From: James Starlight (jmsstarlight_at_gmail.com)
Date: Tue Sep 17 2013 - 14:32:17 CDT
1- its OK!
2- That simulation have finished without any errors. Such problem with psf
file I had only in case when I've tried to make some modifications in the
existing pdb _ psf ( e,g reduce Z layer and remove some water).
One extra question about Charm-gui
I've made new system with embedded protein+ ligand into bilayer (here you
can find it http://www.charmm-gui.org/?doc=input/membrane&time=1379425348 )
Should I create position restrained files for protein and ligand ( in
accordance with namd tutorial ) and make some additions to the
equilibration inp files ?
2013/9/17 Niklaus Johner <niki.johner_at_gmail.com>
> 1) even protonated residues have integer charges, except if you screwed up
> when patching your residues, which is what I suspect happened. Did you get
> any warnings when generating your psf with psfgen, typically that he had to
> guess the position of heavy atoms, or even that he failed to set the
> position of some atoms? My guess is you did something wrong when
> protonating these residues. If they look separated from the residues they
> belong to when you visualize them, something is wrong (be sure to load both
> the psf and pdb files, so that the bonds represented in vmd are the actual
> bonds you have in your structure).
> 2) Are you loading a psf generated with psfgen or by charm-gui? Everything
> that is generated by charm-gui is usually fine, so as you seem new to all
> of this I suspect you introduced some problems later. What happens if you
> simulate the solvated system created by charm-gui, without any of your
> 3)If you can't even load your psf/pdb pair into vmd, you probably have
> something wrong in your files, no point in trying to simulate that, instead
> look for the error in your files. If it looks wrong, it's probably wrong!
> So protons floating around are not normal, and mean your patch wasn't
> applied properly.
> 4) Namd works fine to simulate membrane proteins using standard
> parameters, don't try to change all the simulation parameters to make it
> work. You're wasting your time. It most probably doesn't work because your
> input structure and/or psf files have problems.
> In conclusion find out what the problem in your pdb/psf files is! Good
> advice is to do this systematically to find out in which of your steps the
> problem is created. Also look at the output of psfgen, it is pretty helpful
> to identify problematic atoms. You can also set the output frequency to 1
> so that even when the simulation crashes rapidly you will have some
> trajectory to look at. Typically during minimization and/or MD you'll be
> able to see which atoms move a lot, which bonds stretch exagerately and so
> on, which will help you identify the error in your files.
> Niklaus Johner
> Weill Cornell Medical College
> Harel Weinstein Lab
> Department of Physiology and Biophysics
> 1300 York Avenue, Room D-501
> New York, NY 10065
> On Sep 17, 2013, at 1:12 PM, James Starlight wrote:
> 1) The possible source of error with non-integer charge could arise from
> protonation state set to some titrable residues (e.g I've chosen one asp
> and another glu to be protonated by means of psfgen script)
> but during visualization I've realized that two new added protons looks
> like separate atoms. Also during minimization of such system I've obtained
> some erros with PME so I suppose that such sustem have been prepared with
> errors initially)
> 2) Another problem with PSF file generated by psfgen. I've tried to load
> this psf with the membnrane.pdb (both files created by charm-gui) to vmd
> and obtained error
> psfgen) Created by CHARMM version 36 1
> psfgen) clearing structure, preserving topology and aliases
> psfgen) reading structure from psf file membrane.psf
> psfgen) Error processing bonds
> does it possible to make new PSF via psfgen for membrane.pdb (Assuming
> that my membrane consist of popc pope tip3p as well as ions) ?
> 2013/9/17 Aron Broom <broomsday_at_gmail.com>
>> if you have non-integer net charge for your system, that suggests there
>> may be more important general problems with your system topology. In
>> general, the forcefields tend to be setup in such a way as to give integer
>> or very close to integer values.
>> You may want to inspect all the partial charges and see that they both
>> make sense, and that each individual molecule in your system has an integer
>> charge (i.e. find the molecule that doesn't)
>> On Tue, Sep 17, 2013 at 1:33 AM, James Starlight <jmsstarlight_at_gmail.com>wrote:
>>> Hi Norman!
>>> I've already tried to increased
>>> langevinPistonPeriod 200.
>>> langevinPistonDecay 50.
>>> up to
>>> langevinPistonPeriod 400.
>>> langevinPistonDecay 100.
>>> but simulation have been crushed in any case
>>> by the way the possible source of error could be due to non integer
>>> charge that my system has.
>>> Initialy I had protein with ligand with total charge +3 and neitralized
>>> membrane produced by charm-gui (non charged lipids). After insertion of my
>>> protein into membrane and re-ionization I have obtained total charge 0.45.
>>> I have no idea how I could fix it yet :(
>>> 2013/9/16 Norman Geist <norman.geist_at_uni-greifswald.de>
>>>> Hi James,****
>>>> ** **
>>>> if you’re using a barostat, consider increasing the relax/decay times,
>>>> as fixed atoms lead to high forces due the coordinate rescaling which moves
>>>> the non-fixed into the fixed atoms. Otherwise check your minimization log
>>>> file for messages like “Moving xxx Atoms with bad contacts downhill” or
>>>> even worse “Giving up on xxx Atoms with bad contacts”. If so, you might
>>>> have some superimposed atoms in your structure. Also check if your
>>>> minimization was run for long enough by plotting the TOTAL energy and see
>>>> if it converged.****
>>>> ** **
>>>> Norman Geist.****
>>>> ** **
>>>> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
>>>> Auftrag von *James Starlight
>>>> *Gesendet:* Montag, 16. September 2013 14:08
>>>> *An:* namd-l_at_ks.uiuc.edu
>>>> *Betreff:* Fwd: namd-l: charm-gui membrane builder****
>>>> ** **
>>>> Recently I've forced with new problem during simulation of the membrane
>>>> Following Namd's tutorial I've built my system consisted of receptor
>>>> embedded in the popc bilayer surrounded water and ions.
>>>> After minimization I've launch first stage of equilibration (fixed all
>>>> atoms excepts of the lipid tales)****
>>>> this simulation have been crashed immediately with rattle errors.****
>>>> than I've decreased timestep down to 0.3 and increased cutoffs up to 25
>>>> (because namd told me than I should do it). Within this setup I can run my
>>>> simulation but on each step I obtain
>>>> ERROR: Margin is too small for 2 atoms during timestep 5001.
>>>> ERROR: Incorrect nonbonded forces and energies may be calculated!****
>>>> I have no any margin in my conf file so I have no idea how I can fix it
>>>> and what possible source of errors.****
>>>> Thanks for help****
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
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