AMBER Archive (2009)

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

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Fri Feb 27 2009 - 04:28:02 CST

Dear Amber ,
thank you Ross!
it worked
the force was too ohigh
if i decrease its doing good
but when time goes on
the current rmsd value is not changing
too much it stays to a particular value
and after that the rmsd is not decreasing !
what one have to check for it !

if one like to mask the atoms of his interest
suppose i would like to mask 21-30 or
some specific of like 2,3,8,40
how to give the flag in the
mask option

thanks in advance
balaji
UOM

> From: ross_at_rosswalker.co.uk
> To: amber_at_ambermd.org
> Subject: RE: [AMBER] reg.targeted molecular dynamics
> Date: Wed, 25 Feb 2009 07:12:29 -0800
>
> 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:
>
> tgtfitmask="@*",
>
> 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,
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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