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

[James Lord]

Thanks Justin.

On Wed, May 13, 2015 at 11:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>