[gmx-users] atom type

[Mark Abraham]

On 1/07/2012 1:16 AM, Shima Arasteh wrote:
>
>   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.

Neither can we. Your description could be of H-C(=O)-NXY or H-C(=NX)-OY.

>   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.

If they don't match, you can't use them, but you need to judge that for 
yourself, and be sure to have read the original literature for any 
detail on how these atom types were decided and parametrized. The 
original CHARMM22 forcefield files (freely available via Google) may 
also be instructive.

Mark