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

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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