Hi Pengfei and Elvis,
Thanks for the suggestions.
I need a prepin file as i have 16 complexes of Heme and different
ligands. I don't want to parametize each complex one by one. If i get a
single prepin file (or lib file) i can incorporate it and generate topology
and inpcrd files. In fact i tried, and am now able to generate a single lib
file for HEME. I have not started the simulation but rest looks ok.
I want to lean how this can be done as i have other metal-ligand
complexes too. like CO-METHYLCOBALAMIN (
https://www3.rcsb.org/ligand/COB)
and 2 Iron sulfur clusters (Fe2S2 [
https://www3.rcsb.org/ligand/FES] and
SF4 [
https://www3.rcsb.org/ligand/SF4]).
Currently i am having problem parametizing COB ligand with MCPB.py. I
think i will make this a new thread.
Thanks for the help.
Regards
Abhilash
On Tue, Mar 7, 2017 at 9:30 AM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Hi Abhilash,
>
> Why do you need to make a prepin file? The example in the tutorial (
> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <
> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm>)
> doesn’t need any prepin file to generate the final prmtop and inpcrd files.
>
> Kind regards,
> Pengfei
>
> > On Mar 6, 2017, at 2:34 AM, Abhilash J <md.scfbio.gmail.com> wrote:
> >
> > Hi everyone,
> >
> > I need to make one prepin file and one frcmod file for HEME, like the
> > one in Bryce database of AMBER parameters (
> > http://personalpages.manchester.ac.uk/staff/
> Richard.Bryce/amber/cof/heme_all.in).
> > I was able to prepare the HEME group as mentioned in MCPB tutorial (
> > http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm). I am
> > attaching the mol2, frcmod and other relevent files generated. I want to
> > understand how i can prepare prepin and frcmod files joining the mol2
> files
> > of HEME ring and Iron.
> > I tried using parameters from Bryce database but it is giving error
> > when i load them in tleap
> >
> > Regards
> >
> > Abhilash
> > <comp_tleap.in><FE1.mol2><HM1.mol2><comp_mcpbpy.pdb><HEM.
> frcmod>_______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Mar 08 2017 - 02:00:02 PST
