[gmx-users] How to merge Self-made ammonia .top with tip4p

[Justin Lemkul]

On 12/6/12 6:09 AM, Kenji Mochizuki wrote:
> Dear GMX users
>
> Could you tell me how to make the topology file for ammonia in tip4p water?
>
> I made topology file for ammonia by hand, as shown at end.
> MD dose work when system has only ammonia molecules.
>
> For ammonia in water,
> I had though it needed to add just two line at the top of .top file.
> ------------------------
> #include "ffoplsaa.itp"
> #include "tip4p.itp"
> ------------------------
>
> However, I got "Invalid order for directive defaults" in using grompp_d.
> Should I add this new atoms information into ffnonbonded.itp directly ??
>

That should not be necessary.  If your [defaults] directive is properly 
commented out (as shown), you shouldn't get this error.

The order of inclusion is important.  You have to define all force field-level 
directives (e.g., [defaults], [atomtypes], etc) before you can define any 
[moleculetypes], so you can't #include "tip4p.itp" until after the ammonia 
parameters, since you're introducing new [atomtypes] for that molecule.  The 
easiest solution is simply to move that #include statement right after the end 
of the ammonia [moleculetype] definition (see below).

> ------------------------
> ;[ defaults ]
> ; nbfunc      comb-rule       gen-pairs       fudgeLJ fudgeQQ
> ;1               2               yes             0.5     0.8333
> [ atomtypes ]
> ;name  bond_type    mass    charge   ptype          sigma      epsilon
> FN            FN      0.0000  0.0000  A   3.39000e-01  1.414192e+00
> FH            FH      0.0000  0.0000  A   0.00000e+00  0.00000e+00
> [ moleculetype ]
> ; Name            nrexcl
> AM             3
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB
>       1         FN      1    AM     N       1   -1.03500  14.000000
>       2         FH      1    AM     H1      3    0.34500   1.000000
>       3         FH      1    AM     H2      4    0.34500   1.000000
>       4         FH      1    AM     H3      5    0.34500   1.000000
> [ bonds ]
> ;  ai    aj funct  r  k
>      1     2     1  1.0124e-01  5.0242e+05
>      1     3     1  1.0124e-01  5.0242e+05
>      1     4     1  1.0124e-01  5.0242e+05
> [ pairs ]
> ;  ai    aj funct
> [ angles ]
> ;  ai    aj    ak funct  theta   cth
>      2     1     3     1  1.0670e+02  6.2802e+02
>      2     1     4     1  1.0670e+02  6.2802e+02
>      3     1     4     1  1.0670e+02  6.2802e+02
> [ exclusions ]
> 1       2       3       4
> 2       1       3       4
> 3       1       2       4
> 4       1       2       3

Add #include "tip4p.itp" here.

-Justin

> [ system ]
> ammonia
> [ molecules ]
> AM     11
> ------------------------
>
> K.Mochi
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================