Hi, I agree it could be very useful. You can insert the bond hand-coding it in the topology, but you need also to generate angle and dihedral. This is very boring and error prone.
Francesco Il giorno 08 marzo 2012 12:32, Ehud Schreiber <schr...@compugen.co.il> ha scritto: > Hi,**** > > ** ** > > The mechanism for specifying special bonds for the pdb2gmx program, using > the specbond.dat file (manual section 5.6.7), seems to me not general > enough. The characteristic length of the bond is specifiable, but the range > of lengths for which a bond is assumed is hardcoded as +-10% of the > characteristic length. I, for example, am perturbing structures using the > Concoord method, and lengths of disulfide bonds sometimes vary by more than > 10%.**** > > I therefore suggest that two values would be added at the end of the line > declaring a special bond, specifying the minimum and maximum lengths. These > two values would be optional, so as not to break the existing arrangement, > which would remain as the default. This should not require more than a few > extra lines of code and would be, in my opinion, very useful.**** > > ** ** > > What do you say?**** > > ** ** > > Thanks,**** > > Ehud Schreiber.**** > > ** ** > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Cordiali saluti, Dr.Oteri Francesco
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