<br />Dear All,<br /><br />I used top2psf.pl to visualize bonds in my
coarse grained simulation with MARTINI ff. it worked well. my system
contained a box of 1 protein and several hundreds of water molecules. then
I repeated the box to make a bigger system with command below:<br /><br
/>genconf -nbox 2 2 2 -f 1box.gro -o 8box.gro<br /><br />Now I have 8
proteins. to visualize, I make just proteins .gro file and repair
.top file but I can't visualize bonds in my new system. I think my
.top file has a problem. I examined several ways, but without any results.
Please help me. <br />Regards<br />Kargar<br /><br /><br />--
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