Re: charm-gui membrane builder

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Thu Sep 19 2013 - 01:04:39 CDT

I'd like to point out that I still have been having a problem with edition
of the psf+pdb produced by charm-gui.

E.g this is my system.
http://www.charmm-gui.org/?doc=input/membrane_only&time=1378378701
IT consist of a lot of water from both up and down leaflets so I decide to
remove some water using psfgen script

# Load a pdb and psf file into both psfgen and VMD.
resetpsf
readpsf step5_assembly.xplor_ext.psf
coordpdb step5_assembly.pdb
mol load psf step5_assembly.xplor.psf pdb step5_assembly.pdb
set badwater2 [atomselect top "name OH2 and (z<-47 or z>40)"]
# Delete the residues corresponding to the atoms we selected.
foreach segid [$badwater2 get segid] resid [$badwater2 get resid] {
delatom $segid $resid

writepsf step5_assembly_chopwater.psf
writepdb step5_assembly_chopwater.pdb

using this script I have error

Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
psfgen) clearing structure, preserving topology and aliases
psfgen) reading structure from psf file step5_assembly.xplor_ext.psf
psfgen) Error processing bonds

I'll be thankful if someone provide ne with possible solution

James

2013/9/18 James Starlight <jmsstarlight_at_gmail.com>

> Also I've noticed that charm-gui inp files uses slightly differ simulation
> setup ( in particular shorter cut-offs and lower relaxation times in
> barostat) than in NAMD membrane protein tutorial.
>
>
> >>> 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.
>
>
> 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 modifications?
>>
>> 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.
>>
>> N.
>>
>> 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) ?
>>
>> James
>>
>>
>>
>> 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 :(
>>>>
>>>> James
>>>>
>>>>
>>>> 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 protein.****
>>>>>
>>>>> 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****
>>>>>
>>>>> James****
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Aron Broom M.Sc
>>> PhD Student
>>> Department of Chemistry
>>> University of Waterloo
>>>
>>
>>
>>
>

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