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

James Lord jjamesgreen110 at gmail.com
Wed May 13 12:16:26 CEST 2015

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
resolve this issue, any thought is greatly appreciated?


On Sat, May 9, 2015 at 12:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 5/9/15 3:13 AM, James Lord wrote:
>> Hi Justin,
>> I opened up the strucutre in Swissviewr. Then how can I have a pdb with
>> missing
>> parts added?
> It's done automatically.  You should see a window pop up indicating
> missing atoms and that they have been built back.  Then just save the .pdb
> file.  There are tutorials online for this and you should consult whatever
> documentation and help forums SwissPDBViewer may provide.
> -Justin
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> 20 Penn St.
> Baltimore, MD 21201
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