Navratna Vajpai wrote:
Dear All
I have been able to carry on with the MD run of my peptides. But when I
converted the traj into the pdb file I realized that there are no HA
atoms in the pdb. I checked the rtp file and found that even those atoms
are not defined there. So can anyone tell me how to get the HA (after or
before the MD run) as i need them explicitly . I was trying to look for
the options available in the trjconv but could not find.
Thanks and regards
Does your force field include explicit non-polar hydrogen atoms? Or does
it use united atoms?
Mark
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