[gmx-users] residue not found

[abhisek Mondal]

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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>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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> Blacksburg, VA 24061
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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*