[gmx-users] amber force field in gromacs

Justin A. Lemkul jalemkul at vt.edu
Sat Nov 21 13:23:12 CET 2009

leila karami wrote:
> dear Mark
> your opinion is right [residue number 1 is NGLY in pdb file but residue 
> number 1 is GLY in warning].
> howbeit, what work should I do?

Can you post an actual copy-and-paste snippet from your .pdb file?  So far, you 
have shown a few re-typed parts of lines that, in theory, should work, but 
obviously are not.  I suspect a formatting problem might be the issue. 
Preserving the start position of the residue name and the spacing within all the 
atom information is important, and is the only reason I can think of that NGLY 
gets truncated to GLY when pdb2gmx reads the file.



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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