<br><br><div class="gmail_quote">On Sat, Oct 8, 2011 at 3:10 PM, ITHAYARAJA <span dir="ltr"><<a href="mailto:ithayaraja@gmail.com">ithayaraja@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
only 59 particle variation found out of 230 ligand coordinates.<br><br><div class="gmail_quote">On 8 October 2011 12:22, ITHAYARAJA <span dir="ltr"><<a href="mailto:ithayaraja@gmail.com" target="_blank">ithayaraja@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Sir,<br><br><br>I am actually simulating my protein with its ligand so I incorporated all ligand (3) coordinates to my protein .gro file and placed its .itp file also. I used gromas96 43a1 force field.<br>
<br>I found following error when i was doing grompp for energy minimization.
I went through FAQ and checked all but i couldn't find what exactly it
was. <br><br>So, I attached that files to you. I need your help to solve this<br><br>Program grompp, VERSION 4.5.1<br>Source code file: grompp.c, line: 377<br><br>Fatal error:<br>number of coordinates in coordinate file (GR_b4ion.gro, 66074)<br>
does not match topology (GR.top, 66015)<br></blockquote></div></blockquote><div><br>I used to count the atom numbers in .gro file and manually modify the topology to make them match. <br> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><font color="#888888"><br clear="all"><br>-- <br><font size="2"><b></b></font><br>
Ithayaraja M,<br>Research Scholar,<br>Department of Bionformatics,<br>Bharathiar University,<br>
Coimbatore 641 046,<br>
Tamil Nadu<br>India<br>
</font></blockquote></div><font color="#888888"><br><br clear="all"><br>-- <br><font size="2"><b></b></font><br>Ithayaraja M,<br>Research Scholar,<br>Department of Bionformatics,<br>Bharathiar University,<br>Coimbatore 641 046,<br>
Tamil Nadu<br>
India<br>
</font><br>--<br>
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