[gmx-users] C-terminus residue name in Gromos43a1

Justin Lemkul jalemkul at vt.edu
Tue Feb 25 19:08:58 CET 2014

On 2/25/14, 12:56 PM, Francesca Vitalini wrote:
> Dear Justin,
> Thanks for your answer.
> However I noticed that I had made a mistake and there is no definition of
> NAC in GROMOS53a6, it was the .rtp file of OPLS-AA I was looking at.
> So defining a new residue-type in the rtp file is not as trivial as I had
> hoped.
> I followed the instructions given on the GROMACS wab page
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> and copied the gromos43a1.ff folder and the residuetypes.dat file in my
> local directory.
> I have added the following definition of NAC to the
> gromos43a1.ff/aminoacids.rtp file
> [ NAC ]
>   [ atoms ]
>          N     N    -0.28000     0
>          H     H     0.28000     0
>         CA   CH3     0.00000     0
>   [ bonds ]
>          N    CA    gb_20
>          N     H    gb_2

You're missing a bond here, from N to -C.

>   [ angles ]
> ;  ai    aj    ak   gromos type
>         -C     N     H     ga_31
>          H     N    CA     ga_17
>         -C     N    CA     ga_30
>   [ impropers ]
> ;  ai    aj    ak    al   gromos type
>      N    -C    CA     H     gi_1
>   [ dihedrals ]
> ;  ai    aj    ak    al   gromos type
>    -CA    -C     N    CA     gd_4
> and then tried again the pdb2gmx command as following and obtained this
> error
> Fatal error:
> There is a dangling bond at at least one of the terminal ends. Select a
> proper terminal entry.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> Evidently I have not defined correctly my NAC residue. However, I am not
> sure of how to correctly define the bonds in this specific case. Could you
> possibly identify the error and/or point me where to find detailed
> information? I have already looked at the manual but haven't been able to
> come up with successful definition.

You need to use pdb2gmx -ter and select "None" for the C-terminus, otherwise 
pdb2gmx tries to build a carboxylate.  When it can't find the atoms it needs to 
do this, it fails.



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


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