[gmx-users] amber99sb_virtual site lipids dopc MCH3_N constraint types

[Erik Marklund]

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:song.ke at univie.ac.at
> Molecular Modeling Lab
> Department of Pharmacology and Toxicology
> University of Vienna
> Althanstrasse 14 (UZA 2)
> A-1090 Vienna, Austria
> 
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> 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
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120327/ca9af556/attachment.html>