[gmx-users] error while running pdb2gmx

[Mark Abraham]

Probably the default behaviour of pdb2gmx for termini is not appropriate
for your input. Use pdb2gmx -ter and choose wisely

Mark
On Nov 13, 2013 12:03 PM, "hasthi" <durgs7krish at gmail.com> wrote:

> Hello GROMACS users,
>                               I have phosphorylated Serine residue in my
> protein (140 residues) of interest, now when I run pdb2gmx I get this
> following error
>
> Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms
> while sorting atoms.
>
> I checked aminoacid.rtp, there is no separate entry for OXT there.When I
> did the simulation for the same protein prior phosphorylation I did not get
> this error. What is the reason for this and how should I rectify this
> error?
>
> Please help me with this regard....
>
>
> Regards,
> Hasthi
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