[gmx-users] Re: charge group in topology file

[alkasrivastava at iitb.ac.in]

Hi,
All

I am running gromacs for simulation of 5 peptides. I have a problem with
the topology file in which the charge on each and every charge group is
not coming whole but in some of them it is in fraction which is not
correct. I have used G43a1 as well as OPLS but i am getting the same
problem with both of them. Now i don't know how to deal with it.
here is the part of topology file after pdb2gmx -f 1st.pdb -p 1st.top -o
1st.gro

Can anyone help me.
Thanks in Advance
ALKA

[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
   chargeB      massB
     1   opls_287      1    GLY      N      1       -0.3    14.0067   ;
qtot -0.3
     2   opls_290      1    GLY     H1      1       0.33      1.008   ;
qtot 0.03
     3   opls_290      1    GLY     H2      1       0.33      1.008   ;
qtot 0.36
     4   opls_290      1    GLY     H3      1       0.33      1.008   ;
qtot 0.69
     5  opls_292B      1    GLY     CA      1       0.19     12.011   ;
qtot 0.88
     6   opls_140      1    GLY    HA1      1       0.06      1.008   ;
qtot 0.94
     7   opls_140      1    GLY    HA2      1       0.06      1.008   ;
qtot 1
     8   opls_235      1    GLY      C      2        0.5     12.011   ;
qtot 1.5
     9   opls_236      1    GLY      O      2       -0.5    15.9994   ;
qtot 1
    10   opls_238      2    ASN      N      3       -0.5    14.0067   ;
qtot 0.5
    11   opls_241      2    ASN      H      3        0.3      1.008   ;
qtot 0.8
    12  opls_224B      2    ASN     CA      4       0.14     12.011   ;
qtot 0.94
    13   opls_140      2    ASN     HA      4       0.06      1.008   ;
qtot 1
    14   opls_136      2    ASN     CB      5      -0.12     12.011   ;
qtot 0.88
    15   opls_140      2    ASN    HB1      5       0.06      1.008   ;
qtot 0.94
    16   opls_140      2    ASN    HB2      5       0.06      1.008   ;
qtot 1
    17   opls_235      2    ASN     CG      6        0.5     12.011   ;
qtot 1.5
    18   opls_236      2    ASN    OD1      6       -0.5    15.9994   ;
qtot 1
    19   opls_237      2    ASN    ND2      7      -0.76    14.0067   ;
qtot 0.24
    20   opls_240      2    ASN   HD21      7       0.38      1.008   ;
qtot 0.62
    21   opls_240      2    ASN   HD22      7       0.38      1.008   ;
qtot 1
    22   opls_235      2    ASN      C      8        0.5     12.011   ;
qtot 1.5
    23   opls_236      2    ASN      O      8       -0.5    15.9994   ;
qtot 1
    24   opls_238      3    ASN      N      9       -0.5    14.0067   ;
qtot 0.5
    25   opls_241      3    ASN      H      9        0.3      1.008   ;
qtot 0.8
    26  opls_224B      3    ASN     CA     10       0.14     12.011   ;
qtot 0.94
    27   opls_140      3    ASN     HA     10       0.06      1.008   ;
qtot 1
    28   opls_136      3    ASN     CB     11      -0.12     12.011   ;
qtot 0.88