Dear All I did the Enzyme/drug tutorial and generated complex.gro and complex.top files as was said. Now I want to measure the distance between center of mass of protein and drug I used g_dist but I could not. I entered these commands(of course I made an index.ndx and g-dist.tpr):
I used from an typical .mdp file to generate .tpr file by below command: grompp -c complex.gro -p complex.top -o g-dist.tpr -f g-dist.mdp -maxwarn 3 then, g_dist -f complex.gro -s g-dist.tpr -o g-dist.xvg but the result was an empty g-dist.xvg and: Fatal error: Unexpected end of file in file 631LIG C12 45 -0.475 -0.514 -0.434 at line 2 (Source file ../../../../src/gmxlib/confio. c, line 725) besides,I want to measure this distance befor erunning and as a vector. below is a part of my complex.gro: 631LIG F1 42 -0.701 -0.571 -0.151 631LIG C16 43 -0.534 -0.501 -0.306 631LIG H16 44 -0.491 -0.434 -0.232 631LIG C12 45 -0.475 -0.514 -0.434 631LIG H12 46 -0.394 -0.446 -0.459 thanks in advances
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