[AMBER] The value of NONBONDED_PARM_INDEX pointer

From: Meiting Wang <wangmeitingbetter.163.com>
Date: Mon, 17 Oct 2016 22:57:17 +0800 (CST)

Dear all
  I want to modify the vdW parameters of some atom types in the prmtop file. When I reproduce the prmtop file, I don not know how to calculate the data list in the array of NONBONDED_PARM_INDEX.
Foe example. if the number of atom type is 7 (Ntypes = 7). The LJ_A factor of the first and the second atom type can be calculate as :

 A = LJ_ACOEF[index]

And then is my question. I don not know how to calculate the value of NONBOND_PARM_INDEX[2].
That means that i don not know how to calculate the value of NONBONDED_PARM_INDEX[Ntypes*(ATOM_TYPE(i)-1)+ATOM_TYPE(j)].
I have read the prmtop.pdf again and again, but i can not find the answer.
Thanks for your help and looking forward to your reply ŁĄ
Meiting Wang

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Received on Mon Oct 17 2016 - 08:00:02 PDT
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