AMBER Archive (2006)

Subject: RE: AMBER: identical high energies

From: Ross Walker (
Date: Thu Aug 17 2006 - 21:52:38 CDT

Dear Tanya,

> Conformation 1:
> 1 1.0240E+16 1.5897E+15 6.9165E+17
> O 206760
> BOND = 16415.3128 ANGLE = 27628.7191
> DIHED = 28244.3026
> VDWAALS = ************* EEL = -764301.4029
> HBOND = 0.0000
> 1-4 VDW = 16467.2056 1-4 EEL = 112089.5928
> RESTRAINT = 0.0000

The *'s imply that the value is too big to fit in the space provided in the
output file. Here you see that the VDWAALS energy is huge implying that you
most probably have two atoms sitting almost on top of each other. The bond,
angle and dihedral energies are also fairly high although without knowing ho
many atoms you have in total it is difficult to know if these are 'too
high'. One thing to note is that the minimiser prints out the atom that had
the highest force on it. In this case it was oxygen 206760 which had a
stupidly high force of 6.9x10^17 Kcal/mol/angstrom.

You should try opening your prmtop and inpcrd files in a program such as VMD
and seeing if you can take a look at atom 206760 and the surrounding atoms
to see if anything is wrong.

It is highly unlikely that the minimiser will have been able to successfully
minimise such a problematic structure although steepest descent can
sometimes be robust enough to work. You should probably take a look at the
structure after the minimisation and see how it looks. Compare it to the
initial structure does it look reasonable or has one atom been moved a huge

> offending atom appears to be a water molecule, but I
> don't know why XLeap would have placed a water
> molecule in such an unfavorable position. Does this
> ever happen? I solvated using the solvateBox command,
> and then added explicit salt with addIons2.

Normally you should have no problems with the leap solvatebox command. It
typically adds less water molecules than necessary such that your density is
initially too low. This avoids any problems with atom clashes, particularly
at the box boundaries. However, if you have done something like edit the box
dimensions in the inpcrd file or overidden them in your input files then you
could likely have problems. Other than that I'm not sure why you would see
problems here, especially if your solute has been equilibrated in implicit
solvent first. You could try saving a prmtop and inpcrd file without the
addition of the ions and see if this works okay. You could also try adding
the ions before adding the water. Again though both should work. There is
the possibility that there is a problem with leap and such a large number of
atoms (how many do you have in total?). You should look at things carefully
first to see if you can pin down the problem and afterwards if it still
looks like a problem with leap you could send me the pdb file and I will try
and reproduce it. Please check everything else first though.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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