outdated rdkit?

[fmqeisfeld]

Hi, I've just installed automartini with all its dependencies. However, the following error is reported:

$ ./auto_martini --smi "N1=C(N)NN=C1N" --mol GUA

Traceback (most recent call last): File "./auto_martini", line 1181, in listCGBeads,listBeadPos = findBeadPos(mol, feats, ringAtoms) File "./auto_martini", line 466, in findBeadPos trialEne = evalGaussianInterac(mol, trialComb, ringAtomsFlat) File "./auto_martini", line 298, in evalGaussianInterac listBeads[i], ringAtoms) File "./auto_martini", line 261, in atomsInGaussian distBdAt = Chem.rdMolTransforms.GetBondLength(conf,i,beadId) AttributeError: 'module' object has no attribute 'GetBondLength'

I've checked the Content of rdkit.Chem.rdMolTransforms and there's no function called GetBondLength(...). The only functions are: CanonicalizeConformer,CanonicalizeMol,ComputeCanonicalTransform,ComputeCentroid and TransformConformer.

Coul you please update the source, cuz I really Need to parametrize MAH...I havent found any publications where it has already been parametrized according to the martini-ff.

regards, frank.

[tbereau]

Hi Frank,

You need to update your version of RDKit. Look into your package manager. The more recent RDKit versions have the GetBondLength() function.

Best, Tristan