RE: [AMBER] Leap Questions...

From: Ross Walker <>
Date: Mon, 6 Jul 2009 05:01:34 +0100

Hi Cihan,

> I have a leap-specific question. When I solvate my molecule with
> solvateOct, the water box is situated very near to the boundary of the
> truncated octahedron. That's not the case when I solvate in a normal
> box. So is there any way to avoid this? All the proteins are solvated
> with a 10.0A cutoff for the nearest solute residue. I am attaching the
> PDB's for comparison (bzipped to fit in the message).

I took a look at your pdb's and I can see what you mean although this should
not cause you any problems. It is just an arbitrary choice of origin. The
fact that you are running with periodic boundaries renders this simply a
visualization issue rather than an actual artefact. If you really want you
could use ptraj to reimage your inpcrd file specifying the protein as the
> Another question is - Is there a way to keep track of the crystal
> waters? LEaP loads them as solute so their identity gets lost.

Why would you want to? What makes you think during an MD simulation that the
crystal waters are not degenerate with respect to the leap added waters? In
fact I suspect keeping the crystal waters is what is causing the issue you
see above. You should probably strip them from the pdb and solvate again,
assuming there are not any cavities that do not get filled correctly.

With respect to tagging the crystal waters if you really want to do this I
believe that they should not get reordered by leap. Thus if you have 100
crystal waters your first 100 waters should always be the crystal waters
regardless of whether they diffuse into the bulk solvent or not.
Alternatively you could create your own water residue, called something
different from TP3/WAT and copy the parameters etc from TIP3P water. That
way the crystal waters would have different residue types in the simulation.
This could raise issues with shake though so be careful. You have to
preserve the three bonds for example.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Mon Jul 06 2009 - 17:35:59 PDT
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