[gmx-users] residue not found

[Soham Sarkar]

Use -ter in pdb2gmx command

On Thu, 9 Aug 2018, 9:03 am abhisek Mondal, <abhisek.mndl at gmail.com> wrote:

> Replacing residue names as suggested solved the issue.
> However, I got stuck with atom error now. Same command gives me this now:
>
> *Fatal error:*
> *atom N not found in buiding block 1DT while combining tdb and rtp*
>
> In the pdb (DNA) file there is no N, rather its N1/N2/N3 (link:
>
> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0?ogsrc=32
> )
> ...
> Do I need to reformat the pdb file ? Seems a lot of issue there.
>
>
> On Wed, Aug 8, 2018 at 7:44 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 8/8/18 10:09 AM, Soham Sarkar wrote:
> > > Put your residue name in the residuetypes.dat file and designate it as
> > > nucleic acid. Keep the same file in your ff folder, which in turn
> should
> > be
> > > in the working directory.
> >
> > That won't solve the issue. The problem is that "THY" is not recognized
> > in the force field(s) the OP is trying to use. Consult the .rtp file for
> > the actual nomenclature. Most force fields use DT instead of THY, DA for
> > (deoxy)ADE, RA for ADE (RNA), etc. AMBER uses special residue names for
> > 5'- and 3'-nucleotides, as well.
> >
> > -Justin
> >
> > > On Wed, 8 Aug 2018, 6:54 pm abhisek Mondal, <abhisek.mndl at gmail.com>
> > wrote:
> > >
> > >> Hi,
> > >> I'm facing a very odd issue in gromacs. I'm trying to execute "pdb2gmx
> > -f
> > >> dna1.pdb -o dna.gro" using AMBER/CHARMM forcefield, but getting the
> > >> following error:
> > >>
> > >> *Program pdb2gmx, VERSION 4.6.2*
> > >> *Source code file: /home/user/gromacs-4.6.2/src/kernel/resall.c, line:
> > 642*
> > >>
> > >> *Fatal error:*
> > >> *Residue 'THY' not found in residue topology database*
> > >> *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'm using DNA first time in gromacs.
> > >> What should be the residue name instead of the name of the bases I
> can't
> > >> understand. A little suggestion would be terrific here.
> > >>
> > >> Thank you.
> > >>
> > >> --
> > >> Abhisek Mondal
> > >>
> > >> *Senior Research Fellow*
> > >> *Protein Crystallography Group*
> > >>
> > >> *Structural Biology and Bioinformatics Division*
> > >> *CSIR-Indian Institute of Chemical Biology*
> > >>
> > >> *Kolkata 700032*
> > >>
> > >> *INDIA*
> > >> --
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> > >>
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> > >> posting!
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> > >>
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
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>
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
> *Protein Crystallography Group*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
> --
> Gromacs Users mailing list
>
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