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

Sanku M msanku65 at yahoo.com
Fri Oct 28 23:02:29 CEST 2011

  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.

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