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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Received on Sat Oct 29 2005 - 02:53:00 PDT
