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

[Kenji Mochizuki]

Dear Justin

Thank you for reply. 

I added 
#include "ffoplsaa.itp" into top and 
#include "tip4p.itp"    after [exclusions], as you told. 

Then, I could make tpr file and MD looks working. 

Thank you very much.

Kenji

----- Original Message -----
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Date: 2012-12-06 22:56:19
>> Subject: Re: [gmx-users] How to merge Self-made ammonia .top with tip4p
>> 

>> 
>> 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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>> 

====================
National Institutes of Natural Sciences
  Institute for Molecular Science

  Kenji Mochizuki

  e-mail: kmochi at ims.ac.jp
  phone: 0564-55-7394
====================