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

[Krzysztof Kuczera]

Thanks for the quick response
     - that fixed my problem
Krzysztof

On 9/10/15 5:36 PM, Justin Lemkul wrote:
>
>
> On 9/10/15 6:17 PM, Krzysztof Kuczera wrote:
>> 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
>>
>
> Please get the latest version of the force field from our website.  
> There have been changes related to case sensitivity in the code, and I 
> have updated the force field files accordingly.
>
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
>
> -Justin
>


-- 
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