[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
Tue Jan 27 23:38:56 CET 2015
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> 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>>
> > To: 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>>
> > 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> |
> (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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