[gmx-users] gromacs.org_gmx-users Digest, Vol 171, Issue 108
Mohammad Goodarzi
mohammad.godarzi at gmail.com
Mon Jul 30 16:43:38 CEST 2018
Hi,
I did test it, I cannot resolve it, can you just mutate G2236E and test it ?
I tried to send you the PDB file but the website stopped me
Thanks
On Mon, Jul 30, 2018 at 5:00 AM <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. how to solve a fatal error (Mohammad Goodarzi)
> 2. Re: how to solve a fatal error (Mark Abraham)
> 3. Re: how to solve a fatal error (Mark Abraham)
> 4. Re: Protein_ligand simulation (RAHUL SURESH)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 29 Jul 2018 10:02:53 -0500
> From: Mohammad Goodarzi <mohammad.godarzi at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] how to solve a fatal error
> Message-ID:
> <CAO4=
> jh7Jz77RJAZ+6ZU9vJizDkTxxQsWg+otEqc2DZqLQNt-EQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Fatal Error I got
>
> Basically I am using the following command line
>
> gmx pdb2gmx -f proteinA.pdb -o conf.pdb
>
> Then I selected 20 as follows:
>
> 20: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>
> Then I selected 1 as it was recomended
>
> 1: TIP4P TIP 4-point, recommended
>
> But I got the following error.
>
> Fatal error:
>
> The residues in the chain MET-1--DIO3332 do not have a consistent type. The
>
> first residue has type 'Protein', while residue BR3330 is of type 'Ion'.
>
> Either there is a mistake in your chain, or it includes nonstandard residue
>
> names that have not yet been added to the residuetypes.dat file in the
> GROMACS
>
> library directory. If there are other molecules such as ligands, they
> should
>
> not have the same chain ID as the adjacent protein chain since it's a
> separate
>
> molecule.
>
> The protein I work with is only chain A of
> https://www.rcsb.org/structure/2J3S . I removed the water, chain B from
> the
> file. I mutated one amino acid and saved it in PDB by pymol.
>
> Can anyone tell me what is wrong and how I should solve the issue?
>
> Many thanks
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 29 Jul 2018 17:13:51 +0200
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] how to solve a fatal error
> Message-ID:
> <CAMNuMARAzCUJEN=
> uFCo53wOPxm4nzYeTLxkxEPrOWy4UD8uEKQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> Sounds like your mutated residue has a name that is not one supported by
> the forcefield, so you will need to explore the force field files to see if
> there is a way to name it suitably.
>
> Mark
>
> On Sun, Jul 29, 2018, 17:03 Mohammad Goodarzi <mohammad.godarzi at gmail.com>
> wrote:
>
> > Fatal Error I got
> >
> > Basically I am using the following command line
> >
> > gmx pdb2gmx -f proteinA.pdb -o conf.pdb
> >
> > Then I selected 20 as follows:
> >
> > 20: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> >
> > Then I selected 1 as it was recomended
> >
> > 1: TIP4P TIP 4-point, recommended
> >
> > But I got the following error.
> >
> > Fatal error:
> >
> > The residues in the chain MET-1--DIO3332 do not have a consistent type.
> The
> >
> > first residue has type 'Protein', while residue BR3330 is of type 'Ion'.
> >
> > Either there is a mistake in your chain, or it includes nonstandard
> residue
> >
> > names that have not yet been added to the residuetypes.dat file in the
> > GROMACS
> >
> > library directory. If there are other molecules such as ligands, they
> > should
> >
> > not have the same chain ID as the adjacent protein chain since it's a
> > separate
> >
> > molecule.
> >
> > The protein I work with is only chain A of
> > https://www.rcsb.org/structure/2J3S . I removed the water, chain B from
> > the
> > file. I mutated one amino acid and saved it in PDB by pymol.
> >
> > Can anyone tell me what is wrong and how I should solve the issue?
> >
> > Many thanks
> > --
> > 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.
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 29 Jul 2018 17:13:51 +0200
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] how to solve a fatal error
> Message-ID:
> <CAMNuMARAzCUJEN=
> uFCo53wOPxm4nzYeTLxkxEPrOWy4UD8uEKQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> Sounds like your mutated residue has a name that is not one supported by
> the forcefield, so you will need to explore the force field files to see if
> there is a way to name it suitably.
>
> Mark
>
> On Sun, Jul 29, 2018, 17:03 Mohammad Goodarzi <mohammad.godarzi at gmail.com>
> wrote:
>
> > Fatal Error I got
> >
> > Basically I am using the following command line
> >
> > gmx pdb2gmx -f proteinA.pdb -o conf.pdb
> >
> > Then I selected 20 as follows:
> >
> > 20: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> >
> > Then I selected 1 as it was recomended
> >
> > 1: TIP4P TIP 4-point, recommended
> >
> > But I got the following error.
> >
> > Fatal error:
> >
> > The residues in the chain MET-1--DIO3332 do not have a consistent type.
> The
> >
> > first residue has type 'Protein', while residue BR3330 is of type 'Ion'.
> >
> > Either there is a mistake in your chain, or it includes nonstandard
> residue
> >
> > names that have not yet been added to the residuetypes.dat file in the
> > GROMACS
> >
> > library directory. If there are other molecules such as ligands, they
> > should
> >
> > not have the same chain ID as the adjacent protein chain since it's a
> > separate
> >
> > molecule.
> >
> > The protein I work with is only chain A of
> > https://www.rcsb.org/structure/2J3S . I removed the water, chain B from
> > the
> > file. I mutated one amino acid and saved it in PDB by pymol.
> >
> > Can anyone tell me what is wrong and how I should solve the issue?
> >
> > Many thanks
> > --
> > 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.
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 30 Jul 2018 15:24:17 +0530
> From: RAHUL SURESH <drrahulsuresh at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Protein_ligand simulation
> Message-ID:
> <
> CAAtfiTu71MoJgUswbGnq8RtUj1bT47ZUU2mJfFpZo5v_xdS13Q at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello users.
>
> I overcame the warning errors. The naming is correct now. I tried to update
> the parameters for ffbonded.itp but how will I find the Kb value for F-F ?
>
> On Sat, 28 Jul 2018 at 6:52 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
>
> > Hi all
> >
> > I am performing a simulation between a protein and Fluorine molecule. I
> > have optimized the F2 structure using Gaussian and inserted into the box
> > using gmx insert-molecules command after adding solvent [gmx solvate].
> The
> > topology for fluorine molecule is generated by topolgen.
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *[ moleculetype ]; Name nrexclFLU1 3[ atoms ];
> > nr type resnr residue atom cgnr charge mass typeB
> > chargeB massB 1 opls_164 1 FLU1 F 0
> > -0.206 18.99840 2 opls_164 1
> > FLU1 F 0 -0.206 18.99840 [
> > bonds ]; ai aj funct 1 2 1 ; F F[ pairs ]; ai
> > aj funct[ angles ]; ai aj ak funct[ dihedrals ]; ai aj ak
> > al funct*
> >
> >
> > On command gmx grompp -f em.mdp -c alz_F.gro -p alz.top -o ions.tpr i
> get
> > the following errors
> >
> >
> > *ERROR 1 [file fluorine.itp, line 21]: No default Bond types*
> >
> >
> >
> >
> >
> >
> > *NOTE 1 [file alz.top, line 5915]: System has non-zero total charge:
> > -23.600000 Total charge should normally be an integer. See
> > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> > <http://www.gromacs.org/Documentation/Floating_Point_Arithmetic> for
> > discussion on how close it should be to an integer.*
> >
> >
> >
> >
> >
> >
> > *WARNING 1 [file alz.top, line 5915]: 16639 non-matching atom names
> atom
> > names from alz.top will be used atom names from alz_F.gro will be
> ignored*
> >
> >
> > Indeed there are only 628 atoms in .top file.
> >
> > Any suggestions?
> >
> >
> >
> >
> >
> >
> > --
> > *Regards,*
> > *Rahul *
> >
> --
> *Regards,*
> *Rahul *
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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>
> End of gromacs.org_gmx-users Digest, Vol 171, Issue 108
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