AMBER Archive (2003)

Subject: Re: AMBER: Zn in antechamber

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Mon Sep 29 2003 - 15:15:04 CDT

Hi:
   I followed the manual (page.78) and created 2 resp files by using
respgen, one is like:
Resp charges for organic molecule

 &cntrl

 nmol = 1,
 ihfree = 1,
 ioutopt = 1,

 &end
    1.0
Resp charges for organic molecule
    2 28
    6 0
    6 0
    7 0
    6 0
    6 0
    7 0
    6 0
   16 0
    6 0
   16 8
    9 0
    8 0
    1 0
    1 0
    1 0
    1 0
    1 0
    1 0
    1 0
    1 0
    1 0
    1 0
    1 0
    1 0
    1 24
    1 0
    1 0
    1 27

The first column lookes like atomic mass. I changed '9' into '30',
because that is a Zn. Then I just follow the example in p.78. But it
seems that in the second 'resp' command line (in the manual), the input
file should be 'sustiva.respin2' instead of 'sustiva.respin1'. Finally,
I got the charges, do you think it is right?

Lishan
 
On Mon, 2003-09-29 at 12:38, Junmei Wang wrote:
>
>
>
> If you will make force constants 0.0, it doesn't matter what types they
> are. You may just use "1". You may manually revise resp input files by
> yourself. The amber7 version of respgen doesn't read in total charge
> information from ac input files (If I remember correctly). Best
>
> Junmei
> ===============================================================
> Dr. Junmei Wang
> Chemistry & Biophysics
> Encysive Pharmaceuticals
> 7000 Fannin, Houston TX 77030
> Tel: 713-5786649
> Email: jwang_at_tbc.com
> Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
> ===============================================================

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