Comments (5)
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
[email protected]
949-385-2436
On Thu, Oct 30, 2014 at 4:38 PM, John Chodera [email protected]
wrote:
The Tripos mol2 files in
mol2files_sybyl/
(which I think should be named totripos_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
from freesolv.
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
[email protected]
949-385-2436
On Thu, Oct 30, 2014 at 4:38 PM, John Chodera [email protected]
wrote:
The Tripos mol2 files in
mol2files_sybyl/
(which I think should be named totripos_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
from freesolv.
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?
from freesolv.
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
[email protected]
949-385-2436
On Thu, Oct 30, 2014 at 10:13 PM, John Chodera [email protected]
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)
from freesolv.
These issues were resolved via #28 ; mol2 files use IUPAC names now.
from freesolv.
Related Issues (20)
- Decide any other supporting files/data which ought to be captured when database is re-constructed from primary data HOT 2
- Re-construct database files from primary data HOT 11
- Strip water molecules from all topology/coordinate files in current database HOT 8
- Protocol for generating solvated input files for various codes (AMBER, gromacs) HOT 1
- Have GBSA models been benchmarked on FreeSolv? HOT 4
- Migrate issues and close this repo? HOT 10
- In next update, include a json format version of database HOT 1
- Flag molecules with possibly problematic tautomers (and investigate tautomers for them)?
- Update column names to be more informative HOT 2
- Make CHARMM input files via ParmEd
- Potential duplicate molecules in FreeSolv Set HOT 12
- Set up Travis-CI testing
- GAFF version HOT 5
- Cannot generate GAFF mol2 from Tripos mol2 file HOT 2
- rebuild_freesolv.py script HOT 2
- Problems with processing some SMILES - omega returned error code 0
- Sanitize SDF files
- gromacs-mdp:with verlet lists rcoulomb!= rvdw is not supported HOT 3
- mobley_3323117 (sulfolane) has non-standard SMILES HOT 1
- Is gromacs_energies available to download anywhere? HOT 4
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from freesolv.