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.
!!!!!!!!!!!!!!!
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
>
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Received on Fri Nov 05 2010 - 11:00:02 PDT
