[gmx-users] asking for N and C termini for DNA and giving error

[Justin Lemkul]

On 3/14/14, 7:05 AM, Sucharita Dey wrote:
>
> Hello,
>
> My protein is pr-DNA complex, it is identifying DNA terminus and searching for N and C in tdb  file giving error. When I select -ter and specify none as termini , it still gives error saying
>
> "There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. " Please help.
>
> Error without -ter option:
>
> Processing chain 1 'B' (434 atoms, 21 residues)
> Identified residue DADE1 as a starting terminus.
> Identified residue DTHY21 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Start terminus DADE-1: NH3+
> End terminus DTHY-21: COO-
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.6.3
> Source code file: /home/sucharita/sucharita/softwares/gromacs_all/gromacs-4.6.3/src/kernel/pdb2top.c, line: 1148
>
> Fatal error:
> atom N not found in buiding block 1DADE while combining tdb and rtp
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> with -ter option selecting none
>
> Processing chain 1 'B' (434 atoms, 21 residues)
> Identified residue DADE1 as a starting terminus.
> Identified residue DTHY21 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Select start terminus type for DADE-1
>   0: NH3+
>   1: NH2
>   2: None
> 2
> Start terminus DADE-1: None
> Select end terminus type for DTHY-21
>   0: COO-
>   1: COOH
>   2: None
> 2
> End terminus DTHY-21: None
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.6.3
> Source code file: /home/sucharita/sucharita/softwares/gromacs_all/gromacs-4.6.3/src/kernel/pdb2top.c, line: 1109
>
> Fatal error:
> There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Sucharita Dey,PhD, Research Fellow, Cancer Science Institute of Singapore, National University of Singapore. 14, Medical Drive,  #12-01, Singapore 117599. Tel: (65) 90355220, email: csisd at nus.edu.sg
>

The problem is that DADE, DTHY, etc. are not recognized as normal residue names 
for anything, since they are not defined in residuetypes.dat as being DNA, so 
Gromacs assumes they are protein.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==================================================