Re: [AMBER] Error and sudden halt in equilibration

From: senal dinuka <>
Date: Fri, 22 Feb 2019 09:37:35 +0530

Dear Prof. Case,

All the parameter libraries for ligands of interest were made with gaff
force field and AM1/bcc charge scheme. The same procedure was followed for
all the ligands. A prepin file was created via antechamber which was then
used to create a frcmod for missing parameters.
Only different in my 4th ligand (antibiotic named Moenomycin A) is, it has
5 sugar groups (C69H108N5O34P) which I didn't bother to model using GLYCAM
forcefield libraries. I didn't think of it might be the issue since I was
able to heat the system (100 ps - 300K) without any errors. Would you mind
telling me as to how to check for Lennard-Jones parameters specifically for

Thank you. Regards,

On Thu, Feb 21, 2019 at 6:58 PM David A Case <> wrote:

> On Thu, Feb 21, 2019, senal dinuka wrote:
> >
> >I am running an equilibration on a preheated system of 696 residues in 14A
> >TIP3P waterbox. I did ran 3 MD production runs for same enzyme model with
> 3
> >different ligands successfully and this is the 4th ligand-enzyme complex.
> I
> >was brought up with the following error on equilibration using pmemd.MPI
> >module of amber16 version for a 1ns.
> >
> >mpirun -np 8 pmemd.MPI
> >vlimit exceeded for step 25426; vmax = 42.1209
> >vlimit exceeded for step 25427; vmax = 26.3270
> >vlimit exceeded for step 25434; vmax = 61.5112
> One thing that is certainly possible is that there is something
> different about the force field you use for the 4th ligand. Check to
> see if you have hydrogens with zero Lennard-Jones parameters: these can
> undergo fluctuations that put the hydrogen very close to some other
> atom, leading to gigantic forces and the behavior you report above.
> But this is of course a guess: how did you build your ligand library?
> Is there anything different in the chemistry of the various ligands?
> You might also want to save a restart file right before the system blows
> up, and examine it (say, visually) for bad contacts or other problems.
> ...good luck....dac
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D L Senal Dinuka
Grad.Chem., A.I.Chem.C.
Research Assistant
College of Chemical Sciences
Institute of Chemistry Ceylon
Sri Lanka
+94 77 627 4678
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Received on Thu Feb 21 2019 - 20:30:02 PST
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