Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer

From: Chitrak Gupta (
Date: Wed Dec 16 2015 - 09:21:07 CST

Hi Begum,

Did you remove the overlapping atoms after merging the two structures? This
is how TopoTools does it,-79.9833983,3a,75y,336.15h,68.14t/data=!3m6!1e1!3m4!1sDtWl3tqzmk70PFFMQ0EqRQ!2e0!7i13312!8i6656

If you follow the instructions given here and also renumber your waters, it
should be working.

The other potential issue is the periodic box dimensions. How are you
setting them? I would strongly recommend using the same PBC that the *.inp
scripts generated by charmm-gui has.

This should hopefully solve the issue.

Best regards,

On Wed, Dec 16, 2015 at 4:46 AM, begüm alaybeyoğlu <>

> Hi Chitrak,
> Thank you for the reply. I have checked everything you mentioned.
> 1. I merged the peptide-lipid-water system using psfgen. I will try the
> TopoTools, but I think the problem is not really about the merging of the
> peptide and water-lipid system. I tried minimizion and equilibration of the
> water-lipid system (before adding the peptide and ions) as well and I get
> the same error (and saw that H atoms overlap again).
> 2. I checked my PDBs and I don't have any atoms that were not assigned
> coordinates.
> 3. As you mentioned, I have 13200 water molecules and when I saved the
> coordinates of the equilibrated bilayer (at the end of the step7.1
> production run) VMD messed up the number of the water molecules. So I had
> to split the water molecules into 2 segments manually (1 segment for the
> bilayer) and merged them using psfgen. I believe everythings OK now?
> So, I am still not able to solve the problem.
> Kind regards.
> Begum
> On Tue, Dec 15, 2015 at 8:46 PM, Chitrak Gupta <>
> wrote:
>> Hi Begum,
>> I have never used charmm27, but I have used charmm36 and have ran into
>> this problem quite a few times. Here are my questions/suggestions:
>> 1. How are you merging your lipid with your peptide? In my experience,
>> TopoTools works a lot better than using psfgen
>> 2. Make sure your merged PDB doesn't have anything funny. For example, if
>> some atom has its X,Y,Z coordinates as 0.000,0.000,0.000, it basically
>> means coordinates were not set for that atom. Look through your PDB (maybe
>> generate a script to check it) whether you have such atoms.
>> 3. Also look at the number of waters. When charmm-gui generates a
>> psf/pdb, it assigns all the waters into one segment. Problem with psfgen is
>> that it cannot handle more than 9999 waters within a segment. So, when you
>> take a charmm-gui generated PDB and modify it using psfgen, your water
>> numbers are completely messed up. You now have multiple waters with the
>> same number. You will need to re-segment your waters, keeping 9999 waters
>> in each segment.
>> Hope this helps.
>> Regards,
>> Chitrak.
>> On Tue, Dec 15, 2015 at 11:27 AM, begüm alaybeyoğlu <>
>> wrote:
>>> Dear NAMD users,
>>> I am having trouble with the Charmm Gui generated POPE bilayer. After
>>> having run all the minimization-equilibration-production steps, I ran a 25
>>> ns production simulation (step.7.1) without any problems. What I wanted to
>>> do was to get the last snapshot of my equilibrated bilayer, place my
>>> peptide on top of it, autoionize the system and run a quick minimization &
>>> equilibration before I start the peptide translocation simulation.
>>> Now I keep getting the RATTLE error (for atoms of bilayer always) just
>>> after the minimization is completed and I tried all of the previously
>>> suggested solutions, such as decreasing the timestep or nonbondedFreq or
>>> fullElectFrequency or stepspercycle and increasing the minimization steps
>>> etc. When I plotted the energy I saw that around 2500 steps of minimization
>>> was enough already. I tried slow heating of the system, but the error did
>>> not change. By decreasing my dcdfreq to 10 steps, I observed that H atoms
>>> (bound to C or N) actually start to overlap during the minimization, so the
>>> cause of the error is probably this.
>>> I have run many similar simulations with charmm27 before without any
>>> problems.This is the first time I built the whole system from scratch
>>> using the charmm36 parameters, so I am not sure what is going on. Any
>>> suggestions are welcome.
>>> Thanks.
>>> Begum Alaybeyoglu

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