Hi,
I have a fundamental question, and I would appreciate any help in this regard.
I have a 286 residue protein and I have a acetonitrile molecule and TIP3P waters. Now I want my acetonitrile molecule tethered to a fixed x,y,z location. SO I deleted the x,y,z coordinates of the C2 atom (central Carbon) of ACN and plugged in my x,y,z values. Then I did a transformation in Pymol to put everything in the same reference frame.
Then I setup a initial minimization of my system. My min.in file is
minimise complex
&cntrl
imin = 1,maxcyc = 5000,ncyc = 500,
igb = 0, cut = 10, ntb = 1,
ntr = 1, restraintmask = ':287', restraint_WT = 500,
/
#Hold the ACN molecule tethered to the fixed location
# 500.0
# RES 287
# END
END
/
Before minimization my ACN molecule coordinates is
ATOM 4559 N1 C3N 287 -5.489 13.101 -2.079 1.00 0.00 N
ATOM 4560 C2 C3N 287 -6.000 14.000 -2.500 1.00 0.00 C
ATOM 4561 C3 C3N 287 -6.522 15.193 -3.101 1.00 0.00 C
ATOM 4562 H4 C3N 287 -6.333 15.240 -4.120 1.00 0.00 H
ATOM 4563 H5 C3N 287 -7.606 15.248 -3.037 1.00 0.00 H
ATOM 4564 H6 C3N 287 -6.074 16.053 -2.587 1.00 0.00 H
***************************************************************************************************************************************************
Post minimization, my ACN coordinates are as follows:
ATOM 4562 N1 C3N 287 30.984 59.184 37.642 1.00 0.00 N
ATOM 4563 C2 C3N 287 30.519 60.068 37.172 1.00 0.00 C
ATOM 4564 C3 C3N 287 29.990 61.247 36.574 1.00 0.00 C
ATOM 4565 H4 C3N 287 30.204 61.276 35.535 1.00 0.00 H
ATOM 4566 H5 C3N 287 28.915 61.282 36.642 1.00 0.00 H
ATOM 4567 H6 C3N 287 30.451 62.090 37.082 1.00 0.00 H
There is a huge movement of the x,y,z. Is the 500 restrain force not enough to tether the molecule to that fixed spot?
Am I doing something wrong?
Should I be minimizing the system in a different fashion?
Thanks
Regards
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Received on Tue Oct 15 2019 - 17:00:01 PDT
