James Starlight wrote:
exactly
all hydrogens were represented as a part of the groupd in wich they
were. So is there possible way to explicit it?
I'm not quite sure I follow. A united atom force field, by definition, does not
have aliphatic hydrogens. I suggest you consult the literature and understand
the intrinsics of the chosen force field before you attempt to use it.
Another question about pdb2gmx. about -term
as I understood this must be used only if atoms for CAP groups are
presented in the PDB file mustnt it?
The -ter option can be useful in changing the protonation state of the termini
or in adding caps.
So what term exactly do? Doest it make a connection beetween CAP and C
and N termi or anothing else?
By default, pdb2gmx builds charged termini (NH3+ and COO-), per the typical
protonation states of these groups in aqueous solution. If a cap is present,
then you don't want pdb2gmx doing that, so by choosing "None" for the termini in
conjunction with the caps, only one proton is added to the N-terminus (as in an
amide), and only one carbonyl oxygen remains on the C-terminus, such that the
caps can be added in a sensible way.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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