Dear Mark, Do you mean I will obtain 2 seperate .itp files for CNT and peptide. And I already have spc.itp. Then I will write a short .top file which only consists of include files. Is that all what I will do?
In addition, I think I should combine pdbs od CNT and peptide by pymol,VMD etc. best wishes trevor On 18/01/2011 10:25 AM, trevor brown wrote: > Dear friends, > I have constructed a .top file for a CNT by g_x2top. to do this I > have added C-C interactions in .n2t file and also related ff in > .atomtypes.atp. I have also a .top file for a peptide by pdb2gmx. > My aim is to construct a simulation system in which I want to see the > adsorption. > I don't know the next steps, could you guide me for further steps? You need to end up with a .top file that has the logical structure of #include force field files #include CNT.itp #include peptide.itp #include solvent.itp [molecules] CNT 1 Peptide 1 SOL 10000 and a coordinate file whose molecules are ordered exactly as in the above field, and whose atoms within molecules are ordered exactly as in the [atoms] fields in the .itp file. Your molecule names must match those given in the .itp files. See the examples in section 5.7.1-5.7.3 of the manual. Mark > My second question; I have .gro and .tp files for both CNT and > peptide, do I need any other files such as .itp or .ndx? > Last question: Do you have such a tutorial? > best wishes > trevor
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