[gmx-users] The negative state of a Phe molecule is not parametrized in gromos96 FF?

[Hu Zhongqiao]

Dear all,

 

I wonder if a negative Phe molecule is parametrized in gromos96 FF
properly. I used

 

pdb2gmx -f phe.pdb -o phe.gro -p phe.top -ter

 

I selected "1: NH2" for N-terminus and "0: COO-" for C-terminus. But the
phe.top obtained is not correct

 

 

[ atoms ]

;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB

     1         NL      1    PHE      N      1      -0.83    14.0067   ;
qtot -0.83

     2          H      1    PHE     H1      1      0.415      1.008   ;
qtot -0.415

     3          H      1    PHE     H2      1      0.415      1.008   ;
qtot 0

     4          H      1    PHE     H3      1      0.415      1.008   ;
qtot 0.415

     5        CH1      1    PHE     CA      2          0     13.019   ;
qtot 0.415

     6        CH2      1    PHE     CB      2          0     14.027   ;
qtot 0.415

     7          C      1    PHE     CG      2          0     12.011   ;
qtot 0.415

     8          C      1    PHE    CD1      3       -0.1     12.011   ;
qtot 0.315

     9         HC      1    PHE    HD1      3        0.1      1.008   ;
qtot 0.415

    10          C      1    PHE    CD2      4       -0.1     12.011   ;
qtot 0.315

    11         HC      1    PHE    HD2      4        0.1      1.008   ;
qtot 0.415

    12          C      1    PHE    CE1      5       -0.1     12.011   ;
qtot 0.315

    13         HC      1    PHE    HE1      5        0.1      1.008   ;
qtot 0.415

    14          C      1    PHE    CE2      6       -0.1     12.011   ;
qtot 0.315

    15         HC      1    PHE    HE2      6        0.1      1.008   ;
qtot 0.415

    16          C      1    PHE     CZ      7       -0.1     12.011   ;
qtot 0.315

    17         HC      1    PHE     HZ      7        0.1      1.008   ;
qtot 0.415

    18          C      1    PHE      C      8       0.27     12.011   ;
qtot 0.685

    19         OM      1    PHE     O1      8     -0.635    15.9994   ;
qtot 0.05

20         OM      1    PHE     O2      8     -0.635    15.9994   ; qtot
-0.585

 

The N-terminus is still NH3, not NH2, and the total charge of the system
is -0.585, not -1. I realized that if I removed one of first 3 H atoms
manually, then the total charge is -1. But I think it should be not so
simple. Anyone can give some clues on this? I just want to produce the
topology file of a negative Phe molecule in Gromos99 FF.

 

Best wishes,

Zhongqiao

 

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