[gmx-users] Hi ..
David van der Spoel
spoel at xray.bmc.uu.se
Thu Aug 17 09:11:05 CEST 2006
Navratna Vajpai wrote:
> Dear Mark
> 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
> 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?
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> Navratna Vajpai
> Ph. D student in Prof. Grzesiek's laboratory
> Department of Structural Biology
> Biozentrum, University of Basel
> Klingelbergstrasse 70,
> Basel, Switzerland.
> Phone- +41 61 267 2080(O)
> +41 78 744 0810(M)
> navratna.vajpai at unibas.ch <mailto:navratna.vajpai at unibas.ch>
> gmx-users mailing list gmx-users at gromacs.org
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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
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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