[gmx-users] fatal error

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 21 12:51:58 CET 2011

ahmet yıldırım wrote:
> Dear users,
> Gromacs 4.5.3
> pdb2gmx -f xxx.pdb -water spc
> select Force Field:9
> *Fatal error:*
> atom C not found in buiding block 13NH2 while combining tdb and rtp
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> How can I fixed this error?

You have a carbon atom in a residue that should only contain NH2.  Refer to the 
.rtp file for what is expected, then make a suitable structure that conforms to 
those requirements.

This has been asked and answered hundreds of times, so please make use of the 
mailing list search.  You would have gotten your answer in minutes rather than 


> Thanks in advance
> -- 


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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