AMBER Archive (2006)

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

From: JunJun Liu (ljjlp03_at_gmail.com)
Date: Thu May 25 2006 - 09:01:41 CDT

Thanks to Ilyas and Francois! I have a further question on this issue. I
got the following charge constraints with R.E.D.II for a multi-orientation
calculation. According to my understanding, it means the sum of atom 1
 from all molecule orientation is constrained to be zero. And so does to
atom 2 in all molecules, atom 3 in all molecules.... But this is nonsense
to me. Or does the charge constraint input have another definiation method
for multi-molecules? Thanks!

============
    3
    1 1 2 1 3 1
    3
    1 2 2 2 3 2
.............
============

On Thu, 25 May 2006 05:22:13 -0300, FyD <fyd_at_u-picardie.fr> wrote:

> 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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-- 
JunJun Liu

College of Chemistry
Central China Normal University
WuHan   430079
P.R. China
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