Hi users,
I am trying to setup a LIE calculation of a protein+ligand in solution(TIp3P water)
My lie.in file is ----->
parm com_water.prmtop (this is the complex solvated topology file)
trajin prod*.mdcrd (these are the complex explicit solvent production trajectories)
strip :Na+ (i am stripping na+)
lie RAL :241 :1-240 out lie.out (My ligand residue name is RAL and it is residue no 241, 1-240 is the protein residue numbers)
run
write Eelec.dat RAL[EELEC]
write Evdw.dat RAL[EVDW]
I get the output file lie.out which is as follows: ( i am attaching only 20 lines)
#Frame RAL[EELEC] RAL[EVDW]
1 -43.8652 -63.7259
2 -46.0571 -60.5788
3 -36.7738 -61.5817
4 -39.8252 -63.9710
5 -51.7435 -53.1461
6 -43.4511 -55.3070
7 -33.3594 -61.6698
8 -43.0184 -61.2441
9 -33.4903 -62.0163
10 -35.9071 -56.7356
11 -39.2187 -58.4053
12 -36.8213 -58.3399
13 -43.3488 -58.7945
14 -40.0449 -61.7563
15 -42.9230 -59.1834
16 -34.9556 -62.3135
17 -35.9952 -60.6891
18 -33.1894 -60.4609
19 -36.8168 -54.5597
20 -37.9153 -61.9208
1. In LIE we are supposed to run ligand in water also. where in cpptraj do I do trajin of the sole ligand trajectory in water?
2. Do I need to write a script using equation coefficient_Alpha * EElec + coefficient_beta* Evdw + gamma = delG(bind) ? (as I m trying to find free energy of binding)
3. Cant we have a little tutorial on this like we have for MMPBSA. it will help users to start up and set these types of calculations with ease.
I look forward to hearing from you guys.
Regards
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Received on Tue Feb 05 2019 - 12:30:02 PST
