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

[Krzysztof Kuczera]

Hi
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: 
/home/kuczera/prog/gromacs-5.1/src/gromacs/gmxpreprocess/toppush.c, 
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  
versions
- 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

-- 
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
http://oolung.chem.ku.edu/~kuczera/home.html