Hi,<div><br></div><div><br></div><div>So if I use PME for coloumb interactions, then what are my options? </div><div><br></div><div>Would you then suggest breaking up the 12-atom charge grp in the arginine residue into 2 charge groups? </div>
<div><br></div><div>Would it be enough to make the changes in the .rtp or parameters in other files must be changed?</div><div><br></div><div>POoja<br><br><div class="gmail_quote">On Sat, Jul 17, 2010 at 11:16 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
A charge grp consisting of 12 atoms is created from Arginine residues in my topology file. <br>
; residue 14 ARG rtp ARG q +1.0<br>
476 NH1 14 ARG N 150 -0.47 14.007 ; qtot -3.47<br>
477 H 14 ARG HN 150 0.31 1.008 ; qtot -3.16<br>
478 CT1 14 ARG CA 150 0.07 12.011 ; qtot -3.09<br>
479 HB 14 ARG HA 150 0.09 1.008 ; qtot -3 480 CT2 14 ARG CB 151 -0.18 12.011 ; qtot -3.18 481 HA 14 ARG HB1 151 0.09 1.008 ; qtot -3.09<br>
482 HA 14 ARG HB2 151 0.09 1.008 ; qtot -3 483 CT2 14 ARG CG 152 -0.18 12.011 ; qtot -3.18 484 HA 14 ARG HG1 152 0.09 1.008 ; qtot -3.09 485 HA 14 ARG HG2 152 0.09 1.008 ; qtot -3 486 CT2 14 ARG CD 153 0.2 12.011 ; qtot -2.8 487 HA 14 ARG HD1 153 0.09 1.008 ; qtot -2.71<br>
488 HA 14 ARG HD2 153 0.09 1.008 ; qtot -2.62<br>
489 NC2 14 ARG NE 153 -0.7 14.007 ; qtot -3.32<br>
490 HC 14 ARG HE 153 0.44 1.008 ; qtot -2.88<br>
491 C 14 ARG CZ 153 0.64 12.011 ; qtot -2.24<br>
492 NC2 14 ARG NH1 153 -0.8 14.007 ; qtot -3.04<br>
493 HC 14 ARG HH11 153 0.46 1.008 ; qtot -2.58<br>
494 HC 14 ARG HH12 153 0.46 1.008 ; qtot -2.12<br>
495 NC2 14 ARG NH2 153 -0.8 14.007 ; qtot -2.92<br>
496 HC 14 ARG HH21 153 0.46 1.008 ; qtot -2.46<br>
497 HC 14 ARG HH22 153 0.46 1.008 ; qtot -2 498 C 14 ARG C 154 0.51 12.011 ; qtot -1.49<br>
499 O 14 ARG O 154 -0.51 15.999 ; qtot -2 <br>
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.<br>
<br>
</blockquote>
<br></div>
Strictly speaking, charge groups do not always have to have a net charge, but generally they do.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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.<br>
</blockquote>
<br></div>
Simply breaking the charge group apart seems too arbitrary. If you're not using PME (which you're not), then you need integral charge groups, so it looks like this one has to stay intact. It just seems like there's the potential for inaccurate short-range interactions when the entire sidechain is encompassed by a single charge group. Perhaps for your case it will not matter so much; maybe someone else can comment. There are numerous threads in the list archive discussing this situation, so I won't repeat all of that here.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Also, is there an alternate way by changing the Cut-off?<br>
<br>
</blockquote>
<br></div>
Not really. Any cutoff you choose might be affected by artifacts of a large charge group.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Any thoughts?<br>
Pooja<br>
<br>
<br>
<br>
Pooja<br>
<br>
</blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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