<div>This is the arginine entry in the rtp file. It assigns 12 atoms to charge grp 3.</div><div><br></div><div>[ ARG ]</div><div> [ atoms ]</div><div> N NH1 -0.47 0</div><div> HN H 0.31 0</div>
<div> CA CT1 0.07 0</div><div> HA HB 0.09 0</div><div> CB CT2 -0.18 1</div><div> HB1 HA 0.09 1</div><div> HB2 HA 0.09 1</div><div>
CG CT2 -0.18 2</div><div> HG1 HA 0.09 2</div><div> HG2 HA 0.09 2</div><div> CD CT2 0.20 3</div><div> HD1 HA 0.09 3</div><div> HD2 HA 0.09 3</div>
<div> NE NC2 -0.70 3</div><div> HE HC 0.44 3</div><div> CZ C 0.64 3</div><div> NH1 NC2 -0.80 3</div><div> HH11 HC 0.46 3</div><div>
HH12 HC 0.46 3</div><div> NH2 NC2 -0.80 3 </div><div> HH21 HC 0.46 3</div><div> HH22 HC 0.46 3</div><div> C C 0.51 4</div><div>
O O -0.51 4</div><div><br></div><br><div class="gmail_quote">On Sat, Jul 17, 2010 at 9:17 AM, Sai Pooja <span dir="ltr"><<a href="mailto:saipooja@gmail.com">saipooja@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse"><div>A charge grp consisting of 12 atoms is created from Arginine residues in my topology file. </div>
<div><br></div><div><div>; residue 14 ARG rtp ARG q +1.0</div><div> 476 NH1 14 ARG N 150 -0.47 14.007 ; qtot -3.47</div><div> 477 H 14 ARG HN 150 0.31 1.008 ; qtot -3.16</div>
<div> 478 CT1 14 ARG CA 150 0.07 12.011 ; qtot -3.09</div><div> 479 HB 14 ARG HA 150 0.09 1.008 ; qtot -3 </div><div> 480 CT2 14 ARG CB 151 -0.18 12.011 ; qtot -3.18 </div>
<div> 481 HA 14 ARG HB1 151 0.09 1.008 ; qtot -3.09</div><div> 482 HA 14 ARG HB2 151 0.09 1.008 ; qtot -3 </div><div> 483 CT2 14 ARG CG 152 -0.18 12.011 ; qtot -3.18 </div>
<div> 484 HA 14 ARG HG1 152 0.09 1.008 ; qtot -3.09 </div><div> 485 HA 14 ARG HG2 152 0.09 1.008 ; qtot -3 </div><div> 486 CT2 14 ARG CD 153 0.2 12.011 ; qtot -2.8 </div>
<div> 487 HA 14 ARG HD1 153 0.09 1.008 ; qtot -2.71</div><div> 488 HA 14 ARG HD2 153 0.09 1.008 ; qtot -2.62</div><div> 489 NC2 14 ARG NE 153 -0.7 14.007 ; qtot -3.32</div>
<div> 490 HC 14 ARG HE 153 0.44 1.008 ; qtot -2.88</div><div> 491 C 14 ARG CZ 153 0.64 12.011 ; qtot -2.24</div><div> 492 NC2 14 ARG NH1 153 -0.8 14.007 ; qtot -3.04</div>
<div> 493 HC 14 ARG HH11 153 0.46 1.008 ; qtot -2.58</div><div> 494 HC 14 ARG HH12 153 0.46 1.008 ; qtot -2.12</div><div> 495 NC2 14 ARG NH2 153 -0.8 14.007 ; qtot -2.92</div>
<div> 496 HC 14 ARG HH21 153 0.46 1.008 ; qtot -2.46</div><div> 497 HC 14 ARG HH22 153 0.46 1.008 ; qtot -2 </div><div> 498 C 14 ARG C 154 0.51 12.011 ; qtot -1.49</div>
<div> 499 O 14 ARG O 154 -0.51 15.999 ; qtot -2 </div></div><div><br></div><div>See charge group 153. It has 12 atoms. This is true for all Arginine residues. It seems that charge groups must have an integer net-charge. As you can see, it assigns charge grps 151, 152, 153 etc. till the net-charge becomes an integer.</div>
<div> </div><div>One option would be to manually make them. In this case, I could simply breakdown this particular charge grp into 2 smaller chargegrps but I am sure if that would be consistent with the forcefield and not sure if it would be possible to set the net charge to an integral value to an integer for the smaller charge groups.</div>
<div>Also, is there an alternate way by changing the Cut-off?</div><div><br></div><div>Any thoughts?</div><div>Pooja</div></span></div><div><br></div><font color="#888888"><div><br></div><div><br></div><div><font color="#888888">Pooja</font></div>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>