[gmx-users] After solvation and before adding ions, number of molecules does not agree even though number of H2O molecules

Justin Lemkul jalemkul at vt.edu
Sat Jan 31 23:11:12 CET 2015


Please keep the discussion on the mailing list.

On 1/30/15 10:19 PM, Thomas Lipscomb wrote:
> So you are saying that topol.top [ molecules ] should include 23 DPPC?
>

The topology specifies what is in the system.  If you have 23 DPPC molecules, 
then yes, this needs to be specified.  grompp isn't magic; it only processes 
what you tell it.

> [ molecules ]
> ; Compound        #mols
> Protein_chain_A    1
> DPPC                    23
> SOL                        3625
>
> instead of the original:
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> SOL              3625
>
>
>
> Do I have to do anything else, for example explaining what atoms a molecule of
> DPPC has ... wherever that is needed (model1_solv.gro?)?
>

See the content of any [atoms] directive of your topology files.  You don't need 
to do anything extra.  See Chapter 5 of the manual.

> I am giving you a link to the entire folder of everything, in case that helps.
>   Note that readme_KALP.txt explicitly records everything I did, step-by-step
> (all of the commands, etc.):
> All of my files related to my KALP tutorial with Maximin 3:
> KALP.zip <https://www.dropbox.com/s/pn2xzsoxs7n7uag/KALP.zip?dl=0>
> 	
> image <https://www.dropbox.com/s/pn2xzsoxs7n7uag/KALP.zip?dl=0>
> 	
> 	
> 	
> 	
> 	
> KALP.zip <https://www.dropbox.com/s/pn2xzsoxs7n7uag/KALP.zip?dl=0>
> Shared with Dropbox
> View on www.dropbox.com <https://www.dropbox.com/s/pn2xzsoxs7n7uag/KALP.zip?dl=0>
> 	
> Preview by Yahoo
>
>
>
> About the huge void, actually I am using Maximin 3 instead of KALP so that when
> I complete the tutorial I have data relevant to my project.  I am right now
> trying to find out how many atoms Maximin 3 has but right now I know that its
> amino acid sequence is: GIGGKILSGLKTALKGAAKELASTYLH
>

The topology says how many atoms the peptide has, but that's totally irrelevant. 
  You have large voids in your system; it's physical nonsense to have lipids 
randomly strewn about the system in between two layers of water, which will just 
diffuse into the vacuum space (if the simulation even runs).

> Below is what the solvated (but ions not added, etc.) DPPC membrane looks like
> with Maximin 3.  Right now I'm worried that I have too few DPPC because that
> does not look like much of a membrane (but that is a worry for after I complete
> the tutorial):
>

That's what I was referring to in the last message.  Your random smattering of 
lipids is nonsensical.

-Justin

> Inline image
>
>
>
> On Tuesday, January 27, 2015 5:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> In the coordinate file, you have the peptide, 23 DPPC (surrounded by a huge
> void, so I have no idea what's going on here), and water.  In the topology, in
> [molecules], you specify the protein and water.  With 5 atoms per DPPC, 23 * 50
> = 1150.  That solves the mismatch.  The bigger concern is the huge unoccupied
> volume in the box, but you'll have to sort that out.
>
> -Justin
>
> On 1/27/15 5:10 PM, Thomas Lipscomb wrote:
>  > topol.top already has 241 Protein_chain_A (peptide) atoms (below),  so what else
>  > do I have to do to add the 1150 missing peptide atoms?  I did not get any errors
>  > in step 1 and step 2 (topology steps) of the KALP15 GROMACS tutorial
>  >
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html>
>  >
>  > [ moleculetype ]
>  > ; Name            nrexcl
>  > Protein_chain_A    3
>  >
>  > [ atoms ]
>  > ;  nr      type  resnr residue  atom  cgnr    charge      mass  typeB
>  >  chargeB      massB
>  > ; residue  1 GLY rtp GLY  q +1.0
>  >      1        NL      1    GLY      N      1      0.129    14.0067  ; qtot 0.129
>  > ...
>  >    241        OM    27    HIS    O2    109    -0.635    15.9994  ; qtot 3
>  >
>  >
>  > Below are links to the two files in disagreement in full.
>  >
>  > model1_solv.gro <https://www.dropbox.com/s/l06mkzovev31tp3/model1_solv.gro?dl=0>
>  >
>  > image <https://www.dropbox.com/s/l06mkzovev31tp3/model1_solv.gro?dl=0>
>  >
>  >
>  >
>  >
>  >
>  > model1_solv.gro <https://www.dropbox.com/s/l06mkzovev31tp3/model1_solv.gro?dl=0>
>  > Shared with Dropbox
>  > View on www.dropbox.com
>  > <https://www.dropbox.com/s/l06mkzovev31tp3/model1_solv.gro?dl=0>
>  >
>  > Preview by Yahoo
>  >
>  >
>  > topol.top <https://www.dropbox.com/s/yt6lmtf9882eiaw/topol.top?dl=0>
>  >
>  > image <https://www.dropbox.com/s/yt6lmtf9882eiaw/topol.top?dl=0>
>  >
>  >
>  >
>  >
>  >
>  > topol.top <https://www.dropbox.com/s/yt6lmtf9882eiaw/topol.top?dl=0>
>  > Shared with Dropbox
>  > View on www.dropbox.com
> <https://www.dropbox.com/s/yt6lmtf9882eiaw/topol.top?dl=0>
>  >
>  > Preview by Yahoo
>  >
>  >
>  >
>  > On Wednesday, January 7, 2015 11:51 AM, Justin Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>  >
>  >
>  >
>  >
>  > On 1/6/15 2:45 PM, Thomas Lipscomb wrote:
>  >  > Dear Justin,
>  >  > Message: 2
>  >  > Date: Mon, 05 Jan 2015 18:17:19 -0500
>  >  > From: Justin Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
>  >  > To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>  >  > Subject: Re: [gmx-users] After solvation and before adding ions,
>  >  >      number of molecules does not agree even though number of H2O molecules
>  >  >      does
>  >  > Message-ID: <54AB1B7F.7090706 at vt.edu <mailto:54AB1B7F.7090706 at vt.edu>
> <mailto:54AB1B7F.7090706 at vt.edu <mailto:54AB1B7F.7090706 at vt.edu>>>
>  >  > Content-Type: text/plain; charset=utf-8; format=flowed
>  >  >
>  >  >
>  >  > On 1/5/15 5:21 PM, Thomas Lipscomb wrote:
>  >  >> Dear gmx-users,
>  >  >> I am trying to simulate a Maximin 3 antimicrobial peptide inserted into a
>  > membrane.
>  >  >> The top of this tutorial
>  >
> page:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/04_ions.html
>  >  >>
>  >  >> Has this command (though I changed the name of system_solv.gro to
>  > model1_solv.gro):
>  >  >> /usr/local/gromacs/bin/gmx grompp -f ions.mdp -c model1_solv.gro -p
>  > topol.top -o ions.tpr
>  >  >> Which causes this error:
>  >  >> -------------------------------------------------------Program gmx, VERSION
>  > 5.0.1Source code file:
>  > /home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/grompp.c, line: 603
>  >  >> Fatal error:number of coordinates in coordinate file (model1_solv.gro,
>  > 12266)            does not match topology (topol.top, 11116)For more information
>  > and tips for troubleshooting, please check the GROMACSwebsite
>  >
> athttp://www.gromacs.org/Documentation/Errors-------------------------------------------------------
>  >  >> I know that this is a common error after
>  >
> solvation:http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>  >  >>
>  >  >> So I checked the number of atoms in the topol.top file:
>  >  >> [ molecules ]; Compound        #molsProtein_chain_A    1SOL              3625
>  >  >
>  >  > If you have 3 peptides, shouldn't you have 3 molecules of your protein?
>  >  >
>  >  >> model1_solv.gro agrees that there are 3625 water molecules.
>  >  >>
>  >  >> I know that model1_solv.gro is the "the true value" that topol.top has to
>  > agree
>  >
> with:http://www.researchgate.net/post/How_do_you_match_the_number_of_coordinates_in_the_coordinate_files_topoltop_and_solvgro_in_a_protein_ligand_complex_using_Gromacs
>  >  >>
>  >  >> But I do not know what to do to fix the topol.top file to make it agree with
>  > model1_solv.gro.  Topol.top is missing 12266-11116 = 1150 molecules (or is it
>  > atoms?).
>  >  >
>  >  >
>  >
> -------------------------------------------------------------------------------------------
>  >  >>  It's atoms.  In [molecules], you specify exactly that - how many of each
>  >  >>  [moleculetype] there are; grompp expands the information into number of
> atoms.
>  >  >>
>  >  >>  -Justin
>  >  >
>  >  >
>  >  >
>  >  > Yes but I do not know how to fix the number of coordinates, because:
>  >  > This is what it is supposed to look like:[ molecules ]
>  >  > ; Compound  #mol
>  >  > Protein      1
>  >  > SOL          10189
>  >  > NA+          10
>  >  > But I already checked that SOL has the correct number of water molecules, I
>  > have not added ions yet so NA+ does not apply, and I have only 1 protein as I
>  > should.  So I cannot find anything in [molecules] to fix.
>  >  >
>  >  >
>  >  > So now I am looking at [ moleculetype ] in topol.top:
>  >  > [ moleculetype ]; Name            nrexclProtein_chain_A    3
>  >  > [ atoms ]
>  >  >
>  >  >
>  >  >
>  >  > [atoms] is really big so I don't know how to look through it to add the 1150
>  > missing coordinates.
>  >  > model1_solv.gro
>  >  >
>  >
>  > Given that the number of atoms in disagreement between coordinates and topology
>  > (1150) is exactly the size of one of your peptides, I'd be willing to bet that
>  > that's your issue.
>  >
>  >
>  > -Justin
>  >
>  >  > |  |
>  >  > |  |  |  |  |  |  |  |
>  >  > | model1_solv.groShared with Dropbox |
>  >  > |  |
>  >  > | View on www.dropbox.com | Preview by Yahoo |
>  >  > |  |
>  >  > |  |
>  >  >
>  >  >
>  >  > topol.top
>  >  >
>  >  > |  |
>  >  > |  |  |  |  |  |  |  |
>  >  > | topol.topShared with Dropbox |
>  >  > |  |
>  >  > | View on www.dropbox.com | Preview by Yahoo |
>  >  > |  |
>  >  > |  |
>  >  >
>  >  >
>  >  > Sincerely,Thomas
>  >
>  >  >
>  >
>  > --
>  > ==================================================
>  >
>  > Justin A. Lemkul, Ph.D.
>  > Ruth L. Kirschstein NRSA Postdoctoral Fellow
>  >
>  > Department of Pharmaceutical Sciences
>  > School of Pharmacy
>  > Health Sciences Facility II, Room 629
>  > University of Maryland, Baltimore
>  > 20 Penn St.
>  > Baltimore, MD 21201
>  >
>  > jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu>
> <mailto:jalemkul at outerbanks.umaryland.edu
> <mailto:jalemkul at outerbanks.umaryland.edu>> |
>  > (410) 706-7441
>  > http://mackerell.umaryland.edu/~jalemkul
>
>  >
>  >
>  > ==================================================
>  >
>  >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================


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