Naming convention for 'title' record in Tripos mol2 files

[jchodera]

The Tripos mol2 files in mol2files_sybyl/ (which I think should be named to tripos_mol2/ is a mystery to me. Are these IUPAC names, processed in some way? What is the algorithm for generating these?

[davidlmobley]

Hi,

What I think you’re asking is WHY there are tripos mol2 files containing sybyl atom types (and yes, tripos_mol2 would be an acceptable name) so that’s the question I’ll answer first. But you also asked about “Are these IUPAC names…?” That question doesn’t totally make sense to me, since the files are obviously not IUPAC names. So I’m going to assume that’s not quite what you’re asking. But if it is, please clarify.

In any case - as to why there are two sets of mol2 files, one set which uses gaff atom types and another set which uses sybyl (tripos) atom types: I’ve found this necessary because of issues with Antechamber/Ambertools and OECHEM. Specifically:

• tleap (and presumably derivatives xleap, etc) need mol2 files with gaff atom types, so if you are prepping input for Ambertools you need .mol2 files with gaff atom types as output by Antechamber. This is critical because if you don’t do it, you won’t be able to use these to generate parameters with Ambertools
• OEChem and various other tools often need mol2 files with sybyl atom types, so if you don’t have .mol2 files with sybyl atom types, you won’t be able to use these in OEChem. (For example, while there are SOME GAFF atom types which are understood by OEChem, not all of them are understood, so at least in my experience if you were to read .mol2 files with gaff names into OEChem and use them for, say, charge calculation, you would introduce some errors in the output)

The procedure for converting between the two is to use Antechamber (‘-at sybyl’ for example), which (as far as I am aware) is the only tool which understands both sets of atom type names equally well. Maybe there are others - I have not looked - but certainly OEChem does not. 

Does that answer your question?

David

David Mobley
dmobley@gmail.com
949-385-2436

On Thu, Oct 30, 2014 at 4:38 PM, John Chodera notifications@github.com
wrote:

The Tripos mol2 files in mol2files_sybyl/ (which I think should be named to tripos_mol2/ is a mystery to me. Are these IUPAC names, processed in some way? What is the algorithm for generating these?

Reply to this email directly or view it on GitHub:
#13

[davidlmobley]

So to be totally clear: I generate the sybyl mol2 files by running “antechamber -i gaff.mol2 -fi mol2 -o sybyl.mol2 -fo mol2 -at sybyl” on the gaff mol2 files. 

David

David Mobley
dmobley@gmail.com
949-385-2436

On Thu, Oct 30, 2014 at 4:38 PM, John Chodera notifications@github.com
wrote:

The Tripos mol2 files in mol2files_sybyl/ (which I think should be named to tripos_mol2/ is a mystery to me. Are these IUPAC names, processed in some way? What is the algorithm for generating these?

Reply to this email directly or view it on GitHub:
#13

[jchodera]

What I think you’re asking is WHY there are tripos mol2 files containing sybyl atom types

Sorry to have been unclear!

I was actually looking at the second line of the mol2 files. They contain mangled names like:

pent_1_yne
2_methylpropene
4_methylpyridine
SAMPL4_003
CUP08026_AM1BCC_v1_0

I'm just wondering (1) if these names can be reproducibly generated from some source in what we consider "primary data" now, and (2) if we want something else here instead, like the IUPAC name.

So to be totally clear: I generate the sybyl mol2 files by running “antechamber -i gaff.mol2 -fi mol2 -o sybyl.mol2 -fo mol2 -at sybyl” on the gaff mol2 files.

Wait, if these mol2 files came from the gaff files, where did the gaff mol2 files come from? Didn't you need to start with Tripos mol2 files first to generate the gaff ones?

[davidlmobley]

John,

Ah, OK, I have no idea where the names in the sdf files come from. I’m going to guess this is some sort of glitch with the OEChem SDF writer or something. I certainy didn’t do that on purpose. They’re supposed to contain the iupac name, or at least that’s what I think they ought to contain.

And yeah, sorry. My brain is already fading for the night and I got it backwards. I generate the tripos ones first from OEChem and then use “antechamber -i tripos.mol2 -fi mol2 -o gaff.mol2 -fo mol2”. 

DM

David Mobley
dmobley@gmail.com
949-385-2436

On Thu, Oct 30, 2014 at 10:13 PM, John Chodera notifications@github.com
wrote:

What I think you’re asking is WHY there are tripos mol2 files containing sybyl atom types
Sorry to have been unclear!
I was actually looking at the second line of the mol2 files. They contain mangled names like:

pent_1_yne
2_methylpropene
4_methylpyridine
SAMPL4_003
CUP08026_AM1BCC_v1_0

I'm just wondering (1) if these names can be reproducibly generated from some source in what we consider "primary data" now, and (2) if we want something else here instead, like the IUPAC name.
So to be totally clear: I generate the sybyl mol2 files by running “antechamber -i gaff.mol2 -fi mol2 -o sybyl.mol2 -fo mol2 -at sybyl” on the gaff mol2 files.

Wait, if these mol2 files came from the gaff files, where did the gaff mol2 files come from? Didn't you need to start with Tripos mol2 files first to generate the gaff ones?

Reply to this email directly or view it on GitHub:
#13 (comment)

[davidlmobley]

These issues were resolved via #28 ; mol2 files use IUPAC names now.