hello,
I want to do gromacs simulation of a protein DNA complex along with a small molecule ligand. But unfortunately the bound ligand is not a complete one..its one helix is cut. So, i am following amber forcefield. but unfortunately its not completed. here i am attaching the DNA molecules. so can anyone make the topology files for gromacs simulation.. Its really needful for me.
Thank You. Best regards.
You can assume broken end as 3' and 5' terminal. In fact, pdb2gmx automatically assign broken end as 3' and 5' terminal. If not, just add 3 and 5 to residue name (eg. DG5 DT3 etc.). If it complains atom missing or extra atom then you have to edit the structure accordingly (3' and 5' terminal structure is slightly different from middle ones ).
it is not possible to have a good topology file or correct file when DNA or protein o what you want to simulate in gromacs is broken. Moreover, it is biologically incorrect simulate a broken molecules its do not reflect the reality........... Use modeling softwares to correct your DNA structure and then try again in gromacs.
Best
There are some programs to fix it. You can try the AutodockTools, but i dont know if it works to DNA molecules.
Please, check programs in the web to fix this situation.
Actually the problem was under numbering into the pdb files, so thats why pdb files and topology files didnot matched. i think the problem was on that point.. so thank you everyone.
Fixing periodicity effects with trjconv to suit visualization or analysis can be tricky. Multiple invocations can be necessary. You may need to create custom index groups (e.g. to keep your ligand with your protein) Following the steps below in order (omitting those not required) should help get a pleasant result. You will need to consult trjconv -h to find out the details for each step. That's deliberate - there is no magic "do what I want" recipe. You have to decide what you want, first :-)
With point three, the issue is that trjconv removes the jumps from the first frame using the reference structure provided with -s. If the reference structure (run input file) is not clustered/whole, trjconv -pbc nojump will undo steps 1 and 2
for a fresh dna sequence, topology can be generated using, http://www.swissparam.ch/ website and then you can continue your md simulations.
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