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