Thanks for the reply!
I added this line but I am still getting the same error:
receptor_mask=:0-496,
> It will not, however, try to break
> the ligand into 'pieces' to match the sequence, so if your ligand is not
> comprised of residues that appear continuously in the complex (like your
> ligand_mask tends to suggest), then the default mask guesser will
obviously
>not work.
My ligand consists of 8 separate residues, do you mean that I have to
calculate the modes for each residue separately and include the rest in
receptor?
> This is not enough. You also need to specify receptor_mask. If you only
> specify one mask, MMPBSA.py will attempt to use the defaults (resulting in
> the same error, as you observed). If you are using AmberTools 13, this
> should have been printed as a warning, wasn't it?
I am using AmberTools 12 version.
Best wishes,
Meisam
On Fri, Oct 25, 2013 at 1:22 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Fri, Oct 25, 2013 at 6:29 AM, maghtar <meisam.a63.gmail.com> wrote:
>
> > Dear AMBER users,
> > I am new in AMBER. I have a structure including a protein and
> chromophores.
> > I want to calculate the vibrational modes of the chromophores. I am
> > following the AMBER tutorial for the calculation of binding entropy using
> > MMPBSA; but I am getting the following error:
> >
> > PrmtopError: Couldn't predict mask from topology files!
> > Your ligand residues must be sequential in your complex.
> > There are likely problems with your topology files if this is not the
> case.
> > Exiting. All files have been retained.
> >
> > It seems it is because my ligand is not a protein so the program can not
> > guess the residues of the ligand.
>
>
> The ligand does not have to be a protein for this mask guesser to work.
> The mask guesser works by trying to place the ligand residue sequence
> inside the receptor residue sequence and checking to see if it matches the
> full bound complex residue sequence. It will not, however, try to break
> the ligand into 'pieces' to match the sequence, so if your ligand is not
> comprised of residues that appear continuously in the complex (like your
> ligand_mask tends to suggest), then the default mask guesser will obviously
> not work.
>
> After some search I got to this point
> > that I need to use the ligand_mask option but I am still getting the same
> > error. This is my input file:
> >
> > &general
> > endframe=10, keep_files=2,
> > ligand_mask=:299:477:498:499:501:502:504:505,
> >
>
> This is not enough. You also need to specify receptor_mask. If you only
> specify one mask, MMPBSA.py will attempt to use the defaults (resulting in
> the same error, as you observed). If you are using AmberTools 13, this
> should have been printed as a warning, wasn't it?
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> All the best,
> Meisam
> <http://lists.ambermd.org/mailman/listinfo/amber>
> <http://lists.ambermd.org/mailman/listinfo/amber>
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Received on Fri Oct 25 2013 - 07:30:03 PDT
