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

[Justin Lemkul]

On 4/13/14, 1:15 PM, Albert wrote:
> thank you for kind comments.
>
> I checked that all residues are in the same chain X. I add NMA as Protein in
> residuetypes.dat file and run pdb2gmx command again, it still have some problems:
>
> Linking CYS-121 SG-638 and CYS-198 SG-1229...
> 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 NMA-339
>   0: COO-
>   1: COOH
>   2: CT2
>   3: 3TER
>   4: None
> 3
> End terminus NMA-339: 3TER
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.6.5
> Source code file: /home/albert/gromacs-4.6.5/src/kernel/pdb2top.c, line: 1148
>
> Fatal error:
> atom O3' not found in buiding block 305NMA while combining tdb and rtp
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>

Your ending terminus should be None, not 3TER.  3TER is for nucleic acids.

-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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