ALSO I see that the cpptraj prints this
LIE: 61 Ligand Atoms, 3880 Surrounding Atoms.
I have only 1 ligand with residue no 241 and 34 atoms.. Where is it finding 61 ligand atoms?
My ligand details are as follows:
ATOM 3881 O11 RAL 241 53.802 33.576 39.627 0.00 0.00
ATOM 3883 C11 RAL 241 52.954 34.514 39.155 0.00 0.00
ATOM 3884 C12 RAL 241 53.374 35.772 38.806 0.00 0.00
ATOM 3885 C13 RAL 241 52.407 36.716 38.349 0.00 0.00
ATOM 3888 C10 RAL 241 51.625 34.137 38.948 0.00 0.00
ATOM 3890 C9 RAL 241 50.686 35.042 38.347 0.00 0.00
ATOM 3892 C8 RAL 241 51.105 36.371 38.144 0.00 0.00
ATOM 3893 C7 RAL 241 50.116 37.298 37.586 0.00 0.00
ATOM 3894 S6 RAL 241 48.552 37.317 38.300 0.00 0.00
ATOM 3895 C5 RAL 241 48.097 38.571 37.160 0.00 0.00
ATOM 3896 C4 RAL 241 46.845 39.120 36.974 0.00 0.00
ATOM 3898 C3 RAL 241 46.653 40.051 36.003 0.00 0.00
ATOM 3899 O3 RAL 241 45.409 40.635 35.826 0.00 0.00
ATOM 3901 C2 RAL 241 47.637 40.350 35.017 0.00 0.00
ATOM 3903 C1 RAL 241 48.942 39.851 35.155 0.00 0.00
ATOM 3905 C14 RAL 241 49.109 38.939 36.278 0.00 0.00
ATOM 3906 C15 RAL 241 50.317 38.248 36.592 0.00 0.00
ATOM 3907 C16 RAL 241 51.583 38.538 35.866 0.00 0.00
ATOM 3908 O16 RAL 241 52.174 37.749 35.146 0.00 0.00
ATOM 3909 C17 RAL 241 52.084 39.923 36.048 0.00 0.00
ATOM 3910 C22 RAL 241 51.459 40.837 36.893 0.00 0.00
ATOM 3911 C21 RAL 241 52.033 42.069 37.177 0.00 0.00
ATOM 3914 C18 RAL 241 53.217 40.312 35.372 0.00 0.00
ATOM 3916 C19 RAL 241 53.787 41.541 35.578 0.00 0.00
ATOM 3918 C20 RAL 241 53.186 42.469 36.444 0.00 0.00
ATOM 3919 O23 RAL 241 53.843 43.660 36.731 0.00 0.00
ATOM 3920 C24 RAL 241 54.566 44.394 35.772 0.00 0.00
ATOM 3923 C25 RAL 241 54.811 45.781 36.178 0.00 0.00
ATOM 3926 N26 RAL 241 55.823 46.524 35.403 0.00 0.00
ATOM 3927 C27 RAL 241 55.424 46.975 34.072 0.00 0.00
ATOM 3930 C28 RAL 241 56.450 47.861 33.345 0.00 0.00
ATOM 3933 C29 RAL 241 57.774 47.110 33.183 0.00 0.00
ATOM 3936 C30 RAL 241 58.197 46.644 34.586 0.00 0.00
ATOM 3939 C31 RAL 241 57.159 45.983 35.505 0.00 0.00
________________________________
From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Sent: Wednesday, February 6, 2019 1:58 AM
To: amber.ambermd.org
Subject: [AMBER] Use of LIE command in cpptraj error
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 - 13:00:02 PST
