[gmx-users] No default U-B types in CHARMM36 FF

[Justin Lemkul]

On 4/13/14, 10:20 AM, Albert wrote:
> Hello Mark:
>
> thanks a lot for kind comments. I tried following selections:
>
> Select start terminus type for ACE-35
>   0: NH3+
>   1: NH2
>   2: 5TER
>   3: None
> 3
> Start terminus ACE-35: None
> Select end terminus type for GLY-338
>   0: COO-
>   1: COOH
>   2: CT2
>   3: 3TER
>   4: None
> 4
> End terminus GLY-338: None
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.6.5
> Source code file: /home/albert/gromacs-4.6.5/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
> -------------------------------------------------------
>
>
> It still failed. I don't understand, there is a NMA in the C-term, why the
> second dialog ask the GLY-338 instead of NMA residue?
>

Scroll up in the pdb2gmx screen output.  When it breaks down the chains, it will 
show you what is considered "Protein" and what is considered "Other."  The 
residue "NMA" does not appear anywhere in residuetypes.dat, so pdb2gmx decides 
that you have a "Protein" chain from ACE-1 to GLY-338, and then something else 
to deal with separately.  Add NMA to residuetypes.dat as a Protein type and it 
will work.

-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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