Gee. My mistake then. I did not realize the difference between -COO and Zwitterion_COO-.
However, when I use the zwitterion termini on both ends of the other chain, the total charge is 4.010, which is also *slightly*ยด disturbing. I have seen numbers like 2.999999, which are still better. Is 4.010 acceptable within rounding off errors? thank you for helping -Maria On Thu, Jan 20, 2011 at 2:00 PM, Justin A. Lemkul <[email protected]> wrote: > > > maria goranovic wrote: > >> I did use -ter and chose -COO and NH3+. Am i supposed to chose >> Zwitterion_COO- and Zwitterion_NH3+ ? >> > > That's what I said, and that's what you have, isn't it? A single amino > acid that should have both its termini charged? > > -Justin > > On Thu, Jan 20, 2011 at 12:55 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> maria goranovic wrote: >> >> Hi >> >> I have figured out the vacuum slow problem. It turns out I was >> using PBC in vacuum with PME. It is now fixed. >> >> 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 ? >> >> >> You're not choosing the termini correctly. Use -ter with pdb2gmx >> and select the zwitterion forms of both termini. >> >> -Justin >> >> >> 1 opls_287 484 GLU N 1 -0.3 >> 14.0067 ; qtot -0.3 >> 2 opls_290 484 GLU H1 1 0.33 >> 1.008 ; qtot 0.03 >> 3 opls_290 484 GLU H2 1 0.33 >> 1.008 ; qtot 0.36 >> 4 opls_290 484 GLU H3 1 0.33 >> 1.008 ; qtot 0.69 >> 5 opls_283 484 GLU CA 1 0.04 >> 12.011 ; qtot 0.73 >> 6 opls_140 484 GLU HA 1 0.06 >> 1.008 ; qtot 0.79 >> 7 opls_136 484 GLU CB 2 -0.12 >> 12.011 ; qtot 0.67 >> 8 opls_140 484 GLU HB1 2 0.06 >> 1.008 ; qtot 0.73 >> 9 opls_140 484 GLU HB2 2 0.06 >> 1.008 ; qtot 0.79 >> 10 opls_274 484 GLU CG 3 -0.22 >> 12.011 ; qtot 0.57 >> 11 opls_140 484 GLU HG1 3 0.06 >> 1.008 ; qtot 0.63 >> 12 opls_140 484 GLU HG2 3 0.06 >> 1.008 ; qtot 0.69 >> 13 opls_271 484 GLU CD 4 0.7 >> 12.011 ; qtot 1.39 >> 14 opls_272 484 GLU OE1 4 -0.8 >> 15.9994 ; qtot 0.59 >> 15 opls_272 484 GLU OE2 4 -0.8 >> 15.9994 ; qtot -0.21 >> 16 opls_271 484 GLU C 5 0.7 >> 12.011 ; qtot 0.49 >> 17 opls_272 484 GLU O1 5 -0.8 >> 15.9994 ; qtot -0.31 >> 18 opls_272 484 GLU O2 5 -0.8 >> 15.9994 ; qtot -1.11 >> >> >> >> On Thu, Jan 20, 2011 at 11:55 AM, Mark Abraham >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>> wrote: >> >> >> >> On 01/20/11, *maria goranovic * <[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> >> <mailto:[email protected]>>> wrote: >> >> Hi >> >> 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? >> >> >> Something is materially wrong, like mangled termini. Have a >> look at >> the resulting structure. >> >> >> 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 >> >> >> Have a look at the end of the .log file for some performance >> data. >> How are you assessing "very slow"? >> >> Mark >> -- >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- Maria G. >> Technical University of Denmark >> Copenhagen >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- >> Maria G. >> Technical University of Denmark >> Copenhagen >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Maria G. Technical University of Denmark Copenhagen
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