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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Mar 01 2012 - 07:30:02 PST
