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

[Mark Abraham]

Hi,

-ter does not solve this problem. You should not start new work with such
an old version of GROMACS; I forget when we added -chainsep, but it solves
this problem.

Mark

On Wed, 6 May 2015 15:37 Urszula Uciechowska <
urszula.uciechowska at biotech.ug.edu.pl> wrote:

>
> 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/
>
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