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

[Sucharita Dey]

Hello,
Thanks Justin.
Since my protein has a modified DNA residue (methyl cytosine) I have copied the "gromos53a6.ff" folder as well as the "residuetypes.dat" file in my working directory and modified them, where I have inserted my modified DNA residue as DNA and also have renamed DADE, DTHY ... as DNA. Within "gromos53a6.ff", following "Adding a new residue" from gmx-tutorial, I have modified .rtp, .hdb, atomtypes.atp, and residuetypes.dat. In the rtp, hdb files as well DNA is written as DADE, DTHY.... And I am choosing this force field from the current directory while running pdb2gmx. It is not giving error for the modified residue but giving error for DNA terminal. Am I missing anything for which it is not identifying the DNA as "DNA"?
-Sucharita

 
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
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul [jalemkul at vt.edu]
Sent: Friday, March 14, 2014 8:02 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] asking for N and C termini for DNA and giving error

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

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