Thread: [Apbs-users] gcent question
Biomolecular electrostatics software
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From: ZhouTing <coo...@ho...> - 2007-03-16 21:40:22
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Hi all,My molecule is ATOM 1 C1 LIG 1 -0.257 0.050 -0.010 0.595952 1.870ATOM 2 H2 LIG 1 -1.345 0.058 -0.071 0.130638 1.33ATOM 3 O3 LIG 1 0.314 1.028 0.449 -0.590524 1.52ATOM 4 O4 LIG 1 0.405 -1.028 -0.440 -0.416733 1.55ATOM 5 H5 LIG 1 1.350 -0.951 -0.351 0.280667 0.8The center of it should be 0.4670 -0.8430 -0.4230. My question is why APBS gives such information:Got paths for 1 moleculesReading PQR-format atom data from lig01.pqr. 5 atoms Centered at (2.500e-03, 0.000e+00, 4.500e-03) Net charge 0.00e+00 eI don't know how it gets this center.I look forward to your reply at your earliest convenience. Thank you very much and best wishes from Zurich, Switzerland. Yours very faithfully, Zhou Ting coo...@ho... _________________________________________________________________ 探索 Windows Vista 的世界 http://search.live.com/results.aspx?q=windows+vista&mkt=zh-cn&FORM=LIVSOP |
From: Nathan B. <ba...@cc...> - 2007-03-19 00:44:56
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Hello -- We define the center as xcent =3D 0.5*(xmax + xmin) ycent =3D 0.5*(ymax + ymin) zcent =3D 0.5*(zmax + zmin) as opposed to a center of geometry. Very early versions of APBS used =20= the center of geometry but we found it to be rather unreliable for =20 highly aspherical molecules whose principal axes didn't lie along the =20= axes of the box. Thanks, Nathan On Mar 16, 2007, at 4:40 PM, ZhouTing wrote: > Hi all, > > My molecule is > > ATOM 1 C1 LIG 1 -0.257 0.050 -0.010 0.595952 =20 > 1.870 > ATOM 2 H2 LIG 1 -1.345 0.058 -0.071 0.130638 =20 > 1.33 > ATOM 3 O3 LIG 1 0.314 1.028 0.449 -0.590524 =20 > 1.52 > ATOM 4 O4 LIG 1 0.405 -1.028 -0.440 -0.416733 =20 > 1.55 > ATOM 5 H5 LIG 1 1.350 -0.951 -0.351 0.280667 =20 > &nbs p; 0.8 > > The center of it should be 0.4670 -0.8430 -0.4230. My =20 > question is why APBS gives such information: > > Got paths for 1 molecules > Reading PQR-format atom data from lig01.pqr. > 5 atoms > Centered at (2.500e-03, 0.000e+00, 4.500e-03) > Net charge 0.00e+00 e > > I don't know how it gets this center. > > I look forward to your reply at your earliest convenience. Thank =20 > you very much and best wishes from Zurich, Switzerland. Yours very =20 > faithfully, Zhou Ting coo...@ho... > > =E6=8E=A2=E7=B4=A2 Windows Vista =E7=9A=84=E4=B8=96=E7=95=8C = =E4=BA=86=E8=A7=A3=E6=9B=B4=E5=A4=9A=E4=BF=A1=E6=81=AF=EF=BC=81 > ----------------------------------------------------------------------=20= > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to =20 > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?=20 > page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV____________________________= ____=20 > _______________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |