[gmx-users] How to resolve OXT atom issue?

[RAHUL SURESH]

I think you can go for Swissviewer rather going for modeller
On Sat, 17 Dec 2016 at 12:04 PM, Seera Suryanarayana <palusoori at gmail.com>
wrote:

> Dear Justin,
>
>
>
> I apologize you as I am wasting your  valuable time.
>
>
>
>   I have peptide with 69 residues and some of the SER and THR residues
>
>   are phosphorylated and also some of the missing residues(1 to 6; 36 to 41
>
>   and 69) have been modeled by modeller . I have chosen charmm36 force
>
> field.
>
>   When I executed the command
>
>
>
>   pdb2gmx  -f 1th1.pdb -o 1th1_processed.gro -water spce -ignh
>
>
>
>   I got following error.
>
>
>
>   Fatal error:
>
>
>
>    Atom OXT in residues GLU 69 was not found un rtp enrty GLU with 15
>
>    atoms while sorting atoms.
>
>
>
>  Here I am sending a link which has the coordinate file.
>
>
>
>
>
>
> https://drive.google.com/file/d/0B5HyqLWajWjHWjMyY25Cc3lSRTA/view?usp=drive_web
>
>
>
> Kindly tell me how to solve this error.
>
>
>
> Thanks in advance
>
> Surya
>
> Graduate student
>
> India.
>
> --
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