[gmx-users] gromacs-5.1 with charmm36.ff

Krzysztof Kuczera kkuczera at ku.edu
Fri Sep 11 00:34:21 CEST 2015

I have run into a strange problem when making an urea+tip3p water box
When trying to set up an energy minimization with gromacs-5.1  I get a 
grompp error:

Program gmx grompp, VERSION 5.1
Source code file: 
line: 908

Fatal error:
Unknown bond_atomtype cn9

Here is the strangeness:

- grompp and mdrun work OK with version 5.0.4
- I am using the same force field since winter - from 
charmm36-nov2014.ff.tar, which I add
    manually to the successive 5.x directories as I upgrade the GROMACS  
- my system only has UREA and TIP3P, which do not contain atom names or 
types = CN9
    looking in the CHARMM36 merged.rtp file shows that CN9 atoms are in 
nucleic acids


Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
1251 Wescoe Hall Drive, 5090 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu

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