Dear All,<br><br>I just want to know if the programm PRODRG is able to generate for my ligand files with .top extension.<br><br>I have two files one is itp format and other is gro using PRODRG.<br>If it is possible what is the name here :<a href="http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta#DRGFIN.GRO">http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta#DRGFIN.GRO</a><br>
<br>Yours sincerely,<br>Olga<br><br><div class="gmail_quote">2010/11/10 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
Olga Ivchenko 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 All,<br>
<br>
I have created creating topology file using *prodrg_beta (using gromos 96 ff) <<a href="http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta" target="_blank">http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta</a>>*. When I am trying to run energy minimization it writes an error:<br>
<br>
</blockquote>
<br>
Please consider carefully the caveats about PRODRG noted here (second paragraph):<br>
<br>
<a href="http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips" target="_blank">http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips</a><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Syntax error - File creatine.top, line 19<br>
Last line read:<br>
'[ moleculetype ]'<br>
Invalid order for directive moleculetype<br>
<br>
I looked at previoust mailing lists according this problem. I can not find direct answer.<br>
<br>
</blockquote>
<br>
</div><a href="http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_defaults" target="_blank">http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_defaults</a><br>
<br>
Somehow you've cut and pasted such that you've got a [moleculetype] directive out of order.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I tried to add this line in the topology file<br>
<br>
#include "ffG43a1.ff/DRGGMX.itp"<br>
<br>
An again an error:Fatal error:<br>
Topology include file "ffG43a1.ff/DRGGMX.itp" not found<br>
<br>
</blockquote>
<br></div>
Then either the file doesn't exist or isn't within the search path grompp is trying.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Please can you advice me on this.<br>
<br>
<br>
Yours sincerely,<br>
<br>
Olga<br>
<br>
<br>
<br>
<br>
</blockquote>
<br></div>
-- <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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