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><br><div class="gmail_quote">On Sat, Jan 22, 2011 at 4:43 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><div></div><div class="h5"><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;">
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 the same in all force fields?<br>
Because you have modified charges of your molecules by Gromos96 53A6 while prodrg server is generating topology files in 43A1.<br>
I want to know can I replace charges from gromos 53A6 or other forcefields?<br>
thanks in advance<br>
<br>
</blockquote>
<br></div></div>
Charges are not the same between force fields. We did our study with 43A1 since that is what PRODRG purports to produce. I would say that our recommendations carry to other Gromos force fields, as well, but don't take charges from 43A1 and apply them to 53A6. Be consistent within the force field.<br>
<br>
The atom types produced by PRODRG are largely shared between 43A1 and 53A6, so if you *completely* replace all charges with those from 53A6, you should have a topology that is compatible with 53A6.<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>
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>
<br>
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