Dear Amber usrers,
I am trying to perform PMF calculation for my system using two restrain the distance restrain and plane -plane restrain. I have done minimization using these restrain and in the output file it read two restrains, but the energy showed that NMR restrain for bond only. I have also tried plane to point restrain and it showed that bond and plane to point in NMR restrain is used.
I am applying the plane-plane restrain in order to prevent structure b to move all over structure A in z direction, when i set distance restrain only B structure dose not stay above A at specific distance (z) and location it move around A sheet in z direction.
what is the problem with second restrain highlighted in red, is the angle set right, any other suggestion might be useful please .
I am using sander in amber 12.
The input file for the restrain is
Disance restrian at 11.0 A
&rst
iat=-1, -1,
igr1=531,556,561,560,535,534,
igr2=1095,1096,1097,1098,1099,1100,1101,1102,1103,1104,1105,1106,
r1=0, r2=11.0, r3=11.0, r4=99,
rk2=20.0, rk3=20.0,
/
&rst
iat=1096,1097,1099,1100,560,531,556,561,
r1=-180.0, r2=0.0, r3=0.0, r4=180.0,
rk2=20, rk3=20,
/
note;
plane one atomes are:1096,1097,1099,1100
plane two atoms are: 560,531,556,561,
Regards
Rasha
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Received on Tue Mar 04 2014 - 09:30:02 PST
