[gmx-users] Parametrisation of the heteroatomic pdb

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 28 19:41:59 CEST 2011

James Starlight wrote:
> I understood that but how I can add that groups to termi of the bowh of 
> my chains ?
> I've tried by -ter but pdb2gmx didnt ask me for the addition of the 
> CAPS. May be Amber ff didnt support this feature ?

pdb2gmx does not build things that aren't there.  Your input coordinate file 
needs to have the capping groups present, with all atoms named as the .rtp 
entries expect them, hence the suggestion to investigate the [ACE] and [NME] 


> James
>     You have to build capping groups onto the termini.  See, for
>     instance the [ACE] and [NME] groups in the .rtp file.
>     -Justin


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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