[gmx-users] Did not find any molecules of type ...

Marta Wisniewska marta.d.wisniewska at gmail.com
Mon Feb 22 13:55:05 CET 2016


Hello Justin,

my topology file:
 WAT_GMX.top created by acpypi on Tue Mar  3 13:26:34 2009

; Include forcefield parameters
#include "amber99sb-star-ildnp.ff/forcefield.itp"

[ moleculetype ]
;molname          nrexcl
WAT             2

[ atoms ]
; id  at type     res nr  res name   at name  cg nr  charge    mass
  1   O           1       WAT        O       1      -0.834    16.00000
  2   H           1       WAT        H1      1       0.417     1.00800
  3   H           1       WAT        H2      1       0.417     1.00800

#ifndef FLEXIBLE

[ settles ]
; OW    funct   doh     dhh
1       1       0.09572 0.15139

[ exclusions ]
1       2       3
2       1       3
3       1       2

#else

[ bonds ]
; i     j       funct   length  force_constant
1       2       1       0.09572 502416.0   0.09572        502416.0
1       3       1       0.09572 502416.0   0.09572        502416.0


[ angles ]
; i     j       k       funct   angle   force_constant
2       1       3       1       104.52  628.02      104.52  628.02


; Include water topology
#include "amber99sb-star-ildnp.ff/tip3p.itp"

[ system ]
WAT in water

[ molecules ]
; Compound       #mols
WAT              1
SOL              1023


I have olny one molecule (exactly it is a water molecule. tip3p model).

If I put into topology file:
#include "./wat.itp"

I get a new error, such as : moleculetype WAT is redefined.

How to fix it?

Thank you in advance!

2016-02-19 22:38 GMT+01:00 <
gromacs.org_gmx-users-request at maillist.sys.kth.se>:

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> Today's Topics:
>
>    1. Temperature Calculation in MD (Ray Chao)
>    2. Re: Temperature Calculation in MD (Justin Lemkul)
>    3. Did not find any molecules of type ... (Marta Wisniewska)
>    4. Re: Did not find any molecules of type ... (Justin Lemkul)
>    5. Query regarding energy calculation (Tushar Ranjan Moharana)
>    6. Re: auto-neutralize system (Samuel Flores)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 19 Feb 2016 12:19:31 -0500
> From: Ray Chao <xiaoainisa at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Temperature Calculation in MD
> Message-ID:
>         <CAFm40rDt2CnoQ7Ryiw7Vf6u+Hh=
> uGos-Q1wErFV7zzHpmGDhuw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi, gmx users,
>
> I have a questions regarding the temperature calculation during mdrun. The
> system is periodic in x and y direction, and there a re two groups of
> molecules, polymer and water solvent. The COM motion of the system was
> removed in the mdp file. However, each group has its own COM motion. So in
> calculating the temperature of each group, e.g, gmx traj, is the COM motion
> of each group removed? Or if I want to write my own code to calculate the
> temperature, do I need to cal the COM velocity first and then get rid of
> it?
>
> Thanks for your attention.
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 19 Feb 2016 13:06:17 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Temperature Calculation in MD
> Message-ID: <56C75999.6030208 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 2/19/16 12:19 PM, Ray Chao wrote:
> > Hi, gmx users,
> >
> > I have a questions regarding the temperature calculation during mdrun.
> The
> > system is periodic in x and y direction, and there a re two groups of
> > molecules, polymer and water solvent. The COM motion of the system was
> > removed in the mdp file. However, each group has its own COM motion. So
> in
> > calculating the temperature of each group, e.g, gmx traj, is the COM
> motion
> > of each group removed? Or if I want to write my own code to calculate the
> > temperature, do I need to cal the COM velocity first and then get rid of
> it?
> >
>
> If appropriate comm-grps were used during the simulation, no additional
> correction should be necessary as the output velocities should be correct.
>
> But the temperatures of individual groups are saved in the .edr file
> anyway,
> account for constraints, and are accurate over all MD steps, so it is not
> clear
> to me why you want to re-calculate temperatures using gmx traj.
>
> -Justin
>
> --
> ==================================================
>
> 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
>
> ==================================================
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 19 Feb 2016 19:07:48 +0100
> From: Marta Wisniewska <marta.d.wisniewska at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Did not find any molecules of type ...
> Message-ID:
>         <CAC92+mkowqSs=
> pRL73sQ_-Fr1ov81So9G82-nva1j3Yc2zsnfA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear all,
>
> I'd like perform a free energy binding calculations. I defined my molecules
> by WAT moleculetype in topology and these same name in gro file. I didn't
> include a wat.itp file to .top file.
>
> During grompp command, it shown up an error:
>
> Fatal error:
> Did not find any molecules of type 'WAT' for coupling
>
> I checked out in Internet, but I didn't find any compatible solutions.
>
> Could you help me?
>
> Thank you in advance,
>
> Marta
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 19 Feb 2016 13:09:54 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Did not find any molecules of type ...
> Message-ID: <56C75A72.4010403 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 2/19/16 1:07 PM, Marta Wisniewska wrote:
> > Dear all,
> >
> > I'd like perform a free energy binding calculations. I defined my
> molecules
> > by WAT moleculetype in topology and these same name in gro file. I didn't
> > include a wat.itp file to .top file.
> >
> > During grompp command, it shown up an error:
> >
> > Fatal error:
> > Did not find any molecules of type 'WAT' for coupling
> >
> > I checked out in Internet, but I didn't find any compatible solutions.
> >
> > Could you help me?
> >
>
> Apparently you did not define a [moleculetype] named WAT.  Note that
> residue
> names (e.g. what you're changing in the .gro file) are not relevant here.
> Without seeing your topologies (upload everything to a file-sharing
> service and
> provide a link if you'd like), there's not much more to go on.
>
> -Justin
>
> --
> ==================================================
>
> 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
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Sat, 20 Feb 2016 01:39:48 +0530
> From: Tushar Ranjan Moharana <tusharranjanmoharana at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Query regarding energy calculation
> Message-ID:
>         <
> CAH6CjFirawV9+0bPfAtjYgiifZuM+qOJP+moeRpVAN6kXPwt6g at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi everyone,
> I want to calculate energy (non-bonded) between various amino acids. I have
> the following queries:-
>
> 1)   If an atom belongs to two different energy groups it is showing error.
> Is there any way other than using mdrun -rerun. It is fine for me if energy
> between those groups which share atom/atoms will not be calculated.
> 2)   If a protein is simulated at two local minima (let us say lid open and
> closed form of lipase) and energy is extracted (total or potential) can I
> say the difference in energy is delta G. If not then what is the
> significance of potential and total energy extracted by gmx energy
> (g_energy).
>
> Thanks a lot for the help.
>
>
> "A society with free knowledge is better than a society with free food"
> --
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 19 Feb 2016 22:38:15 +0100
> From: Samuel Flores <samuelfloresc at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] auto-neutralize system
> Message-ID: <B995757C-8F04-4E98-9728-4599D1FBF7DE at gmail.com>
> Content-Type: text/plain;       charset=windows-1252
>
> I?m using 5.1.1 , so I guess -neutral alone should work for me.
>
> Does this just add the minimum number of ions needed to neutralize the
> system?  So for a net-neutral protein (even with several charged residues)
> no ions would be added?
>
> thanks
>
> Sam
>
> > On Feb 19, 2016, at 12:33, Piggot T. <T.Piggot at soton.ac.uk> wrote:
> >
> > In fact, from a very quick test in 4.5.7 -neutral has to be provided
> with -conc (or -np -nn) but in 5.0.6 -neutral seems to work on its own.
> >
> > Cheers
> >
> > Tom
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin
> Lemkul [jalemkul at vt.edu]
> > Sent: 19 February 2016 11:24
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] auto-neutralize system
> >
> > On 2/19/16 6:23 AM, Jo?o Henriques wrote:
> >> Does it work without specifying -nn and -np? I thought it added on top
> of
> >> the ions specified with -np/-nn or -conc, but I am likely to be wrong.
> >>
> >
> > This is what the documentation says, and unless the code has been
> changed, I
> > recall finding that using -neutral on its own has no effect (would be a
> lovely
> > feature to have, though).
> >
> > -Justin
> >
> >> /J
> >>
> >> On Fri, Feb 19, 2016 at 12:18 PM, Piggot T. <T.Piggot at soton.ac.uk>
> wrote:
> >>
> >>> Hi,
> >>>
> >>> The -neutral option of genion should do the trick
> >>>
> >>> Cheers
> >>>
> >>> Tom
> >>> ________________________________________
> >>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> >>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Jo?o
> >>> Henriques [joao.henriques.32353 at gmail.com]
> >>> Sent: 19 February 2016 11:07
> >>> To: Discussion list for GROMACS users
> >>> Subject: Re: [gmx-users] auto-neutralize system
> >>>
> >>> Not that I know of. Anyway, that's like a couple of extra line of
> code...
> >>> Just read the topology and parse the total charge (that's a one-liner
> in
> >>> awk, for example). Then, depending on whether it's positive, negative
> or
> >>> zero, you just set two variables with the correct integer(s) and feed
> it to
> >>> genion like so:
> >>>
> >>> genion ... -np $var1 -nn $var2
> >>>
> >>> Imagine the net charge is +5, then var1=0 and var2=5.
> >>>
> >>> Put this inside a function and you use it over and over without having
> to
> >>> write more code.
> >>>
> >>> /J
> >>>
> >>> On Fri, Feb 19, 2016 at 11:37 AM, Samuel Flores <
> samuelfloresc at gmail.com>
> >>> wrote:
> >>>
> >>>> Guys,
> >>>>
> >>>> Is there a way  you know a way to avoid using e.g. -np to explicitly
> >>>> specify number of ions? I would prefer to let GROMACS figure out how
> many
> >>>> ions it needs to neutralize the system. Mostly this is because I am
> >>> writing
> >>>> a script to generate SLURM job files for a bunch of variants, and
> adding
> >>> up
> >>>> the charges means more coding for me. My system is Staphylococcal
> >>> Protein A
> >>>> , domain B, in solvent.
> >>>>
> >>>> I append below the sort of job file I would be having my script
> generate.
> >>>>
> >>>> Many thanks
> >>>>
> >>>> Sam
> >>>>
> >>>>
> >>>>
> >>>> #!/bin/bash -l
> >>>> #SBATCH -J BF18
> >>>> #SBATCH -p node
> >>>> #SBATCH -n 16
> >>>> #SBATCH -N 1
> >>>> #SBATCH --exclusive
> >>>> #SBATCH -A snic2015-1-443
> >>>> #SBATCH -t 72:00:00
> >>>>
> >>>>
> >>>> module add gromacs/5.1.1
> >>>> cd /home/samuelf/projects/SpA-ZEMu-method-upgrade/C-130-F
> >>>> # was /proj/snic2015-1-317/GROMACS/GROMACS/BF-SPA/C-130-F/
> >>>> echo 6 > temp.txt
> >>>> echo 1 >> temp.txt
> >>>>
> >>>> cat temp.txt | gmx_mpi pdb2gmx -f last.2.pdb -o last.2_processed.gro
> >>> -ignh
> >>>> #6: Amber sb99 , 3 point TIP3P water model: force field was selected
> >>> based
> >>>> on this benchmark article:
> >>>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905107/ <
> >>>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905107/>
> >>>> gmx_mpi editconf -f last.2_processed.gro -o last.2_newbox.gro -c -d
> 1.0
> >>>> -bt cubic
> >>>> gmx_mpi solvate -cp last.2_newbox.gro -cs spc216.gro -o
> last.2_solv.gro
> >>> -p
> >>>> topol.top
> >>>>
> >>>> gmx_mpi grompp -f ions.mdp -c last.2_solv.gro -p topol.top -o ions.tpr
> >>>> echo 13 | gmx_mpi genion -s ions.tpr -o last.2_solv_ions.gro -p
> topol.top
> >>>> -pname NA -np 5
> >>>> mpirun -np 16 gmx_mpi grompp -f minim.mdp -c last.2_solv_ions.gro -p
> >>>> topol.top -o em.tpr
> >>>> mpirun -np 16 gmx_mpi mdrun -v -deffnm em
> >>>>
> >>>> gmx_mpi grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
> >>>> mpirun -np 16 gmx_mpi mdrun -deffnm nvt
> >>>> gmx_mpi grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o
> npt.tpr
> >>>> mpirun -np 16 gmx_mpi mdrun -deffnm npt
> >>>> gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o
> md_0_1.tpr
> >>>> mpirun -np 16 gmx_mpi mdrun -deffnm md_0_1
> >>>>
> >>>>
> >>>> Samuel Coulbourn Flores
> >>>> Associate Professor
> >>>> Computational and Systems Biology Program
> >>>> Department of Cell and Molecular Biology
> >>>> Uppsala University
> >>>>
> >>>> --
> >>>> Gromacs Users mailing list
> >>>>
> >>>> * Please search the archive at
> >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >>>> posting!
> >>>>
> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>>
> >>>> * For (un)subscribe requests visit
> >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>>> send a mail to gmx-users-request at gromacs.org.
> >>>>
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at
> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >>> posting!
> >>>
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
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> >>> send a mail to gmx-users-request at gromacs.org.
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at
> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >>> posting!
> >>>
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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> >>> send a mail to gmx-users-request at gromacs.org.
> >>>
> >
> > --
> > ==================================================
> >
> > 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
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> Samuel Coulbourn Flores
> Associate Professor
> Computational and Systems Biology Program
> Department of Cell and Molecular Biology
> Uppsala University
>
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-request at gromacs.org.
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> *******************************************************
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