Dear amber users and developers,
I am trying do an umbrella sampling of nucleic acid. One of my restraint
co-ordinate is cpd angle (pseudo- dihedral angle ), for that I need to
restraint center of mass of four group of atoms. I am little bit confuse
how to choose the iat value. In the manual I found that it should be
negative, but it is not running in cuda. Here is my restraint file,
*&rstiat=-1,-1,-1,-1igr1=463,482,480,460,462igr2=105,121,119,102,104igr3=170,189,187,167,169igr4=145,147,148,151,152,142,143,144,141,139,138r1
= psu1, r2 = psu0, r3 = psu0, r4 = psu2,rk2 = 50000.0, rk3 = 50000.0,
ialtd=0,&end*
Can anyone suggests what to do ?
Thank you in advance!
--
with regards
Rajarshi Roy
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India
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Received on Thu Mar 15 2018 - 03:30:02 PDT
