<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt;color:#000000;">Dear All,<br><br>I want to simulate DNA-CNT interaction, and reproduce the helical wrapping of DNA around CNT in the first step, and later study the effects of temperature, CNT length etc on the favorable geometries of hybrid.<br><br>I have created .top files for DNA, and CNT separately. To generate the top file of entire system (DNA-CNT), I added CNT in a box with DNA using genbox. But when I try to create .top file using pdb2gmx and Amber forcefield, I get an error that atom C in residue 11 C not found in rtp entry because rtp because .rtp file in Amber only contain dna residues, and if I use some other forcefield like oplsaa then dna residues won't be present. So how do I create the .top file for whole system i.e DNA-CNT?<br><br>Mailing list suggests that another and probably
easier way of doing this is to create .itp file for CNT, and add it to dna.top file using #include file mechanism. So I wanted to ask how can I create .itp file from topology file (because I have the toplogy file for CNT), or do I need to create it manually from scratch?<br><br>Thank You,<br>Majid<br></div></body></html>