[gmx-users] gromacs.org_gmx-users Digest, Vol 181, Issue 27

[Edjan Silva]

HELP - Fatal error gmx pdb2gmx (Justin Lemkul)

Yes. Includes residues in residuetypes.dat. however the same error remains.

Em sáb, 11 de mai de 2019 às 07:01, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> escreveu:

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> Today's Topics:
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>    1. Re: NTMPI / NTOMP combination: 10 threads not "reasonable"
>       for GROMACS? (Szil?rd P?ll)
>    2. Re: HELP - Fatal error gmx pdb2gmx (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 10 May 2019 21:12:12 +0200
> From: Szil?rd P?ll <pall.szilard at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] NTMPI / NTOMP combination: 10 threads not
>         "reasonable" for GROMACS?
> Message-ID:
>         <
> CANnYEw4hu4R4AB2+cERzWvH3XDkJfBAsxzEd26uPHEMUsAvVTA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> That is just a hint, if you measured and you are getting better performance
> with 10 threads, use that setting. (Also note that the message suggests "4
> to 6" rather than "4 or 6" threads).
>
> Do you also get the same note with the 2019 release?
>
> --
> Szil?rd
>
>
> On Fri, May 10, 2019 at 6:27 PM T?letch?a St?phane <
> stephane.teletchea at univ-nantes.fr> wrote:
>
> > Le 20/03/2019 ? 22:42, St?phane T?letch?a a ?crit :
> > > Dear all,
> > >
> >
> > > Those CPUs are 10 cores +HT (so not 4 or 6). Is it only a warning ?
> >
> > Dear all,
> >
> > Any answer from core developpers on this, should a file a bug?
> >
> > Best,
> >
> > St?phane
> >
> > --
> > Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein
> > Design In Silico
> > UFR Sciences et Techniques, 2, rue de la Houssini?re, B?t. 25, 44322
> > Nantes cedex 03, France
> > T?l : +33 251 125 636 / Fax : +33 251 125 632
> > http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
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>
> ------------------------------
>
> Message: 2
> Date: Fri, 10 May 2019 18:00:09 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] HELP - Fatal error gmx pdb2gmx
> Message-ID: <88dab19b-d590-c2dd-8dbb-7ec9ab4ab417 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 5/10/19 2:26 PM, Edjan Silva wrote:
> > I deleted all non-protein molecules and saved the file. I typed the
> > following command:
> >
> > *gmx pdb2gmx -f 4gy7.pdb -o conf.gro -ignh*
> >
> > The error was as follows:
> >
> > *Fatal error:*
> > *The residues in the chain MET1--PHE840 do not have a consistent type.
> The*
> > *first residue has type 'Protein', while residue CME59 is of type
> 'Other'.*
> > *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.*
> >
> > *For more information and tips for troubleshooting, please check the
> > GROMACS*
> > *website at http://www.gromacs.org/Documentation/Errors
> > <http://www.gromacs.org/Documentation/Errors>*
> >
> > I could not run the command without problem. What should I do?
>
> Have you tried following what the error says by adding the nonstandard
> residue to residuetypes.dat?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
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> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
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> End of gromacs.org_gmx-users Digest, Vol 181, Issue 27
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