<div>So, as requested:</div><div><br></div><div>for ions.spc I got info from <a href="http://www.somewhereville.com/?p=114">http://www.somewhereville.com/?p=114</a></div><div><br></div><div>In attach files you may need to reproduce what I am doing here. Assuming you have ffamber installed and GMX 3.3.</div>
<div>Copy ions.itp and tip3p.itp to your _gromacs_/top/ folder.</div><div><br></div><div>tip3p.itp was modified by me.</div><div><br></div><div>I use Mac OSX 10.4.11 intel with Fink</div><div><br></div><div>My commands based on 1BVG.pdb (you can get it at <a href="http://www.pdb.org">www.pdb.org</a>):</div>
<div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000"><br></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000"></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000">
grep 'ATOM ' 1BVG.pdb>| Protein.pdb</p>
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<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000">sed s/PRO\ A\ \ \ 1/NPROA\ \ \ 1/g Protein.pdb | sed s/PRO\ B\ \ \ 1/NPROB\ \ \ 1/g \</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000">| sed s/PHE\ A\ \ 99/CPHEA\ \ 99/g | sed s/PHE\ B\ \ 99/CPHEB\ \ 99/g \</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000">| sed s/O\ \ \ CPHE/OC1\ CPHE/g | sed s/OXT\ CPHE/OC2\ CPHE/g \</p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000">| sed s/HIS\ /HID\ /g | sed s/LYS\ /LYP\ /g | sed s/CYS\ /CYN\ /g >| ProteinAmber.pdb</p>
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<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000">pdb2gmx -ff amber99 -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -water tip3p</p>
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<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000">editconf -bt triclinic -f Protein2.pdb -o Protein2.pdb -d 1.0</p>
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<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000">genbox -cp Protein2.pdb -cs ffamber_tip3p.gro -o Protein_b4ion.pdb -p Protein.top</p>
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<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000">grompp -f em.mdp -c Protein_b4ion.pdb -p Protein.top -o Protein_b4ion.tpr</p>
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<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000">echo 13 | genion -s Protein_b4ion.tpr -o Protein_b4em.pdb -nname Cl -nn 4 -norandom</p>
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<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000">sed s/7274/7270/ Protein.top > temp; echo "Cl 4" >> temp; \mv temp Protein.top</p>
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<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000">grompp -f em.mdp -c Protein_b4em.pdb -p Protein.top -o em.tpr # total charge: 8.000000e+00 !!!!</p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000; min-height: 16.0px">
<br></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000">mdrun -v -deffnm em</p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Monaco; color: #ff0000"><br></p>
<p></p></div><div>Many thanks for your attention.</div><div>Cheers,</div><div>Alan</div><div><br></div><div>-------------------</div><span class="Apple-style-span" style="border-collapse: collapse; ">Can you show us your modified ions.itp file (just the Cl part) and the exact<br>
command options you used for genion?<br>Thanks,<br>Vignesh<br></span><br><div class="gmail_quote">On Thu, Jul 3, 2008 at 7:44 AM, Alan <<a href="mailto:alanwilter@gmail.com">alanwilter@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi List,<div><br></div><div>To people using ffamber.</div><div><br></div><div>I have ffamber with ions.itp modified to recognise ffamber ions. All seems fine and working.</div><div><br></div><div>So, I have a protein, net charge +4 e. In the pdb file there no ions and no water. I modify the pdb as said in ffamber instructions. All fine.</div>
<div>Then, I add water and hence I use genion to neutralise my system. I add 4 Cl. All fine.</div><div><br></div><div>However when using grompp for preparing the inputs for a minimisation, I got a warning saying that my system is now +8 e. It happens no matter what ion I use with ffamber (being it pos or neg, or value 2). It's like if genion were counting only the ions and not reading the ion's charge value.</div>
<div><br></div><div>I know it's reading my modified ions.itp file because otherwise genion will fail to process.</div><div><br></div><div>Has someone else seen that? Any comments?</div><div><br></div><div>Despite this, I can minimise and carry on MD on my system. Is there any other to definitely know if GMX is computing the right charge values?</div>
<div><br></div><div>Many thanks in advance.<br clear="all">Cheers,</div><div>Alan</div><div><br><font color="#888888">-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge.<br>
80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>><a href="http://www.bio.cam.ac.uk/~awd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<
</font></div>
</blockquote></div><br><br clear="all"><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge.<br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<