<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 24/01/2011 10:06 PM, mohsen ramezanpour wrote:
<blockquote
cite="mid:AANLkTi=otHS00mXZ7Z6wcaF4iY786=99PMiS8=e3vYCG@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
Sounds like you've re-learned the lessons here:
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/How-tos/Parameterization">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>
<br>
<blockquote
cite="mid:AANLkTi=otHS00mXZ7Z6wcaF4iY786=99PMiS8=e3vYCG@mail.gmail.com"
type="cite"><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>
</blockquote>
<br>
You should choose a force field based on the likelihood of being
able to successfully make your observations. You want one that has a
record of useful performance on similar systems, for which you can
develop reasonably reliable parameters readily, test them suitably,
and run simulations smoothly. Don't presuppose the form of the
solution.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTi=otHS00mXZ7Z6wcaF4iY786=99PMiS8=e3vYCG@mail.gmail.com"
type="cite">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 moz-do-not-send="true"
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 class="h5">
<br>
On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul <<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a> <mailto:<a
moz-do-not-send="true" 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 moz-do-not-send="true"
href="http://vt.edu" target="_blank">vt.edu</a> <<a
moz-do-not-send="true" href="http://vt.edu"
target="_blank">http://vt.edu</a>> | (540) 231-9080
<div class="im"><br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- gmx-users mailing list <a
moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
</div>
<mailto:<a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>
<div class="im"><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list.
Use the www<br>
interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a><br>
</div>
<mailto:<a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>>.
<div class="im"><br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<br>
</div>
</blockquote>
<div>
<div class="h5">
<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 moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use
the www interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div>
</div>
</blockquote>
</div>
<br>
</blockquote>
<br>
</body>
</html>