Yes, I can see it. The trajectory itself is fine, but the modified residue has one bond which unrealistically stretches and wobbles way beyond the normal H-C bond length. I assume this is what is causing the error, or is at least a symptom of the true cause. It is the hydrogen that was changed from the rest of the side chain to the hydrogen in alanine. Removing all the atoms in the side chain except for CB and letting leap automatically add the remaining hydrogens does not solve the problem. Looking at the mutated residue in the other three systems shows completely normal behaviour.
What can cause this, and why is it happening in this system?
Pietro
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Jason Swails
Sent: 08 May 2014 18:20
To: amber.ambermd.org
Subject: Re: [AMBER] Alanine Scanning MMPBSA
On Thu, 2014-05-08 at 17:08 +0000, Aronica, Pietro wrote:
> 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:
What Bill was referring to were the _MMPBSA_mutant_complex.mdcrd.* files. You can visualize those trajectories with the relevant mutant complex and mutant ligand topology files. Do you see anything strange there?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri May 09 2014 - 04:00:02 PDT
