Hi Matias,
Sorry for massive emails. Thank you for the details.
First of all I don't understand why antechamber changes atoms name and arrangement in mol2???
And I am confuse in editing mol2 file! Should I change it according to PDB file...changing order of atoms along with its coordinates or just rename atoms randomly as mol2 generated-not changing order as its in pdb (it wouldn't effect with different coordinate numbers)??? I rename the atoms but still getting the same problem.
Thanks,Hira
On Wednesday, June 19, 2019, 03:37:49 PM GMT+1, Matias Machado <mmachado.pasteur.edu.uy> wrote:
Dear Hira Jabeen,
Please dig into the mailing list, most answers to your problems are there...
Indeed, I've just answered the issue of properly loading mol2 files two weeks ago!... [
http://archive.ambermd.org/201906/0032.html]
Other very frequent mistakes are:
1) Atom and residue names in the PDB file HAVE TO match those in the residue library (e.g. mol2).
That's causing this error:
"Created a new atom named: O72 within residue: .R<SFR 269>" ... bla bla bla
Which later generates the following issues because no atom types were set to the newly created atoms:
"FATAL: Atom .R<SFR 269>.A<O72 1> does not have a type."... bla bla bla
Solution: rename atom in the PDB or mol2 to be the same.
2) Atom types in the residue library (e.g. mol2) HAVE TO match those at the parameter file (e.g. frcmod).
You haven't seen this error yet, but you would:
"For atom: .R<GOL 291>.A<C1 1> Could not find vdW (or other) parameters for type: C.3"
Solution: It seems gol.mol2 takes parameters from gaff as gol.frcmod is empty, then the former's are the atom types to match.
In case of sfr.mol2, rename atom types to match sfr.frcmod.
Best,
Matias
PS: There is no magic nor artificial intelligence behind AMBER, yet... so user are expected to provide that sense...
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Hira Jabeen" <hira_bioinfo.yahoo.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Miércoles, 19 de Junio 2019 8:20:19
Asunto: Re: [AMBER] Fw: parameterization of ligand+protein complex
Hi Dan,
I tried changing the case sensitive thing...changed all GOL and SFR as uppercase now but still facing the same problem. Looking forward
Thanks,Hira
On Tuesday, June 18, 2019, 05:32:20 PM GMT+1, Daniel Roe <daniel.r.roe.gmail.com> wrote:
Hi,
I think your problem might be that your ligands GOL and SFR are not
being recognized due to case sensitivity. If you look at the leap
output messages you see:
> > loadoff gol.lib
> Loading library: ./gol.lib
> Loading: gol
But in the PDB you're trying to load the residue name is GOL (all
uppercase). I think it might be enough to add PDB resmap entries prior
to trying to load the PDB, e.g.
addpdbresmap { { "GOL" "gol"} {"SFR" "sfr"} }
However, you may want to correct the names in your library files as a
more long term solution.
Hope this helps,
-Dan
On Tue, Jun 18, 2019 at 12:14 PM Hira Jabeen <hira_bioinfo.yahoo.com> wrote:
>
> Hi Dan,I am using Amber18 with Ambertool19. The leap and frcmod files are attached here with. Thanks
> On Tuesday, June 18, 2019, 05:10:52 PM GMT+1, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> You should state the version of AmberTools you are using, as well as
> the exact input you are giving to leap.
>
> -Dan
>
> On Tue, Jun 18, 2019 at 6:28 AM Hira Jabeen <hira_bioinfo.yahoo.com> wrote:
> >
> >
> >
> > ----- Forwarded Message ----- From: Hira Jabeen <hira_bioinfo.yahoo.com>To: amber.ambermd.org <amber.ambermd.org>Sent: Friday, June 14, 2019, 05:09:46 PM GMT+1Subject: parameterization of ligand+protein complex
> > Hi Amber Team,
> > I am using Amber-18 for the parameterization of ligand-enzyme complex through tleap. I have used pdb files to generate mol2 and then libraries in tleap.I have edited mol2 file according to pdb (replaced UNK with ligand names)Still I get this error:Failed to generate parameters
> > Parameter file was not saved.Protein and ligand files are attached here with.Please advice!
> > Thanks,Hira
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jun 20 2019 - 04:00:02 PDT
