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?
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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Received on Thu Mar 01 2012 - 07:00:02 PST
