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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