Hi All,
thanks for the clarification. I did indeed check the Mol2File.c code in the leap src to see if it was worth the effort/possible to create a fork. I have however since realized that I do not need a "perfect" mol2 - since basic connectivity is provided when outputting a mol2 from leap, openbabel is able to, naturally, create a roughly accurate structure internally (albeit without correct characterisation of single/triple bonds). For my case this no longer poses the same problem as I initially thought, since ultimately once I've finished with my modifications through OpenBabel, I'm reading the output back into leap for creation of prmtop/inpcrds files, and hence have access to the .off libraries to produce the correct topology.
What would be a useful fix is for leap to output mol2 files with the correct SYBYL style atom types rather than printing out amber atom types (Which are not compatible with structures designed to load SYBYL atom types...). I've had to make a code that strips faulty c3/C3, ct/CT entries and replace them with their elemental names as a workaround to get OB to interpret it correctly (OB can then assign roughly correct SYBYL atom types e.g C -> C.3, again based on connectivity).
Cheers,
Nick
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of Hannes Loeffler [Hannes.Loeffler.stfc.ac.uk]
Sent: 18 March 2014 16:57
To: amber.ambermd.org
Subject: Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types
Hi Nick,
OB can perceive bonds too but there is a change that it get's it
wrong. Not much else that comes to mind at the moment.
BTW, why exactly do you need to changes atoms in the mol2 file?
Cheers,
Hannes.
On Tue, 18 Mar 2014 16:25:09 +0000
"Browning, Nicholas" <nicholas.browning08.imperial.ac.uk> wrote:
> Hi Hannes,
>
> I'll briefly describe the process of what I'm doing as follows to
> clarify whats happening.
>
> - Obtain starting PDB structure either from some builder or from data
> bank.
> - Load non-standard residue .off files into leap
> - Load PDB file into leap.
> - Create prmtop and mol2 file
> - Modify mol2 file with some atomic modifications to change one
> residue from one non-standard residue to another.
> - Run a minimisation with amber on the new mol2 file.
>
> I realise the modification procecss can be done without OpenBabel,
> however this is somewhat of a focus for me, since my code does a
> number of other things all of which are funnelled through OB - i'd
> like to retain everything being piped through one tool.
>
> Since (as far as I'm aware) it's not possible to load non-standard
> residue lib files into OpenBabel prior to loading a structure, I need
> to create a file which is self-sufficient currently mol2, since leap
> is supposed to support this), such that OpenBabel can load the
> structure correctly internally.
>
> Since I am loading the .off files into leap prior to loading a
> mol2/pdb structure, surely leap would now have both bonding and atom
> type information since these are contained within the lib files?
>
> Kind Regards,
>
> Nick
> ________________________________________
> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf
> of Hannes Loeffler [Hannes.Loeffler.stfc.ac.uk] Sent: 18 March 2014
> 15:23 To: amber.ambermd.org
> Subject: Re: [AMBER] tleap output of mol2 format incorrect bond
> order/atom types
>
> Hi,
>
> ideally you would be using antechamber but strangely (but it should!)
> it doesn't perceive bond orders in the absence of bonds in the mol2.
> If you have bond orders in the mol2 already you may be able to use
> antechamber with -j 4 and -at sybyl (for SYBYL types, assuming the
> current types are GAFF) but I have seen this fail in some cases, i.e.
> unsuitable assignment.
>
> The mol2 reader in Openbabel doesn't know about types other than Sybyl
> though it can assign GAFF types internally.
>
> Tleap would essentially need code from antechamber to be able to
> assign things like bond order and atom types.
>
> Cheers,
> Hannes.
>
>
> On Tue, 18 Mar 2014 14:59:47 +0000
> "Browning, Nicholas" <nicholas.browning08.imperial.ac.uk> wrote:
>
> > Dear All,
> >
> > Having a great deal of trouble trying to find a workaround to this
> > issue. It's been posted about before and it's been deemed unecessary
> > to fix, however I feel this bug is something that needs attending
> > to.
> >
> > Strictly speaking, mol2 files should be self-sufficient units which
> > can be plugged into other tools for
> > visualisation/modification/simulation. The format of the mol2 file
> > output from leap is incorrect, both in terms of how it deals with
> > connectivity (double/triple bonds labelled incorrectly as single
> > bonds) and how it labels atoms (enters data other than the standard
> > SYBYL atom types). This means that mol2 files are only useable for
> > amber, which is giving me a lot of trouble (I am using the c++
> > OpenBabel distributable for atomic modifications).
> >
> > If anyone else has encountered this issue and knows of a workaround
> > then please let me know! I need to be able to obtain self-sufficient
> > mol2 (or any other format with well-defined connectivity/bond-order)
> > in order for OpenBabel to be able to interpret structures correctly.
> >
> > Cheers,
> >
> > Nick
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Scanned by iCritical.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Scanned by iCritical.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 19 2014 - 11:30:03 PDT
