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