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-requ...@maillist.sys.kth.se> escreveu: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 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.szil...@gmail.com> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Cc: Discussion list for GROMACS users > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: Re: [gmx-users] NTMPI / NTOMP combination: 10 threads not > "reasonable" for GROMACS? > Message-ID: > < > cannyew4hu4r4ab2+cerzwvh3xdkjfbasxzed26uphemusav...@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.teletc...@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 > > -- > > 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-requ...@gromacs.org. > > > ------------------------------ > > Message: 2 > Date: Fri, 10 May 2019 18:00:09 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] HELP - Fatal error gmx pdb2gmx > Message-ID: <88dab19b-d590-c2dd-8dbb-7ec9ab4ab...@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 > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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