From: X. Tan <xjtan_at_u.washington.edu>
Date: Tue 12 Mar 2002 13:02:22 -0800 (PST)

Hi, Charles,

I got some replies for my questions, and I 'd like to share the answers
with you and other people.

----------------------------------------------
From: Ramon Garduno<ramon_at_ce.fis.unam.mx>
To: X. Tan <xjtan_at_u.washington.edu>

Mr. Tan: I also had similar questioning some time
ago. In AMBER manuals it is not clear how one should proceed to handle
RESP calculations. After doing my homework I found the following WWW pages
that helped me a lot regarding RESP calculations.

http://signe.teokem.lu.se/~ulf/Methods/resp.html
http://linus.chem.wesleyan.edu/~pearl/icc/Exp_AM08/extend.html

Hope this helps!. Ramon Garduno

--------------------------------------------
From:Mathy Froeyen <Matheus.Froeyen_at_rega.kuleuven.ac.be>
To: X. Tan<xjtan_at_u.washington.edu>

Dear Xiaojian,

The resp doc is indeed not very clear on these points.

"X. Tan" wrote:
> Dear amber user,
>
> Now I am working on RESP. I'd like to fit the charges of
> two or three conformations. So I refer to the example of
RESP/bis-napthyl.
> But there are something in that example I am not very clear. 1. in the
> bis_1.in file, it shows that the charge of napthyl is -99. Here does
this
> "-99" mean charge frozen at initial charge values.
> .....
> napthyl 1-
> -99 29
> 6 0
> 6 0
This could be true. It is indeed something strange.
>
> ....
> 2. what is the exact meaning of the following part.
> ....
> 13 -1.000
> 1 19 1 20 1 21 1 22 1 23 1 24 1 25 1 26 1 27 2 20 2 25 2 26 2 27
> ....
>
This is a charge constraint : first line: nbr-of-atoms charge The total
charge of 13 atoms must be -1.000. The 13 atoms are listed on the
following line: molecule-nbr atom-nbr.
>
> and the part, ....
> 2
> 1 1 2 1
> 2
> 1 2 2 2
> 2
> 1 3 2 3
> 2
> 1 4 2 4
> 2
> 1 5 2 5
> .....
>
Those are restraints between atoms of different molecules. first line:
nbr-of-atoms the two atoms must be treated as if they were the same. The
next line gives mol-nbr atom-nbr. etc.
> 3. in the bis_2.in file, many atoms' ivary were assigned a value "-1",
> what does that mean? .... napthyl 1-
> -99 29
> 6 -1
> 6 -1
> 6 -1
> 6 -1
> ....
>
looking at the output file I think -1 is the same as -99, to freeze the
charge. 0 means to let the charge free a positive number means equivalent
charge, like that numbered atom.
> 4. For the esp.dat file, what I need do is just combine the several
> esp.dat for each confamation into one file. Is that right?
yes.
>
> Thanks for your kind help.
>
> Xiaojian Tan
regards mathy froeyen

--------------------------------------------------------------
Received on Tue Mar 12 2002 - 13:02:22 PST
Custom Search