[gmx-users] 3.3 release and Forcefield nb.itp format

[Erik Lindahl]

Hi Yang,

Please include the header [defaults] section from your forcefield.

The number of columns is flexible, since both atomic number and  
bonded_atomtype fields are optional.

Cheers,

Erik

On Oct 18, 2005, at 7:25 PM, Yang Ye wrote:

> Hi,
>
> I have found that 3.3's grompp generates drastically different  
> LJ_SR and LJ14 parameters for one of my self-defined forcefield  
> (converted from AMBER).
>
> From gmxdump,
> (3.3's tpr) tpx version 40
>         ntypes=72
>            functype[0]=LJ_SR, c6= 2.24468820e-20, c12= 3.18825866e-35
>            functype[1]=LJ_SR, c6= 1.61870333e-32, c12= 0.00000000e+00
>            functype[2]=LJ_SR, c6= 1.43123863e-20, c12= 1.22953165e-35
>            functype[3]=LJ_SR, c6= 1.17580789e-26, c12= 0.00000000e+00
>            ...
>
> They should be
> (3.3b's tpr) tpx version 32
>         ntypes=72
>            functype[0]=LJ_SR, c6= 3.35273775e-03, c12= 3.95092275e-06
>            functype[1]=LJ_SR, c6= 8.76983977e-05, c12= 8.89523299e-09
>            functype[2]=LJ_SR, c6= 3.08322068e-03, c12= 4.16509010e-06
>            functype[3]=LJ_SR, c6= 4.73846623e-04, c12= 2.59686658e-07
>            ...
>
> My ffambernb.itp is
> [ atomtypes ]
> ;name        mass      charge   ptype            c6           c12
>     H     1.008     0.000     A  3.9229141156e-07  5.8568793913e-13
>    HO     1.008     0.000     A  0.0000000000e+00  0.0000000000e+00
> ...
> [ nonbond_params ]
> ; i    j func          c6           c12
>     H     H   1  3.9229141156e-07  5.8568793913e-13
>     H    HO   1  0.0000000000e+00  0.0000000000e+00
>     H    HS   1  3.9229141156e-07  5.8568793913e-13
> ...
> [ nonbond_params ]
> ; i    j func          c6           c12
>     H     H   1  3.9229141156e-07  5.8568793913e-13
>     H    HO   1  0.0000000000e+00  0.0000000000e+00
>     H    HS   1  3.9229141156e-07  5.8568793913e-13
> ...
>
> I found that FF provided by gromacs has different column width. Is  
> this the reason?
>
> Thanks.
>
> Yang Ye
>
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-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214