[gmx-users] Error in DNA.itp file

[Justin Lemkul]

On 11/5/19 11:55 AM, Najamuddin Memon wrote:
> You may use Amber99sb force field  for DNA-protein simulation and also put
> residue type.dat file in your folder. It will work
>

The nucleic acid parameter sets packaged with these GROMACS ports are 
wildly outdated. I suggest finding better parameters from other sources. 
People have ported AMBER parameters, though they should be checked 
thoroughly.

-Justin

> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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