AMBER Archive (2009)

Subject: RE: [AMBER] reg.targeted molecular dynamics

From: Ross Walker (
Date: Wed Feb 25 2009 - 09:12:29 CST

Hi Balaji,

> I tried Targeted Molecular Dynamics
> by giving the mask to all the atoms
> and i gave all the atom flags in the input
> the total number of atoms are 1296
> but when i run the script it shows
> only 1062 atoms matches
> ...
> tgtfitmask= ":1-40 @
> P,O1P,O2P,O5',C5',C4',O4',C1',C6,C5,C2,O2,C4,C3',C2',O3',H5T,1H5',2H5',H4'
> ,H1',N1,C6,H6,H5,N4,1H4,2H4,N3,H3',1H2',2H2',N9,C8,H8,N7,O6,H1,N2,1H2,2H2,
> C7,1H7,2H7,3H7,O4,H3,N6,1H6,2H6,H2,H3T,Na+",
> tgtrmsmask= ":1-40 @
> P,O1P,O2P,O5',C5',C4',O4',C1',C6,C5,C2,O2,C4,C3',C2',O3',H5T,1H5',2H5',H4'
> ,H1',N1,C6,H6,H5,N4,1H4,2H4,N3,H3',1H2',2H2',N9,C8,H8,N7,
> O6,H1,N2,1H2,2H2,C7,1H7,2H7,3H7,O4,H3,N6,1H6,2H6,H2,H3T,Na+",
> /

Are you sure you got all the atoms? Especially all the hydrogens, I suspect
you are missing some. Note your above mask I believe only checks residues
1-40 so you will only get those atom names included if they are also in
residues 1-40. I'm not sure on that since I don't have the ambmask docs to
hand at the moment but you should take a careful look at the syntax
description to make sure the mask is going to do what you want. Note if you
want all the atoms then it is simpler just to write:


you could also write =":1-40"

which should give you all the atoms in residues 1 to 40.

> and the run got stopped with the error
> --------------------------------------------
> vlimit exceeded for step 34; vmax = 20.9476
> Coordinate resetting (SHAKE) was not accomplished
> within 3000 iterations
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
> ----------------------------------------------------------------------
> Is there any problem in the mask atom flags !

This means that some of your atoms moved very fast - this is generally due
to a bad initial structure or in the case of targeted MD being a long way
from the target and having a very large force pulling one towards the
target. This might be because the targeted MD force constant being too high
or in your case a symptom of not having the mask correctly interpreted. I
would suggest setting ntwx=1 and ntpr=1 and rerunning for say 500 steps or
so. Then you will be able to carefully watch what is going on and see where
the problem lies.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

AMBER mailing list