[gmx-users] Error in DNA.itp file

[Najamuddin Memon]

You may use Amber99sb force field  for DNA-protein simulation and also put
residue type.dat file in your folder. It will work


On Tue, Nov 5, 2019, 6:59 PM Paul bauer <paul.bauer.q at gmail.com> wrote:

> 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
>
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