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
>> To: Discussion list for GROMACS users
>> 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_typemasscharge ptype sigma epsilon
>> > FNFN 0. 0. A 3.39000e-01 1.414192e+00
>> > FHFH 0. 0. A 0.0e+00 0.0e+00
>> > [ moleculetype ]
>> > ; Namenrexcl
>> > AM 3
>> > [ atoms ]
>> > ; nr type resnr residue atom cgnr charge mass typeB
>> >chargeB
>> > 1 FN 1AM N 1 -1.03500 14.00
>> > 2 FH 1AM H1 30.34500 1.00
>> > 3 FH 1AM H2 40.34500 1.00
>> > 4 FH 1AM H3 50.34500 1.00
>> > [ bonds ]
>> > ; aiaj 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 ]
>> > ; aiaj funct
>> > [ angles ]
>> > ; aiajak 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
>>
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
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>>
>>
National Institutes of Natural Sciences
Institute for Molecular Science
Kenji Mochizuki
e-mail: kmo...@ims.ac.jp
phone: 0564-55-7394
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