<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>Dear Mark</span></div><div><span>Thanks for your complete explanation. </span></div><div>Now I have a question about adding ions to this system. I see the chain A has qtot=-1 and also the chain B has qtot=-1.</div><div><br></div><div>Now If I add two positive ions using the genion command, is it ok to make my system neutral?</div><div>I mean is it the same as the case where two negative ions were on a single protein?</div><div>------------------------------</div><div>Thanks again</div><div>Regards</div><div>D.M<br></div><div><br></div><div><br></div> <div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"><br><br><b><span style="font-weight:bold;">From:</span></b> Mark
Abraham <Mark.Abraham@anu.edu.au><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Saturday, 16 June 2012, 12:15<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] simulating dimer proteins<br> </font> </div> <br><div id="yiv270411724">
<div>
On 16/06/2012 5:31 PM, delara aghaie wrote:
<blockquote type="cite">
<div style="color:#000;background-color:#fff;font-family:arial, helvetica, sans-serif;font-size:12pt;">
<div><span>Dear Gromacs Users</span></div>
<div><span><br>
</span></div>
<div><span>Running pdb2gmx on a pdb file containing a dimer
protein, I used option (( chainsep id_or_ter)))</span></div>
<div><span>This resulted in separated topologies for each chain
and separated posre files. Also in the .gro file, the
aminoacides of the second chain started from number 1.
(Without this option the second chain aminoacides will
receive numbers in continuation of numbers of first
chain))....</span></div>
<div><br>
<span></span></div>
<div><span>Now:</span></div>
<div><span>Can I use these files to continue the simulations or
again it is necessary to follow the procedure explained in
multiple chains gromacs???</span></div>
<br>
</div>
</blockquote>
<br>
By definition of pdb2gmx function, you now have a topology and a
coordinate file that matches. That is the minimum requirement for
grompp to succeed later. grompp doesn't care about some aspects of
atom numbering - including your observation above.<br>
<br>
Mark<br>
</div>
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