Hi Rahul,<br>
<br>
Apparently, in your structure file the sodium ions are placed before
the solvent. That means that in the .top file they should also be
placed before as follows:<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
Protein 1<br>
Na 10 <br>
SOL 182 <br><br>
This section needs to correspond to the structure file.<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<br><div><span class="gmail_quote">On 9/6/05, <b class="gmail_sendername">Rahul Karyappa</b> <<a href="mailto:r.karyappa@ncl.res.in">r.karyappa@ncl.res.in</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Respected Sir,<br>
I am generating my structure (.pdb) using Cerius2
software. There I am putting my model in the box and performing energy
minimization. As you told I first removed Na+ ions from the .pdb
file. Then I generated .gro and .top files using PRODRG website. Then I
added Na+ ions again in the .gro file. But my question is where to add
Na+ ions in the .top file? In the beginning of the file I added
#include "ions.itp" and in the last like this:<br>
[ system ]<br>
; Name<br>
Protein<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
Protein 1<br>
SOL 182 <br>
Na 10 <br>
But after this when I ran grompp it gave me following errors:<br>
<font size="2">processing coordinates...<br>
Warning: atom names in topol.top and out1.gro don't match (OW - NAA)<br>
Warning: atom names in topol.top and out1.gro don't match (HW1 - NAB)<br>
Warning: atom names in topol.top and out1.gro don't match (HW2 - NAC)<br>
Warning: atom names in topol.top and out1.gro don't match (OW - NAD)<br>
......<br>
<br>
<font size="3">And when I ran mdrun it gave me following errors:<br>
<br>
</font>Back Off! I just backed up step5.pdb to ./#step5.pdb.1#<br>
Wrote pdb files with previous and current coordinates<br>
Warning: 1-4 interaction between 15 and 20 at distance larger than 1 nm<br>
These are ignored for the rest of the simulation<br>
turn on -debug for more information<br>
<br>
Back Off! I just backed up step6.pdb to ./#step6.pdb.1#<br>
Wrote pdb files with previous and current coordinates<br>
<br>
Back Off! I just backed up step7.pdb to ./#step7.pdb.1#<br>
Wrote pdb files with previous and current coordinates<br>
<br>
</font>Where am I going wrong? Is it correct? Or I need to add them where we specify other atoms in the .top file.<br>
waiting for your kind reply.<br>
Rahul Karyappa<br>
NCL, Pune<br>
<br><font face="Arial" size="2"><table style="border-color: blue; border-left: 1px solid blue; padding-left: 5px;"><tbody><tr><td><b><i>-- Original Message --</i></b><br>From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
spoel@xray.bmc.uu.se</a>><br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users@gromacs.org</a>><br>Date: Mon, 05 Sep 2005 09:06:03 +0200
<br>Subject: Re: [gmx-users] problem with Na+ ions....<br><br><br>On Mon, 2005-09-05 at 11:41 +0530, Rahul Karyappa wrote:<br>> Dear all,<br>> I have structure with defined Na ions in it. I have a .pdb file of<br>
> that structure and I want to convert it to .gro and .top files. When I<br>> tried it on PRODRG website it gave me error that Na+ is not supported.<br>> Then I defined all the atoms in .rtp file also Na. But it's not
<br>> working. What can I do for this? I have included "ions.itp" file in<br>> the .top file. Do I need to delete the Na+ entry in the .top file. I<br>> can't delete them from .gro file because their coordinates are
<br>> specified. What Should I do?<br>take out Na from your pdb file, make the topology and add the Na back in<br>manually. check chap. 5 in the manual.<br>> Thanking you in advance.<br>> <br>> Rahul Karyappa<br>
> NCL, India<br>> *****************************************************************<br>> This email is virus free by TrendMicro Inter Scan Security Suite.<br>> *****************************************************************
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