Now I changed the .top file in this way and I am getting this error now :-<br><br>change :- ; Include forcefield parameters<br>#include "charmm27.ff/forcefield.itp"<br><br>;Include ligand topology<br>#include "PTR.itp"<br>
<br>[ moleculetype ]<br>; Name nrexcl<br>Protein_chain_A 3<br><br>=====================<br><br>error:-<br><br><br>Ignoring obsolete mdp entry 'title'<br><br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#<br>
Generated 23220 of the 23220 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 1<br>Generated 20092 of the 23220 1-4 parameter combinations<br>Excluding 3 bonded neighbours molecule type 'Protein_chain_A'<br>
<br>-------------------------------------------------------<br>Program grompp, VERSION 4.5.4<br>Source code file: toppush.c, line: 1987<br><br>Fatal error:<br>No such moleculetype LIG<br>For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>-------------------------------------------------------<br><br>"I Had So Many Problem, and Then I Got Me a Walkman" (F. Black)<br>
<br><br><br><br><br><div class="gmail_quote">On Tue, Jun 21, 2011 at 1:56 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im">On 21/06/2011 2:51 PM, bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
ok now I am doing the things again and here is the result of output of each command till adding ions. At the time of executing the command grompp for reading em.mdp file for ions.tpr generation, I am getting the following error:-<br>
<br>
<br>
Fatal error:<br>
Syntax error - File PTR.itp, line 7<br>
Last line read:<br>
'[ atomtypes ] '<br>
Invalid order for directive atomtypes<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/<u></u>Documentation/Errors</a><br>
------------------------------<u></u>-------------------------<br>
<br>
"Everything's formed from particles" (Van der Graaf Generator)<br>
<br>
here's a list of output , I obtained till the step of adding ion ??<br>
</blockquote>
<br></div>
You haven't followed the steps of the tutorial well enough. Specifically, you've edited a .top or .itp file in the wrong place.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>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 href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>
Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>