Thanks v much for the info. :)
On 5 November 2010 18:03, Jason Swails <jason.swails.gmail.com> wrote:
> 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
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> > > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Nov 05 2010 - 11:30:03 PDT
