AMBER Archive (2006)

Subject: Re: AMBER: Qestion about input for RESP program

From: FyD (fyd_at_u-picardie.fr)
Date: Thu May 25 2006 - 03:22:13 CDT

Quoting JunJun Liu <ljjlp03_at_gmail.com>:

> On the page 235 of Amber8 manual, it states that 7.1th "area" is the list
> of atoms that need constraints. Now, I have a question, this constraint
> list can be written in the following two ways:
> === 1st way ===
> 6 0.0
> 1 1 1 2 1 3 1 4 1 5 1 6
> 6 0.0
> 1 17 1 18 1 19 1 20 1 21 1 22
> ================
>
> === 2nd way ===
> 12 0.0
> 1 1 1 2 1 3 1 4 1 5 1 6
> 1 17 1 18 1 19 1 20 1 21 1 22
> ===============
>
> These two ways of defining the list of charge constrained atoms are the
> same to me. But the results are different. Can anybody tell me why there's
> such a difference? I checked the source code and found it's related the
> 'nlgrng" varible. What's the role of this varible?

In 1st way:
you want that the charge value of the atoms 1-6 of molecule 1 to be set = 0
            the charge value of the atoms 17-22 of molecule 1 to be set = 0

In the 2nd way:
you want that the charge value of the atoms 1-6 & 17-22 of molecule 1 to be set
= 0
(However, the format is not the one used by RESP, it should be 16I5 and not 12I5
as in it is represented in the 2nd way)

It is normal you get different results...

Please see the R.E.DD.B. central aminoacid projects: You get a quick overview
using the new R.E.DD.B. browser "List projects" selecting "molecule
fragment"...
By clicking on the download link you can download RESP inputs used for the
project reported.

regards, Francois

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