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

[James Lord]

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?
https://drive.google.com/file/d/0B0YMTXH1gmQsSWlXTU56R0FYcVk/view?usp=sharing

Cheers
James


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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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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