[gmx-users] special bond

[Nicola Staffolani]

OK, the use of the same name and type is a bit confusing, so it wasn't
clear from the last post that this should work.

​I beg your pardon but I think I am doing confusing things because I am
confused myself and that's why I am looking for help ;)​


In this case, it should (though of course you will get fatal errors
regarding missing angles unless you define suitable [angletypes], but
that's a separate issue).
​
Indeed I do get fatal errors regarding missing angles, but unfortunately
the gb's corresponding to the special bonds the atoms are supposed to make
are *not* there, this is the alarming point...
​

> So the net effect of what you are saying is:
> ​​
> pdb2gmx writes the bond between ATM1 and ATM2, but does not write gd_99
> into the .top as reference to the parameters, do I have that correct?
>

​Yes, you have it correct, where "​​pdb2gmx writes the bond between ATM1
and ATM2" means that during the compilation the correct couples of atoms
corresponding to the couples defined in specbond.dat are linked... These
couples  then, as said, are present in the .top file, but without any gb
aside...


-- 
Nicola Staffolani PhD
Biophysics & Nanoscience Centre CNISM <http://www.unitus.it/biophysics>
Università della Tuscia
Largo dell'Università s.n.c., I-01100 Viterbo
email: n.staffolani at unitus.it
tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36