No. There is one original trajectory file which I am analysing which is the solvated complex. The prmtop files are the solvated prmtop, the complex, the ligand, the receptor, the mutated ligand and the complex with the mutated ligand. Only the first one is able to visualise the trajectory properly (for obvious reasons) and the others cannot be used to look at it.
In case it's needed, the MMPBSA command is like this:
MMPBSA.py -O -i MMPBSA.in MMPBSA.out -sp Unstapled_solvated.prmtop -cp Unstapled_complex.prmtop -rp Unstapled_receptor.prmtop -lp Unstapled_ligand.prmtop -y Total_run.mdcrd -mc L146A_complex.prmtop -ml L146A_ligand.prmtop
The "Unstapled_X" files are the native versions of the system, and the "L146A_X" files are generated using the simple PDB manipulation outlined before.
Pietro
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Bill Miller III
Sent: 08 May 2014 17:51
To: AMBER Mailing List
Subject: Re: [AMBER] Alanine Scanning MMPBSA
Are you able to visualize the mutated trajectories made by MMPBSA.py using the mutated prmtop files you created?
On Thu, May 8, 2014 at 12:45 PM, Aronica, Pietro < pietro.aronica07.imperial.ac.uk> wrote:
> I have already checked. The error is large, and there is a discrepancy
> that I cannot identify in the prmtops themselves. As far as I can
> tell, all is it should be and it should work. What's even more
> puzzling, is that the exact same procedure and method of prmtop
> generation gives no error whatsoever in other residues. Most of the
> files are simply copy-pasted, and I cannot understand why in one case it works and in another it does not.
> Where can I look to see where this difference arises from?
> Pietro
>
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Bill Miller III
> Sent: 08 May 2014 17:12
> To: AMBER Mailing List
> Subject: Re: [AMBER] Alanine Scanning MMPBSA
>
> In the typical single-trajectory MM-PBSA approach, the bonded terms
> should cancel out exactly when the receptor and ligand energies are
> subtracted from the complex energies. Thus, the delta values for the
> BOND, ANGLE, DIHED, and 1-4 bonded interaction terms should be zero.
> This error message you are seeing is due to one or more of these delta terms being non-zero.
> You should check the values of those terms in your
> FINAL_RESULTS_MMPBSA.dat file for the inconsistencies. If they are
> near-zero, the warning probably just occurred because of a round-off error.
> If they significantly deviate from zero, this may show that you have
> some deeper issues with your prmtop files being incompatible with the
> mutated trajectory.
>
> I hope that helps.
>
> -Bill
>
>
> On Thu, May 8, 2014 at 11:56 AM, Aronica, Pietro <
> pietro.aronica07.imperial.ac.uk> wrote:
>
> > Hello,
> > I'm having problems with MMPBSA. I'm trying to run an Alanine
> > Mutagenesis Scan across a peptide, and it worked fine for the first
> > three residues I tried. On the fourth one, the MMPBSA.out file
> > returns a "INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS"
> > error and
> unusable data.
> > The mutated prmtop was generated in each case by taking the pdb of
> > the original file and manually deleting extraneous atoms to make an
> > alanine out of the original residue. This modified pdb was made into
> > a prmtop using leap, which was then used to make ligand, receptor
> > and complex prmtops with ante-MMPBSA. This process worked fine with
> > the first three mutations I attempted and gave realistic values, but
> > I cannot understand what I did that was wrong in the fourth case. I
> > have diffed all the files involved between working and non-working
> > versions
> and found no relevant differences.
> > What can give rise to the "INCONSISTENCIES" error? Where should I
> > look to troubleshoot this?
> > Cheers
> > Pietro
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Post-doc
> University of Richmond
> 417-549-0952
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Post-doc
University of Richmond
417-549-0952
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Received on Thu May 08 2014 - 10:30:03 PDT
