Dear Dr.justin<br>Actually by doing this we are using two different force fields in one simulation.<br>I had done it before and the result was that I discussed before in gmx-users(LINCS Error,Exploding system,Bad contacts between atoms)<br>
Then,this approch seems to doesn't work about my system.<br><br>Then I want to find charges and charge groups for gromos 43A1 and replace them for my drug(to edit PRODRG file manually) and work totally in gromos 43A1.<br>
Unfortunately I can't obtain these parameter.<br>Please let me have if you have it.<br>Can I use some Ab Initio software for determining partial charges of my drug?<br>for example ABINIT or Gaussian!<br><br>Thanks in advance<br>
<br><div class="gmail_quote">On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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;">
<div class="im"><br>
<br>
mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Ok<br>
then,I can use PRODRG server to generate .top and .gro files for drug.<br>
since it's reported charges are not very accurate ,we can replace all charges completely with them in 53A6(if was present).<br>
But it means we are working in 53A6 force field.<br>
then,we must generate .top and .gro files for our protein with 53A6 too.<br>
and work completely with 53A6.<br>
Am i right?<br>
thanks in advance<br>
</blockquote>
<br></div>
That sounds like a reasonable approach. Be sure to validate the drug topology. In my experience, this procedure is pretty good, but you always have to convince reviewers...<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;"><div><div></div><div class="h5">
<br>
On Sat, Jan 22, 2011 at 4:43 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>
mohsen ramezanpour wrote:<br>
<br>
Dear Justin<br>
<br>
I read your articles about PRODRG server,they were very useful.<br>
But I have a question:<br>
are charges of functional groups and generally other atom groups<br>
the same in all force fields?<br>
Because you have modified charges of your molecules by Gromos96<br>
53A6 while prodrg server is generating topology files in 43A1.<br>
I want to know can I replace charges from gromos 53A6 or other<br>
forcefields?<br>
thanks in advance<br>
<br>
<br>
Charges are not the same between force fields. We did our study<br>
with 43A1 since that is what PRODRG purports to produce. I would<br>
say that our recommendations carry to other Gromos force fields, as<br>
well, but don't take charges from 43A1 and apply them to 53A6. Be<br>
consistent within the force field.<br>
<br>
The atom types produced by PRODRG are largely shared between 43A1<br>
and 53A6, so if you *completely* replace all charges with those from<br>
53A6, you should have a topology that is compatible with 53A6.<br>
<br>
-Justin<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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