[gmx-users] atom type

Shima Arasteh shima_arasteh2001 at yahoo.com
Sat Jun 30 17:16:45 CEST 2012

 Hi dear gmx friends,

I have a C atom which its neighbors are N, O, H atoms and then sp2 hybridization. I wanna add this atom to the CHARMM36, but I don't know its atom type. I checked the atomtypes.atp file in CHARMM36 package, the C types are as below:
C    12.01100 ;    carbonyl C, peptide backbone 
CA    12.01100 ;    aromatic C 
CT1    12.01100 ;    aliphatic sp3 C for CH 
CT2    12.01100 ;    aliphatic sp3 C for CH2 
CT3    12.01100 ;    aliphatic sp3 C for CH3 
CPH1    12.01100 ;    his CG and CD2 carbons 
CPH2    12.01100 ;    his CE1 carbon 
CPT    12.01100 ;    trp C between rings 
CY    12.01100 ;    TRP C in pyrrole ring 
CP1    12.01100 ;    tetrahedral C (proline CA) 
CP2    12.01100 ;    tetrahedral C (proline CB/CG) 
CP3    12.01100 ;    tetrahedral C (proline CD) 
CC    12.01100 ;    carbonyl C, asn,asp,gln,glu,cter,ct2 
CD    12.01100 ;    carbonyl C, pres aspp,glup,ct1 
CPA    12.01100 ;    heme alpha-C 
CPB    12.01100 ;    heme beta-C 
CPM    12.01100 ;    heme meso-C 
CM    12.01100 ;    heme CO carbon 
CS    12.01100 ;    thiolate carbon 
CE1    12.01100 ;    for alkene; RHC=CR 
CE2    12.01100 ;    for alkene; H2C=CR 
CST    12.01100 ;    CO2 carbon 
CT    12.01100 ;    aliphatic sp3 C, new LJ params, no hydrogens (see toppar_all22_prot_aliphatic_c27.str) 
CT1x    12.01100 ;    aliphatic sp3 C for CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) 
CT2x    12.01100 ;    aliphatic sp3 C for CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) 
CT3x    12.01100 ;    aliphatic sp3 C for CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) 
CN    12.01100 ;    C for cyano group (see toppar_all22_prot_pyridines.str) 
CAP    12.01100 ;    aromatic C for pyrimidines (see toppar_all22_prot_pyridines.str) 
COA    12.01100 ;    carbonyl C for pyrimidines (see toppar_all22_prot_pyridines.str) 
C3    12.01100 ;    cyclopropyl carbon

Am I supposed to add a new atom type? I think this C type is not existed here.

Thanks for your  suggestions.


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