I did use -ter and chose -COO and NH3+. Am i supposed to chose Zwitterion_COO- and Zwitterion_NH3+ ?
On Thu, Jan 20, 2011 at 12:55 PM, Justin A. Lemkul <[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]>> wrote: >> >> >> >> On 01/20/11, *maria goranovic * <[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]> >> >> 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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