<div dir="ltr">Thanks Justin!<br><br>There is one script in User Contributions page, but it does not work.<br>I totally changed my way, I will use NAMD in this case...<br><br><br><br><div class="gmail_quote">On Fri, Jan 27, 2012 at 2:11 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="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="im"><br>
<br>
Dariush Mohammadyani wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Is there any similar script to change it for this reason?<br>
<br>
</blockquote>
<br></div>
If there is one that exists, it may have been posted to the User Contributions page of the Gromacs website. If not, maybe someone will post one for you.<br>
<br>
I've seen this question asked before with no answer, so likely it's time to break out the NAMD and Gromacs manuals in concert with your favorite text editor and scripting language, and have at it.<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 class="im">
<br>
On Fri, Jan 27, 2012 at 11:26 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>
Dariush Mohammadyani wrote:<br>
<br>
Hi all,<br>
<br>
I have two files (Topology and Parameter files) in NAMD format<br>
(*.inp). I am going to use them in GROMACS.<br>
Can you help me how can I use them?<br>
<br>
<br>
You'll have to have a good working knowledge of all file formats<br>
involved (which, for Gromacs, requires a thorough read through<br>
Chapter 5 of the manual) and design a script that will parse the<br>
relevant information from your existing files and write them into<br>
Gromacs format.<br>
<br>
-Justin<br>
<br></div>
-- ==============================<u></u>__==========<div class="im"><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>
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</blockquote><div class="HOEnZb"><div class="h5">
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-- <br>
==============================<u></u>==========<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="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br><div dir="ltr"><div>Kind Regards,<br>Dariush Mohammadyani<br>Department of Structural
Biology<br>University of Pittsburgh School of Medicine<br>Biomedical Science
Tower 3<br>3501 Fifth Avenue<br>Pittsburgh, PA 15261<br>USA</div></div><br>
</div>