[gmx-developers] Charmm27 and RNA gives No default Angle types errors

[David van der Spoel]

On 2010-07-08 13.05, Daniel Larsson wrote:
> On Jul 8, 2010, at 12:46 , Daniel Larsson wrote:
>
>> Hi all,
>>
>> Is the nucleic acid support still under development? I tried to process a small RNA molecule with the latest head version of Gromacs. pdb2gmx is fine, but grompp chokes when building the topology since it can not find any angle parameters and gives one of these errors for each angle:
>>
>> ERROR 1 [file topol.top, line 479]:
>>   No default Angle types
>
> After some digging, the problem seems to be that the function type set by pdb2gmx is 1 (default), but the ffnabon.itp file lists all the angles as function type 5.
>
> The angletype is set to 5 in the [ bondedtypes ] record in aminoacids.itp, but somehow pdb2gmx does not seem to adhere to this.
>
Fixed this by replicating the bondedtypes information in each file. It 
might be better to have just one file with this information, but now it 
works anyway.

>> Regards,
>> Daniel
>>
>> --
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-developers-request at gromacs.org.
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se