From bond lengths, center of mass for the group and the moment of inertia. Erik
27 mar 2012 kl. 14.54 skrev Song Ke: > Dear All, > > I have a question about create and simulate dopc lipid virtual sites. I > noticed in ffbonded.itp > > [ constrainttypes ] > ; this section is implemented manually from bond & angle values > > ; constraints for rigid CH3 groups > MCH3 CT 2 0.166426 > MCH3 S 2 0.193875 > MCH3 MCH3 2 0.092163 > ; constraints for rigid NH3 groups > MNH3 CT 2 0.158254 > MNH3 MNH3 2 0.080229 > > ; angle-derived constraints for OH and SH groups in proteins > ; The constraint A-C is calculated from the angle A-B-C and bonds A-B, B-C. > C HO 2 0.195074 > CA HO 2 0.195074 > CT HO 2 0.194132 > CT HS 2 0.235935 > > > However, there is no MCH3 N constraint types, how can I get this value? > > Meanwhile, Is there a website or scripts to generate the dopc virtual > sites bonded itp instead of do it manually? > > Many thanks in advance, > > > -- > Song KE > PhD Candidate > Mailto:[email protected] > Molecular Modeling Lab > Department of Pharmacology and Toxicology > University of Vienna > Althanstrasse 14 (UZA 2) > A-1090 Vienna, Austria > > -- > 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 ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 [email protected] http://www2.icm.uu.se/molbio/elflab/index.html
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