[AMBER] questions for mdgx-virtual site

From: Gao J <21919039.zju.edu.cn>
Date: Fri, 29 May 2020 16:29:44 +0800 (GMT+08:00)


I want to perform mix-solvent MD in amber and to prevent aggregation ofbenzene probes, I need to set virtual sites on the probes with L-J repulsions between themselves merely. My parameters for &rule were as follows and I got an error said "ReadEPRuleFile >> Error. Extra point name unspecified." So I wonder what the correct format of "epname" or "atom" required. What's more, I am a little confused if any parameters needed for "excl[1,2]".

I really appreciate for your help!


  frame[1,2]: C1 C4

  epname: VSB

  atom: VSB

  style: 1


  v12: 0.5

  Sig: 21

  eps: 0.01

  residue: UNK


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Received on Fri May 29 2020 - 02:00:02 PDT
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