Hira,
Thankyou for your suggestion. The same we are doing using tleap, but the
problem is in my initial file i hadnot added TER card between protein and
ligand, so while preparing parameter file for receptor
some extra H are coming which are not in my mdcrd
On Tue, Jun 21, 2011 at 9:39 PM, Hirdesh Kumar <hirdesh.iitd.gmail.com>wrote:
> Bajite,
> You need to provide the protein structure without bound ligand for mmpbsa
> analysis. You can do so either using ptraj or simply by tleap using the
> same files which you have used previously for system preparation but
> excluding ligand information from complex this time to generate parameter
> and coordinate file for protein atoms only.
>
>
> Hirdesh
>
> On Tue, Jun 21, 2011 at 7:55 PM, baljinder <baljinder7.gmail.com> wrote:
>
> > Dear all,
> > We are calculating the binding free energy using two steps viz.
> extraction
> > of coordinates and binding free energy calculation.
> > While doing the second step the error message i am getting is "
> >
> > odd number of probe positions on torus!
> >
> > /root/amber/amber10/exe/sander -O -i sander_rec.in -o
> > sander_rec.1.out -c ./snapshot_rec.crd.1 -p ./receptor-vac.prmtop not
> > successful
> > "
> >
> > We tried to increase the PRBRAD from 1.4 to 1.6, but the same error
> > message.
> > While trying to make pdb from extracted coordinate we are not able to
> make
> > PDB from extracted cordinated of receptor, while for complex and ligand
> > there is no such problem. The mistake from my side is initially i dint
> > saved
> > the receptor (protein only without ligand)prmtop along with ligand and
> > complex, saved it separetly .
> > Kindly suggest the solution if possible.
> >
> > Thanks in advance
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 21 2011 - 10:30:03 PDT
