Navratna Vajpai wrote:
Dear Mark
Hello.
The force field I used is g43b1 from GROMOS96. I checked the g43b1.atp
file and fond that the HC is defined there which corresponds to Hydrogen
attached to the Carbon. But somehow in the pdb outcome this is not
there. the output pdb file contains only H atoms corresponding to HN.
Now I exactly don't know which type of atoms are defined there. Kindly
let me know what should I do to bring HA into the scene.
use an all atom force field.
Best regards
Nav
On Aug 17, 2006, at 5:46 AM, Mark Abraham wrote:
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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*******************************************
Navratna Vajpai
Ph. D student in Prof. Grzesiek's laboratory
Department of Structural Biology
Biozentrum, University of Basel
Klingelbergstrasse 70,
CH-4056
Basel, Switzerland.
Phone- +41 61 267 2080(O)
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
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