[gmx-users] modelling/adding missing residues in case of Fatal error: Incomplete ring in HIS3

[Justin Lemkul]

On 5/13/15 6:16 AM, James Lord wrote:
> Many thanks Justin,
> I created a new .pdb file with SwissPDBViewr  but again executing pbd2gmx is
> giving the following warning and error
>
>
> Warning: Starting residue CA584 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue CA585 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue CA586 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue ACT587 in chain not identified as Protein/RNA/DNA.
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.
> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
> 8 out of 8 lines of specbond.dat converted successfully
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION -4.5.4
> Source code file: /home/James/gromacs-4.5.4/src/kernel/resall.c, line: 642
>
> Fatal error:
> Residue 'ACT' 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
> -------------------------------------------------------
>
> Here is the link to new PDB, my question is what is ACT residue? and how to

Did you read the contents of the PDB file?

REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CA ACETATE, 20% PEG3350, 0.1 M
REMARK 280  TRIS HCL, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K

If you visualize ACT you will see it is acetate.

> resolve this issue, any thought is greatly appreciated?

Given that it's a crystallization co-solvent it's unlikely to be functional in 
any way, so you can likely delete it.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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