Dear justin,<br> I have no clues about rewriting a force field so i think i can t proceed with this anymore.<br><br>thanks a lot for your patient reply.<br>sree.<br><br><br><br><div class="gmail_quote">On Wed, Dec 22, 2010 at 9:32 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>
<br>
sreelakshmi ramesh wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear justin,<br>
I am sorry the file is <a href="http://ffG43a1nb.itp.It" target="_blank">ffG43a1nb.itp.It</a> <<a href="http://ffG43a1nb.itp.It" target="_blank">http://ffG43a1nb.itp.It</a>> was a typing mistake.<br>
<br>
</blockquote>
<br>
The points I raised before still stand:<br>
<br>
1. You're not using 43A1, you're using ffgmx, according to that message from grompp.<br>
<br>
2. You can't make a simple change to any of the force fields included in Gromacs to magically convert them into using Buckingham potentials. None of them were designed to do that. You'll have to basically re-write the entirety of the ff*nb.itp file, and then validate that such a force field model is even valid, because none of them were parameterized to be.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
On Wed, Dec 22, 2010 at 9:26 AM, 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>
Justin A. Lemkul wrote:<br>
<br>
<br>
<br>
sreelakshmi ramesh wrote:<br>
<br>
I am using gromos force field fotr my work and This force<br>
field's files come filled<br>
with LJ functions and now if i want to work with<br>
buckingham potential i changed in default section of force<br>
field ffG34a21.itp file but it gives me the follwing errors<br>
<br>
<br>
ERROR 77 [file ffgmxnb.itp, line 144]:<br>
Trying to add LJ (SR) while the default nonbond type is<br>
Buck.ham (SR)<br>
<br>
<br>
I should also add that if you think you're using Gromos96 (although<br>
from "ffG34a21.itp" it's not at all clear to me that you're using<br>
any legitimate form of it - 43A1? 43A2? something else?), you're<br>
not. The "ffgmx" force field is a modified form of Gromos87 that is<br>
antiquated and should not be used for new simulations, as described<br>
in detail in the manual.<br>
<br>
-Justin<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></div></div>
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<div class="im"><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>
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<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> | (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>
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