Hi Amber users,
I have been trying to work out someway to analyse my protein+ mixed solvent simulation to get peaks of solvent density and use them to get SPAM energies out of my trajectories. Till now, I have little luck as it has not been easy,
So here is the system "ABL Kinase in 5% acetonitrile 95% TIP3P water box"... I get certain spots on the protein where the acetonitrile probe (in short C3N) bind and thus probability of C3N is higher in that pocket than the probability of that C3N to be in bulk mixture.
I have density peaks, and also occupancies for 10 such sites on ABL kinase.
When I use these peaks as input file for "spam" action in cpptraj (the latest version on Github), I get positive deltaG and positive enthalpies. That is not quite possible as I have used LIE, SILCS type ,MDMix (Xavier Barril method) types methodologies and they all have favorable energies of binding to that spot/location.
Can anyone explain how is it so? Is there something wrong that I am setting up the system?
Any scientific explanation might help me a lot.
Also when i say interaction, in SPAM is it hard coded for water interactions only? Will it be able to get me C3N+protein interaction energies/ C3N+water interaction energies/C3N+ another C3N interaction energies as in one hotspot we may have all these 3 interactions happening simultaneously.
My input file is attached below: If you have any idea where I may be going wrong, Please help me.
parm ablkinase_3KFA/ACN_H2O_5-95vv_layered/RUNS/3kfa_md_9pmemdcuda/3kfa_layer_ACN_H2O_5-95vv.prmtop
trajin 3kfa_md_1-pmemdMPI/New4G_production.1.crd 1 1250 1
trajin 3kfa_md_1-pmemdMPI/New4H_production.1.crd 1 1250 1
solvent :C3N, WAT
center :1-286 mass origin
image origin familiar com :1-286
###Align trajectory to reference structure by minimizing RMSD
reference solvbox/3kfa_layer_ACN_H2O_5-95vv.pdb
#
strip :Na+,Cl-,WAT
spam 3kfa_ACN_peak.xyz solv C3N reorder cut 12 sphere site_size 6 info info.txt summary spam_summary.out out spam_energies.out
run
rms reference mass :1-286.CA
average 3kfa_avg.pdb :1-286 pdb
run
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Received on Tue Jun 25 2019 - 07:00:03 PDT
