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

[David van der Spoel]

alkasrivastava at iitb.ac.in wrote:
> 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

in the example below the charge is integer after every residue. See 
column with qtot.

> 
> 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
> 
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se