[gmx-users] Terminal_ARG_residue causing problem in pdb2gmx

[Mark Abraham]

On 14/12/2010 6:35 PM, shahid nayeem wrote:
> Dear Gromacs User
> My pdb is homodimer with  Arg as c-terminal residue. With this pdb I 
> am etting following error in pdb2gmx command
> Program pdb2gmx, VERSION 4.0.7
> Source code file: pdb2gmx.c, line: 429
>
> Fatal error:
> Atom OXT in residue ARG 107 not found in rtp entry with 17 atoms
>              while sorting atoms
> The command executed is as follows
>  pdb2gmx   -f    .pdb   -o    .gro   -p  .top
> I tried to change the OXT atom name in pdb file to O2, then also I am 
> getting the same error.
> In .rtp entry there is ARG residue as N-ter  but for C-ter ARG there 
> is no residue.
> Please suggest.
> Waiting for  helps from gromacs users.
> Shahid Nayem

There have been problems with terminal oxygen atoms. Please upgrade to 
4.5.3 and see if you still have problems.

Mark