I want to do an MD simulation of a dipeptide which contains two alanine and in one of the alanine in place of the methyl group a CH2CN group is present. I have attached the .gro file of my structure here. I am using OPLS-AA force field. But when I am running grompp I am getting the following error-
NOTE 1 [file minim.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to 1981633587
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
ERROR 1 [file topol.top, line 152]:
No default Angle types
ERROR 2 [file topol.top, line 188]:
No default Ryckaert-Bell. types
ERROR 3 [file topol.top, line 192]:
No default Ryckaert-Bell. types
ERROR 4 [file topol.top, line 196]:
No default Ryckaert-Bell. types
I believe this is because in my ffbonded.itp file there is no definition of angle type and dihedral type for the following combination of atoms -
CA CB CZ
N CA CB CZ
HA CA CB CZ
C CA CB CZ
Therefore, my question is, from where can I get the parameters needed to edit the above-mentioned angle type and dihedral types in my ffbonded.itp file? I have attached my topol.top file and ffbonded.itp file here. Any suggestion regarding this will be highly appreciated.
If no one has already parametrized and published suitable parameters, you'll have to do it yourself, following the protocol described in the force field's primary literature.
For the 1st option, you can consider Justin's suggestion but sometimes it takes long time to get proper parameters.
2nd option, I recommend to use ambertools and using tleap you can create a topology for your system applying amber99sb force field. I think amber FF handles this kind of problem.
AMBER requires the same approach as any force field - one needs to generate appropriate parameters. AMBER99sb doesn't automatically support this residue, either. One would have to proceed through a parametrization protocol, presumably aided by antechamber or other utilities, and then still verify that the generated topology (which by default may be a combination of standard protein and GAFF atom types, which may not be preferred) is valid. It may be "easier" to generate a topology this way, but it is always difficult to verify and refine it.
Hi, try this server:
http://zarbi.chem.yale.edu/ligpargen/ to generate the missing information.
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