nice one! i will give it a go. thanks for your help. :)
On 29 February 2012 21:59, Jason Swails <jason.swails.gmail.com> wrote:
> What version of tleap are you using? The intrinsic GB radii section has
> been written in topology files as long as I can remember.
>
> It may help to put in a command like
>
> set default pbradii mbondi2
>
> or something like that (whichever PBRadii you want to use) into your script
> before you write the topology files. This should add the radii information
> for you.
>
> HTH,
> Jason
>
> On Wed, Feb 29, 2012 at 7:32 AM, g t <sketchfoot.gmail.com> wrote:
>
> > Hi,
> >
> > I am trying to run an mmpbsa calculation using the perl script. I have
> > created the input topology files for complex, ligand and receptor.
> However
> > upon submission the job does not complete properly. The error I have been
> > able to find is in the file X_ThX_Complex_com.pdb.1:
> >
> > ERROR: Flag "RADII" not found in PARM file
> >
> > If I load my parm files into ptraj i also get the following errors
> related
> > to the generalised born intrinsic dielectric radii:
> >
> > PRMTOP does not contain %FLAG RADIUS_SET
> > PRMTOP does not contain %FLAG RADII
> > PRMTOP does not contain %FLAG SCREEN
> >
> > The following is an example set-up file I use to create the parm files.
> Is
> > there a command I am missing that sets the radii?
> >
> > ##########
> > source leaprc.gaff
> > source leaprc.ff03.r1
> > loadoff all_aminoct02.lib
> > loadoff ${dirNo}_final.lib
> > mol = loadpdb ${dirNo}_complex_unsolvated.pdb
> > bond mol.64.SG mol.157.SG
> > solvatebox mol TIP3PBOX 10.0
> > charge mol
> > #addions2 mol K+ 14.0
> > #savepdb mol ${dirNo}_complex_SOLVATED.pdb
> > saveamberparm mol dehydrated2a_${dirNo}.parm dehydrated2a_${dirNo}.crd
> > (i later use rdparm to strip out the water molecules to create the
> > dehydrated complex)
> > #######
> >
> > Any help would be greatly appreciated.
> >
> > Best regards,
> > ET
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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Received on Thu Mar 01 2012 - 07:00:02 PST
