[AMBER] problems on amoeba force filed implemented in amber

From: fjliu <fjliu.itcs.ecnu.edu.cn>
Date: Fri, 10 Jul 2015 16:53:01 +0800

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:
                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
        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

       Torsion 1-C 2-C 7-N 8-C 40 3
    1 40

       MECHANIC -- Some Required Potential Energy Parameters are

       TINKER is Unable to Continue; Terminating the Current Calculation

       What is wrong with it? Also I do the example in
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? Thanks for your help!Fengjiao

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Received on Fri Jul 10 2015 - 02:00:03 PDT
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