[gmx-developers] Charmm27 and RNA gives No default Angle types errors
hess at cbr.su.se
Mon Jul 19 10:59:34 CEST 2010
David van der Spoel wrote:
> 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.
I did this on purpose, such that you can have different bondedtypes for
different types of molecules,
if a force field requires this (and it makes the files independent,
which prevents lots of bugs/mistakes).
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