[gmx-users] How to run pdb2gmx with -ter flag?

[Urszula Uciechowska]

Hi,

I have problems with using -tar flag in pdb2gmx, after running
pdb2gmx -f COM-oH.pdb -o COM-oH.gro -p COM-oH.top -ter -ignh -water tip3p

I do not get any errors however after generating a pdb using editconf I am
getting a complex where the receptors are connected with bonds.
What I am doing wrong?
I have also tried to put the "ter" cards in my pdb (COM-oH.pdb):


ATOM   2779  O2  DC3   136      96.011  58.127 145.405  1.00  0.00        
  O
ATOM   2780  C3' DC3   136      94.583  61.640 142.148  1.00  0.00        
  C
ATOM   2781  C2' DC3   136      95.682  60.578 142.176  1.00  0.00        
  C
ATOM   2782  O3' DC3   136      94.914  62.682 143.055  1.00  0.00        
  O
ter
ATOM   2784  N   MET   137     -55.937  52.177 172.707  1.00  0.00        
  N
ATOM   2785  CA  MET   137     -57.391  52.043 172.937  1.00  0.00        
  C
ATOM   2786  CB  MET   137     -58.028  53.416 173.205  1.00  0.00        
  C
but after running pdb2gmx
I am getting an error message:

-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2gmx.c, line: 655

Fatal error:
Atom OXT in residue ARG 421 was not found in rtp entry ARG with 24 atoms
while sorting atoms.
.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

How to run it correctly?

Urszula Uciechowska

University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk
Poland


-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/