[gmx-users] N-terminus type PRO-NH

Mark Abraham Mark.Abraham at anu.edu.au
Sun Apr 2 01:16:45 CEST 2006

Nguyen Hoang Phuong wrote:
>>Is pdb2gmx recognising the N-terminal residue as PRO?
> I think so. However in my case pdb2gmx does not read the entry PRO-NH in
> the ffG43a1-n.tdb file. Only NH3+,NH2, or None are read. I cheat
> pdb2gmx by replacing the header [ PRO-NH ] by [ NH2 ] and it works
> for me now.

This immediately indicates that there is nothing wrong with the format 
(and functionality) of the [ PRO-NH ] section, and suggests that the 
problem is pdb2gmx recognising the applicability of this capping to your 
N-terminal residue. I suggest stripping off any capping on the PRO in 
your input file, and carefully comparing the atoms with those in 
ffG43a1.rtp for PRO. You might also try an input of a plain PRO amino acid.


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