Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer

From: Chitrak Gupta (
Date: Fri Dec 18 2015 - 09:08:27 CST

Hi Jim,

Thanks for the information. This could really make life a lot easier in

Best regards,

On Thu, Dec 17, 2015 at 8:49 PM, Jim Phillips <> wrote:

> Actually, psfgen can handle resids > 9999 in the psf file. The problem is
> that the coordpdb command relies on the truncated resid in the pdb file, so
> you end up re-assigning the same residue multiple times. The trick is to
> load the exactly corresponding pdb file at the same time as the
> (extended-column-width) psf file via:
> readpsf mymol.psf pdb mymol.pdb
> In this case the atoms in the pdb file are assumed to exactly match the
> atoms in the psf file, in the same order, just as VMD would assume. You
> can also read binary coordinate files the same way:
> readpsf mymol.psf pdb mymol.pdb namdbin mymol.coor
> 2.11 and the upcoming VMD also support velnamdbin. See readpsf at
> Jim
> On Tue, 15 Dec 2015, 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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