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
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Received on Wed Jun 19 2019 - 04:30:02 PDT
