<br>Thanks everyone,<br>you were right, it doesn't work if I only take off one phosphate from GTP. I was using the wrong parameters, now I have an integer total charge.<br><br>Carla<br><br><div class="gmail_quote">On Thu, Jan 21, 2010 at 2:36 PM, Thomas Piggot <span dir="ltr"><<a href="mailto:t.piggot@bristol.ac.uk">t.piggot@bristol.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">If using an amber forcefield and GTP/GDP you can use the parameters on the following website. I have used the ATP/ADP ones and have had no problems with many different systems and ATP/ADP conformations with which I used to test these parameters.<br>
<br>
<a href="http://www.pharmacy.manchester.ac.uk/bryce/amber#cof" target="_blank">http://www.pharmacy.manchester.ac.uk/bryce/amber#cof</a><br>
<br>
Tom<div><div></div><div class="h5"><br>
<br>
Justin A. Lemkul wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
Carla Jamous wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thank you Justin,<br>
but I ran a simulation before this one with GTP & it worked fine. GDP & GTP parameters are identical except for GDP having less atoms.<br>
This is why I can't understand why I don't get an integer charge while I did in my previous simulation.<br>
<br>
</blockquote>
<br>
OK, but this still doesn't help anyone give you any advice. Please refer to my previous post - which case applies to you: almost integer, or way off?<br>
<br>
It is also potentially faulty logic to suggest that GDP parameters can be generated from GTP parameters by simply chopping off a phosphate. Under most force field parameter sets, the charges on the beta-phosphate will have to change since the electronic properties of the molecule are now different.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Carla<br>
<br>
On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Carla Jamous wrote:<br>
<br>
Hi,<br>
<br>
In order to run my simulation, I had to insert GDP parameters in<br>
ffamber94 (the force field I'm using).<br>
However, I'm having a problem with GDP charge.<br>
the charge of every charge group in top file should be an<br>
integer. But I'm getting a decimal charge which gives me<br>
naturally a decimal total charge of my molecule.<br>
I checked number of atoms, it's correct, their charge also.<br>
But it seems it's having trouble adding charges & giving an<br>
integer charge.<br>
Does anyone have an idea where is the source of the problem?<br>
<br>
<br>
What is the charge? If it is a small difference between an integer<br>
and your charge (i.e., the difference between +1.9999 and +2) then<br>
there is no problem. The issue there is the inherent limitation of<br>
doing a lot of floating-point operations to sum the total charge.<br>
If, however, you have a charge of +1.9256 when you wanted +2, then<br>
your parameters are simply wrong.<br>
<br>
-Justin<br>
<br>
Thanks<br>
<br>
Carla<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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