cheers jason, i will look into this
On 1 March 2012 15:24, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Mar 1, 2012 at 9:59 AM, g t <sketchfoot.gmail.com> wrote:
>
> > Hi. i think i figured out the issue.
> >
> > i was using ptraj to solvate the complex, then using rdparm to strip the
> > waters from the topology file. this way the box information would be
> > preserved. i wanted to keep the box in case (don't know for sure) it
> > created problems with calculations later on.
> >
> > upon rewriting the file with rdparm, the radii information gets lost. is
> > there any way to get round this within rdparm?
> >
>
> No, you cannot do it with rdparm. rdparm only writes old-style topology
> files (pre-Amber 7 style). You will have to use tleap to generate your
> topology file (there will be a program in AmberTools 12 called ParmEd that
> can do this type of thing, but nothing reliable in AmberTools 1.5).
>
> HTH,
> Jason
>
>
> >
> > best regards,
> > ET
> >
> > On 1 March 2012 14:40, g t <sketchfoot.gmail.com> wrote:
> >
> > > 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
> > >> > _______________________________________________
> > >> > AMBER mailing list
> > >> > 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
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> > _______________________________________________
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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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Mar 01 2012 - 09:00:02 PST
