Amir Abbasi wrote:
Hi Dear Users!
I'm Using MMB to produce initial structures for my simulations.
This program creating a .pdb file in output.
The output file containing Hydrogen atoms that are not recognized by
gromos53a5.
I want to edit my pdb file but I can't find anything about hydrogen
types in gromos!
any suggestion?
The Gromos force fields are united-atom, so most H atoms are not used. Aromatic
hydrogens are type HC and polar hydrogens are type H.
If you're trying to run your structure through pdb2gmx and it's complaining, use
-ignh and only necessary hydrogens will be built back on.
-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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