[gmx-users] Adding Hydrogens by pdb2gmx
jmsstarlight at gmail.com
Mon Oct 31 14:09:03 CET 2011
all hydrogens were represented as a part of the groupd in wich they were.
So is there possible way to explicit 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?
So what term exactly do? Doest it make a connection beetween CAP and C and
N termi or anothing else?
2011/10/31 Justin A. Lemkul <jalemkul at vt.edu>
> James Starlight wrote:
>> Its very unclear for me because after pdb2gmx -f 1.pdb -o conf.gro -ignh
>> with gromos force field
>> I've checked conf.gro by VMD and this structure didnt contains any
>> hydrogens ;o
> I highly doubt that. I've used one of the Gromos96 force fields for
> nearly all of my work and it has never failed in any Gromacs version.
> Perhaps you're simply not taking into account the fact that Gromos96
> parameter sets are united atom, meaning that aliphatic hydrogens are not
> represented explicitly.
> 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
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