[gmx-users] Hi ..

Navratna Vajpai navratna.vajpai at unibas.ch
Thu Aug 17 09:00:27 CEST 2006

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.
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?
> 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,
Basel, Switzerland.
Phone- +41 61 267 2080(O)
	       +41 78 744 0810(M)

navratna.vajpai at unibas.ch

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