[gmx-users] Error in DNA.itp file

[Paul bauer]

Hello,

the error states that you are missing parameters for your system. Did 
you check that the forcefield contains all the special parameters you 
need for the conjugate molecule?
Also, I would recommend to not use a prehistoric version of GROMACS for 
new studies, if there are no specific reasons preventing you from using 
a more recent one that is still supported (such as 2018 or 2019).

Cheers

Paul

On 05/11/2019 14:47, Ayesha Kanwal wrote:
> Hi all,
> i am preparing system of DNA-protein complex, downloaded it from RCSB website, by using GROMACS-version 4.5.5; force field AMBER03WS with water Model TIP4P (2005). The DNA chain contains DA, DT, DG, DC atom type.
> but the problem is that when i use command for energy minimization the following error has occurred. Error shows that problem is in .itp file Dih. types. For protein .itp files,there was no problem. Only DNA .itp files have issue. Its my first time i am preparing this kind of system please let me know how can i resolve this problem and why these errors were generated ? I have searched out previous mail but could not find relevant answer so i am posting it now here. i have attached .mdp file with this e-mail.
>
> checking input for internal consistency...
> Generated 2412 of the 2415 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 2415 of the 2415 1-4 parameter combinations
>
> ERROR 1 [file dna-his_DNA_chain_I.itp, line 44148]:
>    No default Improper Dih. types
>
>
> ERROR 2 [file dna-his_DNA_chain_J.itp, line 44148]:
>    No default Improper Dih. types
>
>

-- 
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594