still im getting problem, i checked the funct its have numerical value..stilll getting problem..do i have to install gromac 3 version for that..coz i having 4.0.5 version...<br><br><div class="gmail_quote">On Thu, Aug 6, 2009 at 3:22 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>
mohit kumar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
but i dnt find any 'type' column in my topology file..the grompp programm with this top file works gud in 3.3 version..im having 4.0.5 version..is that can be issue?? shud i try in 3.3 version<br>
<br>
</blockquote>
<br></div>
This may be some new error-checking mechanism introduced in version 4.0. In your topology, a function type for pairs should be defined, according to the header of this section (from pdb2gmx):<br>
<br>
[ pairs ]<br>
; ai aj funct c0 c1 c2 c3<br>
<br>
If your "funct" column is blank or says "0" then that could be giving the error.<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 class="im">
On Thu, Aug 6, 2009 at 2:48 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>
mohit kumar wrote:<br>
<br>
im running energy minimization for POPC bilayer but its showing<br>
error which i cant figure out<br>
<br>
-- -------------------------------------------------------<br>
Program grompp, VERSION 4.0.5<br>
Source code file: topdirs.c, line: 99<br>
<br>
Fatal error:<br>
Invalid pairs type 0<br>
<br>
what does this pair type mean and how can i solve it?? plz help me<br>
<br>
<br>
The error message is pretty clear. Somewhere within the topology,<br>
you have a "0" in the "type" column, which doesn't correspond to any<br>
known pair type.<br>
<br>
-Justin<br>
<br>
<br>
<br>
MOHIT KUMAR<br>
Molecular Biochemistry & Biophysics<br>
Graduate Student<br>
Illinois Institute of Technology<br>
Chicago,IL, USA<br>
<br>
<br>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></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>
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<br>
-- <br>
MOHIT KUMAR<br>
Molecular Biochemistry & Biophysics<br>
Graduate Student<br>
Illinois Institute of Technology<br>
Chicago,IL, USA<br>
<br>
</div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<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>
========================================<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>MOHIT KUMAR<br>Molecular Biochemistry & Biophysics<br>Graduate Student<br>Illinois Institute of Technology<br>Chicago,IL, USA<br><br>