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

From: Vlad Cojocaru <>
Date: Fri, 02 Jun 2006 11:54:20 +0200

Dear Zhao,

I believe Moil-View should have a LES-friendly interface. HHowever, my
advice is to split the LES trajectory into different trajectories for
each copy. If you do that you can further use ptraj or any other tool to
analyze the new trajectories....

One way you can split the trajectory is to assign different beta values
for the different copies in a pdb file of the entire system... Then you
can load that pdb as topology into vmd and add the trajectory ... You
can use VMD to save each frame as a new pdb file for each beta value
(copy) ... Then if you want you can use ptraj to create an amber traj
from the newly created pdb file. ... This is just an idea... You can do
it differently of course ...

Best wishes

pang zhao wrote:

> 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.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,
> 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.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!
> ------------------------------------------------------------------------
> ------------------------------------------------------------------------

Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Jun 04 2006 - 06:07:15 PDT
Custom Search