Yes and no. The atom types and bonded terms are likely available, but there may not be an existing residue topology in the distributed files.
A couple quick searches with grep did not find BOC alone, but there are some complex molecules with the fragment in top_all36_cgenff.rtf which could probably be used as a basis to create a patch (PRES) for replacing an amino group.
Probably, but I'd use existing fragments from the CGenFF topology file (search for Tert.Butyl) if I needed this for my work. The CGenFF guidelines advise using existing topologies when available, instead of those from cgenff program or its web interface, ParamChem.
Ya, I have the received the parameter file from CGenFF paramchem in .str format.
the group is defined as "RESI/ scrat". this I have written it as PRES BOC.
(since the atom name C (CG202) should bind with +N of Resi Trp)
in the bond defination i have replaced H02 atom with +N (which earlier binds with C) and following an earlier example i have scripted the setup file as
read sequ card * peptide seq * 5 trp thr val ser ala
gener pep setup warn first boc last ct3
the warning in the output as
PARAMETER FILE BEING READ FROM UNIT 99 RDTITL> * PARAMETERS GENERATED BY ANALOGY BY RDTITL> * CHARMM GENERAL FORCE FIELD (CGENFF) PROGRAM VERSION 1.0.0 RDTITL> * PARRDR> WARNING: ATOMS IN BOND CG2O OG2D 750.00000 1.22000 DONT EXIST PARRDR> WARNING: ATOMS IN BOND CG2O OG30 150.00000 1.33400 DONT EXIST PARRDR> WARNING: ATOMS IN BOND CG2O N 260.00000 1.30000 DONT EXIST PARRDR> WARNING: ATOMS IN BOND CG30 CG33 222.50000 1.53800 DONT EXIST PARRDR> WARNING: ATOMS IN BOND CG30 OG30 340.00000 1.43000 DONT EXIST PARRDR> WARNING: ATOMS IN BOND CG33 HGA3 322.00000 1.11100 DONT EXIST PARRDR> WARNING: ATOMS IN ANGLE OG2D CG2O OG30 90.00000 125.90000 DONT EXIST **** Warning **** The following extraneous characters were found while command processing in PARRDR 160.00 2.25760
* Toppar stream file generated by * CHARMM General Force Field (CGenFF) program version 1.0.0 * For use with CGenFF version 3.0.1 *
read rtf card append * Topologies generated by * CHARMM General Force Field (CGenFF) program version 1.0.0 * 36 1
! "penalty" is the highest penalty score of the associated parameters. ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization.
RESI /scrat 0.000 ! param penalty= 108.000 ; charge penalty= 8.368 GROUP ! CHARGE CH_PENALTY ATOM C CG2O2 0.557 ! 7.505 ATOM C1 CG331 -0.270 ! 0.622 ATOM O1 OG2D1 -0.456 ! 0.525 ATOM C2 CG331 -0.270 ! 0.622 ATOM O2 OG302 -0.445 ! 8.368 ATOM C3 CG331 -0.270 ! 0.622 ATOM CT CG301 0.232 ! 4.616 ATOM H01 HGA3 0.090 ! 0.025 ATOM H02 HGR52 0.112 ! 2.610 ATOM H03 HGA3 0.090 ! 0.025 ATOM H04 HGA3 0.090 ! 0.025 ATOM H05 HGA3 0.090 ! 0.025 ATOM H06 HGA3 0.090 ! 0.025 ATOM H07 HGA3 0.090 ! 0.025 ATOM H08 HGA3 0.090 ! 0.025 ATOM H09 HGA3 0.090 ! 0.025 ATOM H10 HGA3 0.090 ! 0.025
BOND C O1 BOND C O2 BOND C H02 BOND C1 CT BOND C1 H03 BOND C1 H06 BOND C1 H09 BOND C2 CT BOND C2 H04 BOND C2 H07 BOND C2 H10 BOND O2 CT BOND C3 CT BOND C3 H01 BOND C3 H05 BOND C3 H08 IMPR C O1 O2 H02
END
read param card flex append * Parameters generated by analogy by * CHARMM General Force Field (CGenFF) program version 1.0.0 *
! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization.
