Dear all,
I am going to run a SMD for umbrella sampling, but in the pull step I met an error in the mdout file: jar option running Error: No atom in residue 189. Here is my RST file:
&rst
iat=-1,-1,
r2=5.4,
rk2=1,
r2a=-23.6,
iresid=1,
fxyz=0,0,1,
outxyz=1,
igr1=189,
igr2=8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,
/
My plan is to pull a molecule(res number=189) starting in the middle of the channel of the protein to the outside in the +z direction, so I set igr1=189, and I would like to use the COM of the protein as the distance reference, so for igr2 is the residue number of my protein. I am not sure if my settings are right or not, could anybody give me some advice? Thank you in advance!
Best regards,
Meng Wu
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Received on Thu Jul 05 2018 - 06:00:08 PDT
