Hi<div><br></div><div>I have figured out the vacuum slow problem. It turns out I was using PBC in vacuum with PME. It is now fixed.</div><div><br></div><div>The other problem is still there. My protein has 2 chains. one chain is simply a glutamate residue. Its charge (both terminii charged is -1.11 instead of -1). here is the section of the topology with the charges. Why does pdb2gmx assign a charge of -1.11 instead of -1 if there is a free glutamate molecule with NH3+ and COO- at the terminii ? </div>
<div><br></div><div><br></div><div><div> 1 opls_287 484 GLU N 1 -0.3 14.0067 ; qtot -0.3</div><div> 2 opls_290 484 GLU H1 1 0.33 1.008 ; qtot 0.03</div><div>
3 opls_290 484 GLU H2 1 0.33 1.008 ; qtot 0.36</div><div> 4 opls_290 484 GLU H3 1 0.33 1.008 ; qtot 0.69</div><div> 5 opls_283 484 GLU CA 1 0.04 12.011 ; qtot 0.73</div>
<div> 6 opls_140 484 GLU HA 1 0.06 1.008 ; qtot 0.79</div><div> 7 opls_136 484 GLU CB 2 -0.12 12.011 ; qtot 0.67</div><div> 8 opls_140 484 GLU HB1 2 0.06 1.008 ; qtot 0.73</div>
<div> 9 opls_140 484 GLU HB2 2 0.06 1.008 ; qtot 0.79</div><div> 10 opls_274 484 GLU CG 3 -0.22 12.011 ; qtot 0.57</div><div> 11 opls_140 484 GLU HG1 3 0.06 1.008 ; qtot 0.63</div>
<div> 12 opls_140 484 GLU HG2 3 0.06 1.008 ; qtot 0.69</div><div> 13 opls_271 484 GLU CD 4 0.7 12.011 ; qtot 1.39</div><div> 14 opls_272 484 GLU OE1 4 -0.8 15.9994 ; qtot 0.59</div>
<div> 15 opls_272 484 GLU OE2 4 -0.8 15.9994 ; qtot -0.21</div><div> 16 opls_271 484 GLU C 5 0.7 12.011 ; qtot 0.49</div><div> 17 opls_272 484 GLU O1 5 -0.8 15.9994 ; qtot -0.31</div>
<div> 18 opls_272 484 GLU O2 5 -0.8 15.9994 ; qtot -1.11</div><div><br></div><div><br></div><br><div class="gmail_quote">On Thu, Jan 20, 2011 at 11:55 AM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</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><span>On 01/20/11, <b>maria goranovic </b> <<a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a>> wrote:</span><blockquote style="border-left:1px solid rgb(0, 0, 255);padding-left:13px;margin-left:0pt" type="cite">
<div>Hi<div><br></div><div>I have a protein whose topology I built using pdb2gmx with the -ss option and the opls-aa force field. When I run grompp, the total charge on the protein is reported as 2.9 (not 2.999). Why a non-zero charge? Does this have something to do with the disulfide bridge?</div>
</div></blockquote><br></div>Something is materially wrong, like mangled termini. Have a look at the resulting structure.<div class="im"><br><br><blockquote style="border-left:1px solid rgb(0, 0, 255);padding-left:13px;margin-left:0pt" type="cite">
<div><div>Secondly, when I run a simulation of the same protein (7000 atoms) with certain restraints in vacuum, the simulation runs very slow. I am wondering why. I am not using particle decomposition. the box size is 50 x 50 x 50 nm. Using 4.5.3</div>
</div></blockquote><br></div>Have a look at the end of the .log file for some performance data. How are you assessing "very slow"?<br><font color="#888888"><br>Mark
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