MOL2 Format for Maestro

Hi,

When trying to import a structure exported as MOL2, Maestro from Schrodinger crashes.

Apparently the @<TRIPOS>MOLECULE declaration in incomplete in the second line, only

num_atoms num_bonds 

are present and Maestro needs the all

num_atoms [num_bonds [num_subst [num_feat [num_sets]]]]

line... namely the substructure count, features count, and sets sount - usually 1 0 0, but a bit inconvenient!
Do you think you can fix it?

Cheers,

Nicolas

Hi Nicolas,

We are considering your request and we will get back with an answer soon.

Regards,

Erika

Hi Nicolas, 

According to the mol2 format (as you also quoted in you post)  only the 'number of atoms'  is mandatory parameter, the rests are optional. So strictly speaking Maestro's import does not comply the original Tripos specification. Have you contacted Schrödinger yet? ;-)

Anyway, we have experienced similar problems related to other file formats and other vendors, so it's fairly normal for us to try to adjust our software to these external circumstances.

In case of MOL2 it is the 3rd optional field that might be relevant, as far as I understood it represents the number of disconnected fragments in the molecule, though Tripos did apply a quite unusual terminology when they called them substructures. Is my understanding correct?

The features field is 0 at present, though in the longer term we may consider to implement some of these features - depending on the progress and goals of our 3D searching projects. Till then this value can be 0 by default.

I did not manage to figure out the meaning of the last fields, number of sets, though. Do you have any idea regarding the possible meaning of this last value? As we cannot write the SET record in the MOL2 export, we set this 5th field to 0.

We will implement this extra bit for you (and for other Maestro users :) ) though we cannot assign high priority to this task.

Btw, may I ask what do you use Maestro for?

 

Best regards

Miklos

Hi Miklos,

Investigating further I found that only the 3 first numbers are necessary... (the last being the number of disconnected fragments, you may be right). I will send a report to Schrodinger, if it can help but I doubt they can be as reactive as you guys ;-)
Right now I can open the mol2 files in Accelrys DViewer and re-save it in the mol2 format recognizable by Maestro, but it is a bit of a pain.

I use Maestro academic edition (hence, free) for 2 things

- to manipulate molecules (dihedrals, etc...) and fragments, once you get used to it it is pretty powerful
- to run molecular dynamics calculations thanks to Desmond (also free for academics!)

Cheers,

Nicolas

 

 

 

Schrodinger was very nice, they are looking into it for the next release, and here is their answer for the current "fix"

It seems 
to be a Maestro problem, as mol2convert utility does not have any 
problems converting this file to .mae format, e.g. (all on one line) :

$SCHRODINGER/utilities/mol2convert -imol2 test_notworking.mol2 -omae 
file.mae

It also appears that this issue will be fixed in the next (2010) release 
and test_notworking.mol2 can be imported into Maestro without any 
problems.

In the meantime, there are several option for dealing with this 
behavior:

1) Manually edit the file to add the [num_subst] field, as you have done
2) Convert the file to .mae using mol2convert command line utility
3) Process the file with OpenBabel (if you have it installed) as:

babel -imol2 test_notworking.mol2 -omol2 fixed.mol2

Thank you for the detailed analysis and description of the situation. If it is only the third field, fragment count, that is wrongly handled as mandatory, we can easily export it. It's planned to be released in version 5.3.1 (around March).

 

Regarding structure manipulation: can you tell us more about it? We've plans to add such features to MarvinSpace. Btw, it already enables user to tweak torsional angles manually, are you aware of this functionality?

Regarding MD, have you tried ours, available in the Conformers plugin? Feedback is warmly welcome!

 

Best regards

Miklos

Hi Nicolas,

I would like to inform you that we had to make an urgent patch release that was named 5.3.1, therefore the feature promised in this topic will be included only in the patch release coming at the end of March (probably named 5.3.2).

Best regards,

Akos

Thank you Akos!

Cheers