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wildly outdated.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 paramet
Residue type.dat file having definition of nucleotides
On Tue, Nov 5, 2019, 9:55 PM 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
>
>
> On Tue, Nov 5, 2019, 6:59 PM Paul bauer wrote:
>
>>
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 wrote:
> Hello,
>
> the error states that you are missing parameters for your system. Did
> you check that the forcefield contain
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 reas
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
foll
