AMBER Archive (2006)

Subject: AMBER: How to analyze the trajectory generated by LES simulation

From: pang zhao (zhao.pang_at_gmail.com)
Date: Fri Jun 02 2006 - 02:08:03 CDT

Dear All,
I performe a LES simulation for 500 ps with 5 copys of the ligand.
I first run 2 ns NPT MD with explicit solvent and then with use the restrt
file "2ns.restrt" and prmtop file "npt.prmtop"
to generate the two files for LES, les.top, les.crd. I successfully run 500
ps LES simulation.

But I could not know how to analyze the trajectory generated by LES
simulation. Because the LES trajectory is different
from the normal trajectory.

when I try to do analyze hydrogen bond using ptraj with the file les.top,
the error occurs: ERROR in readParm: ...failed to find SOLVENT_POINTERS

When I use npt.prmtop for the ptraj analysis, it works.
But I find the analysis result is too different from that with the first 2
ns NPT trajectory.

Such as the RMSD analysis for the LES trajectory, for the protein the C
alpha RMSD is too big.

the picutre about the RMSD analysis is attached, one is the C alpha RMSD,
the second is that of the ligand.

the ptraj input :
trajin lesnpt.mdcrd
center :1-343 origin mass
image origin center familiar
rms first out protein_les_rms.out :1-342_at_CA
rms first out lig_les_rms.out :343

For the hydrogen analysis, I could not find the hydrogen bond of the ligand
with the LES trajectory,
but I can find the two hydrogen bonds of the ligand with the 2 ns NPT
trajectory.

Because the LES trajectory is different from the normal trajectory. I think
there the LES analysis may be diffrent from
the Normal MD simulations. But How to correctly analyze the LES trajectory?

Can I use the LES trajectory for MM-PBSA?

Great thanks!


C_alpha_RMSD.jpg
lig_rmsd.jpg -----------------------------------------------------------------------
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