Hello:
I am trying to calculate ligand binding energy for protein/ligand
system. The enthapy part was done by GMXPBSA. Now I would like to
evalutate the entropy part with g_covar + g_anaeig.
Here I got some questions:
--- is it necessary using double precison Gromacs for entropy evaluation?
--- I googled a lot concering on this topic from Gromacs mailist. If I
understand correctly, we should
(1) generate eigenvec.trr as input file for g_anaeig
(2) use g_anaeig calculate the entropy
is it correct?
---I am trying to run command:
g_covar -f input.xtc -s input.tpr -n -o eigenval.xvg -v eigenvec.trr -av
average.pdb -l covar.log -ascii covar.dat -xpm covar.xpm -xpma covara.xpm
The trajecotry I am using for above commend was extracted from MD
simulations and water/ions were removed from the system. When g_covar
pop up a dialoug asking which compoenent I am going to analyze, I
selected "System" which contains protien+ligand
Is it correct to do so?
---I am planning to run g_anaeig with following command for entropy
evaluation:
g_anaeig -v eigenvec.trr -entropy -s input.tpr -comp
Shall I speicify additional options for this purpose?
Thank you very much.
Albert
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