follows : > > > >atomtypes.atp > > > > > >opls_079 1.00800 ; H(O) ALCOHOLS JPC,90,1276 (1986) > > opls_080 15.03500 ; CH3 IN METHANOL JPC,90,1276 (1986) > > opls_081 14.02700 ; CH2 IN ETHANOL JPC,90,1276 (1986) > > opls_082 32.06000 ; S IN H2S JPC,90,6379 (1986) > > opls_083 32.06000 ; S IN RSH JPC,90,6379 (1986) > > opls_084 32.06000 ; S IN RSR JPC,90,6379 (1986) > > opls_085 32.06000 ; S IN RSSR JPC,90,6379 (1986) > > opls_086 1.00800 ; H IN H2S JPC,90,6379 (1986) > > opls_087 1.00800 ; H(S) IN RSH JPC,90,6379 (1986) > > opls_088 15.03500 ; CH3 IN CH3SH JPC,90,6379 (1986) > > opls_089 14.02700 ; CH2 IN CH3CH2SH JPC,90,6379 (1986) > > opls_090 15.03500 ; CH3 IN CH3SR JPC,90,6379 (1986) > > opls_091 14.02700 ; CH2 IN RCH2SR JPC,90,6379 (1986 > > > >The ffbonded.itp is as follows ; Some esoteric OPLS atomtypes are not > >freely available (or depreciated). > >; Interaction types involving these have been commented out. [ bondtypes ] > >; i j func b0 kb OW HW 1 0.09572 502080.0 > > ; For TIP4F Water - wlj 1/98 OW LP 1 0.01750 753120.0 ; > > -idem- C* HC 1 0.10800 284512.0 ; C C3 1 > > 0.15220 265265.6 ; END C_2 C3 1 0.15220 265265.6 ; > >END C_3 C3 1 0.15220 265265.6 ; END C CA 1 > >0.14900 334720.0 ; wlj 8/97 C_2 CA 1 0.14900 334720.0 ; > >wlj 8/97 C_3 CA 1 0.14900 334720.0 ; wlj 8/97 C CB > >1 0.14190 374049.6 ; GUA C_2 CB 1 0.14190 374049.6 ; > >GUA C_3 CB 1 0.14190 374049.6 ; GUA C CM 1 > >0.14440 343088.0 ; THY C_2 CM 1 0.14440 343088.0 ; THY > >C_3 CM 1 0.14440 343088.0 ; THY C CS 1 0.14900 > > 334720.0 ; C_2 CS 1 0.14900 334720.0 ; C_3 CS 1 > > 0.14900 334720.0 ; C CT 1 0.15220 265265.6 ; C_2 > >CT 1 0.15220 > > 265265.6 ; C_3 CT 1 0.15220 265265.6 ; C CT_2 1 > > 0.15220 265265.6 ; AA Calpha C_3 CT_2 1 0.15220 265265.6 > >; AA C-term NO ON 1 0.12250 460240.0 ; wlj nitro CS CW > > 1 0.13670 456892.8 ; wj/nm CS CS 1 0.14240 > >392459.2 ; -idem- CS CB 1 0.14240 392459.2 ; -idem- CS > > HA 1 0.10800 307105.6 ; -idem- CU NB 1 0.13200 > >343088.0 ; -idem- CU CA 1 0.14210 392459.2 ; -idem- CU > > HA 1 0.10800 307105.6 ; -idem- NA NB 1 0.13490 > >334720.0 ; -idem- OS NB 1 0.13990 386601.6 ; -idem- OS > > CR 1 0.13570 386601.6 ; -idem- C3 C3 1 0.15260 > >217568.0 ; Ethane C! C! 1 0.14600 322168.0 ; wlj C! > >CS 1 0.14600 322168.0 ; wlj > >-- > >gmx-users mailing list [email protected] > >http://lists.gromacs.org/mailman/listinfo/gmx-users > >* Please search the archive at > >http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
