[gmx-users] Re: Seeking solution for the error Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms while sorting atoms.

I have tried it Tsjerk.. But the same error is shown again.. - Santhosh Kumar Nagarajan MTech Bioinformatics SRM University Chennai India -- View this message in context:

Re: [gmx-users] Re: Seeking solution for the error Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms while sorting atoms.

Please answer all of Justin's questions. What is in the PDB file - what should the C terminus be! Mark On Tue, Sep 17, 2013 at 2:27 AM, Santhosh Kumar Nagarajan santhoshraja...@gmail.com wrote: I have tried it Tsjerk.. But the same error is shown again.. - Santhosh Kumar Nagarajan MTech

[gmx-users] Re: Seeking solution for the error Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms while sorting atoms.

This is the command I used pdb2gmx -f protein.pdb -o processed.gro -water spce -ignh And I used OPLS-AA/L all-atom force field.. -- View this message in context:

Re: [gmx-users] Re: Seeking solution for the error Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms while sorting atoms.

Hi Santhosh, Try renaming the atom (mind the space): sed 's/OXT/O2 /' pdbfile fixed.pdb And then run pdb2gmx on that. Cheers, Tsjerk On Tue, Sep 17, 2013 at 6:05 AM, Santhosh Kumar Nagarajan santhoshraja...@gmail.com wrote: This is the command I used pdb2gmx -f protein.pdb -o