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

[Urszula Uciechowska]

Hi,

Now I have GROMACS v 5.0. What option should I select for -chainsep?
-chainsep <enum> (id_or_ter)
     Condition in PDB files when a new chain should be started (adding
     termini): id_or_ter, id_and_ter, ter, id, interactive

Should I change something in my PDB file?  This is not clear for me.
Thank you for your help

Urszula

> 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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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/