<br><br><div class="gmail_quote">On Tue, Feb 15, 2011 at 5:25 PM, Parul tew <span dir="ltr"><<a href="mailto:parultew@gmail.com">parultew@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<pre style="font-family:comic sans ms,sans-serif">Hi all,<br>first I would like to thank Justin A. Lemkul for the tutorials provided which are very helpful for new users like me.<br>I am doing a membrane protein simulation and now doing packing of the lipids around the protein. I had run the <a href="http://inflategro.pl" target="_blank">inflategro.pl</a> script and <br>
and now I am facing a problem doing energy minimization of my inflated system (contatining protein and the lipid membrane) using grompp. <br>I have updated my topology file accordingly ie removed the spc.itp, ions.itp it now only contains protein and dppc <br>
the protein is of 3881 atoms but after updating my topolgy it still gives the following error:<br>Fatal error:<br>number of coordinates in coordinate file (system_inflated.gro, 9331)<br> does not match topology (topol.top, 10281)<br>
As i understand it could be because of the deleted lipids of the system, if so how can I know the deleted number of lipids.<br><br>My topology file looks like <br>-----------------------------------------------------------------------------------------------------------------------------<br>
;
<br>; This is your topology file
<br>; protein
<br>;
<br>; Include forcefield parameters
<br>#include "ffG53a6_lipid.itp"
<br>
<br>[ moleculetype ]
<br>; Name nrexcl
<br>Protein_A 3
<br>
<br>[ atoms ]<br>.<br>.<br>.<br>.<br>; Strong position restraints for InflateGRO
<br>#ifdef STRONG_POSRES
<br>#include "strong_posre.itp"
<br>#endif
<br>
<br>; Include DPPC chain topology
<br>#include "dppc.itp"
<br>
<br>
<br>#ifdef POSRES_WATER
<br>; Position restraint for each water oxygen
<br>[ position_restraints ]
<br>; i funct fcx fcy fcz
<br> 1 1 1000 1000 1000
<br>#endif
<br>
<br>
<br>[ system ]
<br>; Name
<br>protein<br>128-Lipid DPPC Bilayer
<br>
<br>[ molecules ]
<br>; Compound #mols
<br>Protein_A 1<br>DPPC 128<br></pre></blockquote><div><br></div><div>After insertion, there are probably several DPPC molecules removed. Check outputs from <a href="http://inflategro.pl">inflategro.pl</a>, then update accordingly.</div>
<div><br></div><div>Terry</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><pre style="font-family:comic sans ms,sans-serif">----------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br>
<br>thank you,<br>Parul Tewatia<br></pre><p style="margin-bottom:0in">
<br>
</p>
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