[gmx-users] error while running pdb2gmx

hasthi durgs7krish at gmail.com
Wed Nov 13 12:02:59 CET 2013


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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