[gmx-users] pdb2gmx problem with ACE N-cap

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 28 23:04:52 CEST 2011

Sanku M wrote:
> Hi,
>   I have a protein pdb file with ACE as N-cap and I am trying to use 
> pdb2gmx ( within gromacs 4.5.4 ) to generate a topology file using 
> opls/AA . the ACE is present in opls aminoacids.rtp files. But, on 
> issuing the pdb2gmx command, I get following error message:
> Program pdb2gmx_44, VERSION 4.5.4
> Source code file: pdb2top.c, line: 1070
> Fatal error:
> atom N not found in buiding block 1ACE while combining tdb and rtp
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> I wonder how I can make sure that ACE can be used as N-terminus.

You've somehow constructed the cap wrong.  There is no N atom in ACE.  Check the 
.rtp for what's required, check your coordinate file, and make sure you're using 
"-ter none" with pdb2gmx.  If that's still not working, post your command and 
relevant snippet of your coordinate 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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