AMBER Archive (2005)

Subject: AMBER: rounding in xleap when using saveoff command...

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Oct 28 2005 - 20:26:22 CDT

Dear All,

I have calculated the RESP charges for some structures by doing
multimolecular charge fitting. I followed the RESP protocol. I have
created the .prepi files for these structures using the new RESP charges,
and everything is fine; namely, the charges of each structure looks ok.
(By ok, I mean the following: The RX5' and RX3' parts add to -1 while the
intermediate residues (RX) have -1 charge) Then I have loaded these
structures into xleap and entered the perturbed charge information (also
the other parameters needed to do perturbation) in the "Edit Selected
Atoms" window. In that window, I kept the "unused" parts blank. Then I
have saved the structures using saveoff command. Here, I am copy/pasting
some part of a file created:

.
.
.
 "C6" "CM" 0 1 131073 29 6 -0.040620
 "H6" "H4" 0 1 131073 30 1 0.225025
 "C3'" "CT" 0 1 131073 31 6 0.176434
 "H3'" "H1" 0 1 131073 32 1 0.069871
 "O3'" "OH" 0 1 131073 33 8 -0.660896
 "H3T" "HO" 0 1 131073 34 1 0.442954
!entry.RC3.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
 "P" "P" 0 -1 0.0
 "O1P" "O2" 0 -1 0.0
 "O2P" "O2" 0 -1 0.0
 "O5'" "OS" 0 -1 0.0
 "C5'" "CT" 0 -1 -0.001094
 "H5'1" "H1" 0 -1 0.002027
 "H5'2" "H1" 0 -1 0.002027
 "C4'" "CT" 0 -1 -0.028908
 "H4'" "H1" 0 -1 -0.000479
.
.
.

When I use the command "charge <name of the structure>", it is giving me
the expected charge informations. As an example;

> charge RC3
Total unperturbed charge: -0.6805
Total perturbed charge: -0.6805
>

or

> charge RC
Total unperturbed charge: -1.0000
Total perturbed charge: -1.0000
>

Now, when I put the 'true' variable into the "unused" parts of the
perturbed atoms (in the "Edit Selected Atoms" window), and saveoff the
structures, the charges I see in the files are rounded off. As I an
example, I am getting the following charges compared to the charges I
copy/pasted above:

.
.
.
 "C6" "CM" 0 1 131073 29 6 -0.040600
 "H6" "H4" 0 1 131073 30 1 0.225000
 "C3'" "CT" 0 1 131073 31 6 0.176400
 "H3'" "H1" 0 1 131073 32 1 0.069900
 "O3'" "OH" 0 1 131073 33 8 -0.660900
 "H3T" "HO" 0 1 131073 34 1 0.443000
!entry.RC3.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
 "P" "P" 0 -1 0.0
 "O1P" "O2" 0 -1 0.0
 "O2P" "O2" 0 -1 0.0
 "O5'" "OS" 0 -1 0.0
 "C5'" "CT" 0 -1 -0.001100
 "H5'1" "H1" 0 -1 0.002000
 "H5'2" "H1" 0 -1 0.002000
 "C4'" "CT" 0 -1 -0.028900
 "H4'" "H1" 0 -1 -0.000500
.
.
.

The problem is when I check out the total charge of the structures. When I
use the "charge" command in xleap for these .lib filed structures, I am
getting the following results:

> charge RC3
Total unperturbed charge: -0.6805
Total perturbed charge: -0.6806
> charge RC
Total unperturbed charge: -1.0000
Total perturbed charge: -1.0001
>

In this example, the difference is small, but in some other examples, the
difference is 0.0002 or 0.0003. This happens because of the roundoff. I
wonder if I HAVE to use 'true' variables in the "Edit Selected Atoms"
window (for the perturbed atoms) if I want to do perturbation simulation.
If the answer is yes, how can I solve the problem I am having here?
Thanks in advance.

Best, 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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