<div>Maybe in other words:</div>
<div> </div>
<div>Can I create dipol in my aminoscids.rtp file which will be positively charged (+1) - NH+</div>
<div> </div>
<div>[ POS ]</div>
<div> [atoms]</div>
<div> N N 0.7 0</div>
<div> H H 0.3 1</div>
<div> [bonds]</div>
<div> N H</div>
<div> </div>
<div>Please, help whether this is not a mistake adding new residue with such charges?<br><br></div>
<div class="gmail_quote">On Mon, Jan 23, 2012 at 9:31 AM, Steven Neumann <span dir="ltr"><<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div>Hi Gmx Users,</div>
<div> </div>
<div>I am building a surface as a reperesentation of protein surface. In this case I divide amino acids as: polar, nonpolar, positively charged and negatively charged. Representation of 3 atoms constitutes one residue. I created new residues (Charmm27) using exsiting charges:</div>
<div> </div>
<div>e.g. Residue - Negative [ NEG ]</div>
<div> </div>
<div> </div>
<div><span lang="EN-GB">
<p>[ NEG ]</p>
<p>[ atoms ] </p>
<p>CC C 0.34 0</p>
<p>OT1 OC -0.67 1</p>
<p>OT2 OC -0.67 2</p>
<p>[ bonds ]</p>
<p>CC OT1</p>
<p>CC OT2</p></span></div>
<div>Theses charges are taken from COO- group of terminal residue [ GLY ]. I am able to find partial charges for Hydrophobic (CH2). However, I cannot find for positive representation of 3 atoms) for positive or hydrophilic residues. They always come as 2 or 4 atoms giving positive (+1) of neutral (hydrophilic).</div>
<div> </div>
<div>My question: Can I create me own partial charges for given positive or hydrophilic group? Is that ok for the force field? As different atoms in different groups have different charges it should be fine in this case... </div>
<div> </div>
<div>I will appreciate your response. Thank you!</div><span><font color="#888888">
<div> </div>
<div>Steven</div></font></span></blockquote></div><br>