Thanks for your reply. So I can not do the QM/MM calculation with the
amoeba water. Can you give me some advice about which program maybe I
can use for do this ? Will you write this part in future? Thank you!
On 07/10/2015 07:54 PM, Jason Swails wrote:
> On Fri, 2015-07-10 at 16:53 +0800, fjliu wrote:
>> Dear all:
>> I want to imitate the tutorial A2 to do the QM/MM
>> simulation
>> with the water model replaced by amoeba. Then I do as follows:
>> leapin
>> xleap -s -f
>> NMA = loadpdb NMA_skeleton.pdb
>> edit NMA (do the relax)
>> solvatebox NMA TIP3PBOX 15
>> savepdb NMA NMA_slv.pdb
>> saveamberparm NMA NMA_slv.top NMA_slv.crd(save to see the
>> box
>> information)
>> quit
>> Then:
>> pdbxyz NMA_slv
>> the NMA_slv.key:
>> parameters /home/fjliu/software/tinker/params/amoebabio09
>> a-axis 40.18
>> b-axis 39.30
>> c-axis 39.56
>>
>> I get the NMA_slv.xyz. Followed by: analyze NMA_slv PC >
>> NMA_slv.analout, I got the error message:
>>
>> Undefined Torsional Parameters :
>>
>> Type Atom Names
>> Atom
>> Classes
>>
>> Torsion 1-C 2-C 7-N 8-C 40
>> 3
>> 1 40
>>
>> MECHANIC -- Some Required Potential Energy Parameters are
>> Undefined
>>
>> TINKER is Unable to Continue; Terminating the Current
>> Calculation
>>
>> What is wrong with it?
> As the error message states, the Tinker parameter set does not define
> all of the torsions defined in your molecule. In particular, the atom
> types C-C-N-C has no torsion defined. So you need to add a definition
> for this torsion to your key file so Tinker knows how to assign it.
>
> What I did to parametrize NMA was to look through the amoebabio09
> parameter set, look for a torsion parameter whose atom types are as
> close as possible to the ones in NMA, and copy those parameters to my
> key file. Ultimately, however, this is a question about Tinker, not
> really Amber, so we may not be the most expert authorities on what went
> wrong.
>
>> Also I do the example in
>> /home/fjliu/software/amber14/src/pmemd.amoeba/build_amoeba/examples/JAC,thre
>> is no problem with the given jac.pdb. But if I extracted a water
>> molecule to do the pdbxyz, the atom type information will not give
>> out,
>> then it will be wrong when I do the analyze.
>>
>> Another question is can I do the QM/MM calculation with amoeba
>> water model?
> Not with Amber.
>
> HTH,
> Jason
>
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Received on Tue Jul 14 2015 - 03:00:02 PDT
