Hello,
My comments are below:
On Fri, Nov 5, 2010 at 1:43 PM, g t <sketchfoot.gmail.com> wrote:
> Hi!
> Thanks for your reply, I didn't spot that error, so I deleted the extra 0
> and put residue 158 (the ligand) back into LRES like so:
>
> INPUT FILE:
> Receptor
> RRES 1 157 172 174 1242 1244 2539 2541 4578 4580 6117 6119 7038 7040 8001
> 8003 8013 8014
> END
> Ligand
> LRES 158
> END
> Residues_TOprint
> RES 1 158 172 174 1242 1244 2539 2541 4578 4580 6117 6119 7038 7040 8001
> 8003 8013 8014
> END
> END
> EOF
> ##############################################
>
> The OUTPUT file:
> Receptor
>
> RRES 1 157 172 174 1242 1244 2539 2541 4578 4580 6117 6119 7038 7040 8001
> 8003
> END
>
> Ligand
>
> LRES
> 158
> END
>
> Residues_TOprint
>
> RES 1 158 172 174 1242 1244 2539 2541 4578 4580 6117 6119 7038 7040 8001
> 8003 8
> END
>
> END
> ####################
>
> Is there a character limit on the number of residues amber prints?
> I opened up the file with a text editor to be sure, but the outfile seems
> to
> have chopped of 8013 & 8014. Moreover energies are only given up till
> residue 7040. The last ones specified (i.e. 8001-8003 and 8013-8014) are
> not
> processed.
>
> More importantly, residue 158 (ligand) is not printed either.
>
>
> If I specify just the RRES mask as 1-8014, then all residues are printed.
> Therefore I think it is to do with a character limitation. i.e. you can
> only
> specify limited groups of atoms to monitor.
>
Yes, there is a hard limit of 7 "fields" that you may specify, which I only
just came to learn a couple days ago. It is actually (very poorly and
difficult-to-find) documented in the Amber11 manual (see the section about
groups, where it says that it prints from 1 to 7 in a couple locations). It
is a hard-coded limit that is integrated into the rgroup/rfree code in
several places. I just modified the current code to accept more, and
removed the hard limits to an adjustable parameter for the residue cards,
which will be available in the next release. It may also turn into a bugfix
for Amber11 if the powers that be decide it's worthwhile (but it does not
really fix a bug).
Hope this helps,
Jason
> !!!!!!!!!!!!!!!
>
> I also tried the following input files:
> Receptor
> RRES 1 157 159 8014
> END
> Ligand
> LRES 158
> END
> Residues_TOprint
> RES 1 8014
> END
> END
> EOF
>
> In this case the program recognised the LRES card and printed out energies
> for all the residues
>
> Cheers!
> GT
>
>
>
>
> On 1 November 2010 20:06, Jason Swails <jason.swails.gmail.com> wrote:
>
> > On Mon, Nov 1, 2010 at 3:54 PM, g t <sketchfoot.gmail.com> wrote:
> >
> > > Hi,
> > >
> > > I'm doing a TI calculation and have encountered a few issues with
> setting
> > > idecomp to 2 and the RRES and LRES cards.
> > >
> > > input file:
> > > Receptor
> > > RRES 1 158 172 174 1242 1244 2539 2541 4578 4580 6117 6119 7038 7040
> 8001
> > > 8003 80013 8014
> > >
> >
> > 80013 should be 8013. I don't know how this is handled. Do you still
> get
> > the error if you correct this?
> >
> >
> > > END
> > > Ligand
> > > LRES 158
> > > END
> > > Residues_TOprint
> > > RES 1 158 172 174 1242 1244 2539 2541 4578 4580 6117 6119 7038 7040
> 8001
> > > 8003 80013 8014
> > >
> >
> > Same error here.
> >
> >
> > > END
> > > END
> > >
> > >
> > >
> >
> ################################################################################
> > > My output files comes out as:
> > > Receptor
> > >
> > >
> > Good luck!
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Nov 05 2010 - 11:30:02 PDT
